Sequence Modifications Mass Mass Fractional Part Protein Groups Proteins Gene Names Protein Names Unique (Groups) Unique (Proteins) Acetyl (Protein N-term) Oxidation (M) Missed cleavages Identification type Control 1 Identification type Control 2 Identification type Control 3 Identification type PEI Infil 1 Identification type PEI Infil 2 Identification type PEI Infil 3 Identification type PEI LL 1 Identification type PEI LL 2 Identification type PEI LL 3 Identification type SHP20 Infil 1 Identification type SHP20 Infil 2 Identification type SHP20 Infil 3 Identification type SHP20 LL 1 Identification type SHP20 LL 2 Identification type SHP20 LL 3 Experiment Control 1 Experiment Control 2 Experiment Control 3 Experiment PEI Infil 1 Experiment PEI Infil 2 Experiment PEI Infil 3 Experiment PEI LL 1 Experiment PEI LL 2 Experiment PEI LL 3 Experiment SHP20 Infil 1 Experiment SHP20 Infil 2 Experiment SHP20 Infil 3 Experiment SHP20 LL 1 Experiment SHP20 LL 2 Experiment SHP20 LL 3 Retention time Calibrated retention time Charges PEP MS/MS scan number Raw file Score Delta score Reverse Potential contaminant Intensity Intensity Control 1 Intensity Control 2 Intensity Control 3 Intensity PEI Infil 1 Intensity PEI Infil 2 Intensity PEI Infil 3 Intensity PEI LL 1 Intensity PEI LL 2 Intensity PEI LL 3 Intensity SHP20 Infil 1 Intensity SHP20 Infil 2 Intensity SHP20 Infil 3 Intensity SHP20 LL 1 Intensity SHP20 LL 2 Intensity SHP20 LL 3 id Protein group IDs Peptide ID Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs MS/MS Count Taxonomy IDs AAAAGFEKGIDR Unmodified 1204.62 0.62003536 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 1 By matching By matching By matching By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 1 1 1 1 1 1 2 2 2 1 1 1 9.2752 9.1568 2;3 3.2757E-06 3995 22-052-Murphy-SHP20-LL-3 56.043 46.155 121710000 768080 1216000 692390 6255400 4161200 2480200 21791000 27747000 21246000 0 6725200 19126000 0 0 9502400 0 121 0 0;1;2;3;4;5;6;7;8;9;10;11;12;13;14 0;1;2;3;4;5 0 6 AAALNIVPTSTGAAK Unmodified 1383.7722 0.7721789 90 P25857 GAPB Glyceraldehyde-3-phosphate dehydrogenase GAPB, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 30.895 30.785 2 1.2923E-29 23461 22-052-Murphy-SHP20-PEI-LL-1 107.15 77.681 131130000 8536600 9896300 8026500 16574000 0 0 36115000 0 31077000 0 0 0 0 0 20907000 1 90 1 15;16;17;18;19;20;21;22;23 6;7;8;9;10;11 10 5 AAEDPAPASSSSK Unmodified 1216.5572 0.55716033 205 Q9S831 PSAE1 Photosystem I reaction center subunit IV A, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 3 1 1 2 1 1 1 4 7.9145 7.7934 2 2.0542E-41 2495 22-052-Murphy-SHP20-LL-3 110.87 99.024 209410000 6724500 6105000 10739000 20137000 18187000 0 57660000 0 0 0 26296000 36970000 26595000 0 0 2 205 2 24;25;26;27;28;29;30;31;32;33;34;35;36;37;38;39;40;41 12;13;14;15;16;17;18;19;20;21;22;23;24;25;26;27;28;29;30;31;32;33;34;35 27 24 AAEDTPPATASSDSSSTTAAAAPAKVPAAK Unmodified 2741.3355 0.33554682 201 Q9S714 PSAE2 Photosystem I reaction center subunit IV B, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 2 2 2 2 2 2 2 2 2 2 22.591 22.39 3;4 2.5669E-95 14598 22-052-Murphy-SHP20-PEI-LL-1 74.876 74.876 3627300000 0 5159300 105630000 187870000 169610000 89860000 442320000 356680000 386240000 197430000 312800000 770580000 245320000 97753000 260070000 3 201 3 42;43;44;45;46;47;48;49;50;51;52;53;54;55;56;57;58;59;60;61;62;63;64;65;66;67;68 36;37;38;39;40;41;42;43;44;45;46;47;48;49;50;51;52;53;54;55;56;57;58;59;60;61;62;63;64 57 29 AAENVFIKKMEQEK Unmodified 1663.8603 0.86034198 235 Q9ZUX4 Uncharacterized protein At2g27730, mitochondrial yes yes 0 0 2 By MS/MS By MS/MS By matching By matching By MS/MS 1 1 1 1 1 25.116 25.034 3 0.019145 10863 22-052-Murphy-control-1 49.423 44.793 18962000 3729100 2671300 5155100 1870900 0 0 0 5535300 0 0 0 0 0 0 0 4 235 4 69;70;71;72;73 65 65 1 AAFPNLNSDAGLK Acetyl (Protein N-term) 1358.683 0.68302954 24 A8MRC4;P48006 At1g30230 Elongation factor 1-delta 1 yes no 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 50.408 50.295 2 1.7121E-14 42712 22-052-Murphy-SHP20-PEI-LL-3 79.906 70.125 231010000 3997900 2828900 2417600 19820000 8206500 2881800 47978000 35612000 29829000 9265500 14982000 36118000 8778600 0 8297900 5 24 5 74;75;76;77;78;79;80;81;82;83;84;85;86;87 66;67;68;69;70;71;72 72 7 AAFPNLNSGSGLK Acetyl (Protein N-term) 1316.6725 0.67246486 212 Q9SI20 Elongation factor 1-delta 2 yes yes 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 47.724 47.611 2 0.00097675 45816 22-052-Murphy-SHP20infil-3 57.859 43.185 17665000 0 0 0 4398000 3178500 2126900 0 0 0 0 0 7961200 0 0 0 6 212 6 88;89;90;91 73 73 1 AAGAVAKLIAK Unmodified 1011.6441 0.64406526 123 P56791 rpl2-A 50S ribosomal protein L2, chloroplastic yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 18.169 17.94 2 3.1345E-08 9163 22-052-Murphy-SHP20-PEI-LL-2 72.355 52.995 82964000 0 348710 6033000 0 0 0 20216000 20363000 15281000 2160900 3117500 11120000 0 1687600 2636700 7 123 7 92;93;94;95;96;97;98;99;100;101 74;75;76 76 3 AAGAVAKLIAKEGK Unmodified 1325.8031 0.8030851 123 P56791 rpl2-A 50S ribosomal protein L2, chloroplastic yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 15.094 14.894 3 7.3109E-44 9888 22-052-Murphy-SHP20-PEI-LL-1 90.614 75.074 58004000 5858800 7525200 2681500 0 0 0 20317000 9798400 4734800 0 2120000 3882200 0 1086500 0 8 123 8 102;103;104;105;106;107;108;109;110 77;78;79;80;81 79 5 AAQPEPVAPVENAGEK Unmodified 1605.7999 0.79985021 38 F4I420 At1g76810 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21.607 21.439 2 1.5969E-17 13246 22-052-Murphy-SHP20-PEI-LL-2 79.974 70.287 68642000 2083200 3114200 4201000 4662500 3236700 2090400 7576500 7596400 4914800 3582700 4996600 12001000 3623500 0 4962600 9 38 9 111;112;113;114;115;116;117;118;119;120;121;122;123;124 82;83 83 2 ADAVNAQTPSLSEQYHLEK Acetyl (Protein N-term) 2142.0229 0.022926872 203 Q9S7L9 COX6B-1 Cytochrome c oxidase subunit 6b-1 yes yes 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 2 2 2 1 1 2 1 1 1 38.924 38.788 2;3 2.0001E-60 36746 22-052-Murphy-SHP20infil-3 110.66 97.681 108120000 2188200 2599600 2379600 4301800 4287300 3808900 11966000 10174000 10283000 3973900 9004100 30438000 5787100 2529700 4402600 10 203 10 125;126;127;128;129;130;131;132;133;134;135;136;137;138;139;140;141;142;143 84;85 84 2 ADDEVVDPKK Acetyl (Protein N-term) 1156.5612 0.56118307 139 Q0WWE3 At1g15120 Cytochrome b-c1 complex subunit 6 yes yes 1 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 16.962 16.763 2 1.0039E-15 13536 22-052-Murphy-SHP20infil-3 101.33 89.12 66910000 0 0 0 711340 0 3672800 2809300 3621100 0 7456300 8485500 25856000 8399300 0 5898000 11 139 11 144;145;146;147;148;149;150;151;152 86;87;88;89;90;91;92 88 7 ADKLKQSLPPGLSVQDL Unmodified 1808.0044 0.0043636815 67 O22860 RPL38A 60S ribosomal protein L38 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 41.424 41.327 3 0.0037573 28026 22-052-Murphy-control-3 51.771 51.771 75149000 7336500 11086000 25010000 0 0 0 15672000 9727500 6316800 0 0 0 0 0 0 12 67 12 153;154;155;156;157;158 93;94 93 2 ADQQAGTIVGGVR Acetyl (Protein N-term) 1312.6735 0.67352749 169 Q945Q1 CYS1 Cysteine proteinase inhibitor 1 yes yes 1 0 0 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 34.872 34.752 2 1.2737E-26 19925 22-052-Murphy-control-2 93.551 93.551 42402000 4588900 4495200 0 3502600 0 2114900 9052500 7695500 6961900 0 0 0 0 1485600 2505300 13 169 13 159;160;161;162;163;164;165;166;167 95;96;97;98;99 96 5 ADSVSKNAPPEFQNTK Unmodified 1731.8428 0.84277766 87 P23321 PSBO1 Oxygen-evolving enhancer protein 1-1, chloroplastic yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 9.5556 9.3764 3 5.6552E-43 4214 22-052-Murphy-SHP20-LL-3 85.45 70.981 81342000 0 0 0 0 0 9942200 0 0 0 0 17257000 19082000 17906000 0 17155000 14 87 14 168;169;170;171;172 100;101;102;103 103 4 ADVEPEVAAAGVPKKR Acetyl (Protein N-term) 1677.905 0.90498399 39 F4I472;Q08112;Q9FY64 RPS15;RPS15A;RPS15D 40S ribosomal protein S15-1;40S ribosomal protein S15-4 yes no 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 27.417 27.289 3 4.0417E-21 19301 22-052-Murphy-SHP20-PEI-LL-3 59.185 59.09 100530000 6046500 0 0 0 0 0 0 43450000 37579000 0 0 0 0 13456000 0 15 39 15 173;174;175;176 104;105;106 106 3 AEDSPAVTSTPLVVTEHPVEPTTELPVEHPEEK Unmodified 3563.7519 0.75190355 93 P31168 COR47 Dehydrin COR47 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 41.212 41.092 4 1.2469E-95 34182 22-052-Murphy-SHP20-PEI-LL-1 75.103 75.103 67656000 0 0 8278600 3021400 6951100 4475700 31531000 13398000 0 0 0 0 0 0 0 16 93 16 177;178;179;180;181;182 107;108;109 108 3 AEEIKNVPEQEVPK Acetyl (Protein N-term) 1650.8465 0.84646606 99 P42763 ERD14 Dehydrin ERD14 yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 33.147 33.03 2 3.6801E-47 24426 22-052-Murphy-SHP20-PEI-infil-2 123.86 105.11 228790000 17474000 24979000 36420000 8985900 20779000 11350000 27534000 21790000 19933000 15546000 23997000 0 0 0 0 17 99 17 183;184;185;186;187;188;189;190;191;192;193 110;111;112;113;114;115;116;117;118;119;120 116 11 AEKAVTIRTR Acetyl (Protein N-term) 1185.683 0.68296996 0 A0A1I9LMY7;Q9SS17;Q8LC83 RPS24A;RPS24B 40S ribosomal protein S24-1;40S ribosomal protein S24-2 yes no 1 0 2 By matching By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By matching 1 1 2 2 1 1 2 2 2 1 1 1 1 8.9993 8.8942 2;3 0.0056744 5167 22-052-Murphy-SHP20infil-3 44.203 36.316 633190000 2319000 1824900 26634000 93024000 61090000 72660000 0 22200000 158130000 44742000 40480000 106820000 1872000 0 1398500 18 0 18 194;195;196;197;198;199;200;201;202;203;204;205;206;207;208;209;210;211 121;122 121 2 AEKTDSSAAAAAAPATK Unmodified 1559.7791 0.77911477 202 Q9S7H1 psaD1 Photosystem I reaction center subunit II-1, chloroplastic yes yes 0 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 2 2 2 2 2 2 2 2 2 2 2 8.1409 8.0135 2;3 0 3763 22-052-Murphy-SHP20infil-3 255.52 254.05 663060000 2395600 12903000 21442000 45991000 34871000 23890000 81335000 51808000 53569000 35025000 57456000 118290000 70459000 0 53632000 19 202 19 212;213;214;215;216;217;218;219;220;221;222;223;224;225;226;227;228;229;230;231;232;233;234;235;236;237 123;124;125;126;127;128;129;130;131;132 126 9 AEKTDSSAAAAAAPATKEAPVGFTPPQLDPNTPSPIFAGSTGGLLR Unmodified 4477.2765 0.27652238 202 Q9S7H1 psaD1 Photosystem I reaction center subunit II-1, chloroplastic yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 52.79 52.644 4 1.6447E-08 45021 22-052-Murphy-SHP20infil-1 20.352 19.16 91341000 0 1409300 0 0 0 0 0 30401000 0 14074000 15673000 12363000 6797200 5385100 5238500 20 202 20 238;239;240;241;242;243;244;245 133;134;135;136;137;138;139;140 134 8 AEKTESSSAAPAVKEAPVGFTPPQLDPNTPSPIFAGSTGGLLR Unmodified 4292.1965 0.19648115 207 Q9SA56 PSAD2 Photosystem I reaction center subunit II-2, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By matching By MS/MS By matching By matching 1 1 1 1 1 1 52.553 52.435 4 3.7525E-07 44526 22-052-Murphy-SHP20-PEI-LL-3 27.873 27.873 37588000 0 0 0 0 0 0 0 11211000 10546000 3580800 6397800 0 3258900 0 2593900 21 207 21 246;247;248;249;250;251 141;142 142 2 AEQTEKAFLK Acetyl (Protein N-term) 1205.6292 0.62920306 84 P16181;P42733;O65569 RPS11A;RPS11C;RPS11B 40S ribosomal protein S11-1;40S ribosomal protein S11-3;40S ribosomal protein S11-2 yes no 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 30.719 30.56 2 0 18043 22-052-Murphy-control-3 160.91 141.55 723320000 30051000 34871000 76682000 20417000 0 2140600 198340000 148030000 127950000 15800000 18058000 25297000 10767000 4427500 10490000 22 84 22 252;253;254;255;256;257;258;259;260;261;262;263;264;265 143;144;145;146;147;148;149 143 4 AEQTEKAFLKQPK Acetyl (Protein N-term) 1558.8355 0.83550744 84 P16181;P42733;O65569 RPS11A;RPS11C;RPS11B 40S ribosomal protein S11-1;40S ribosomal protein S11-3;40S ribosomal protein S11-2 yes no 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 2 1 1 2 2 2 2 2 1 1 1 1 1 1 26.432 26.289 2;3 8.5239E-35 18278 22-052-Murphy-SHP20-PEI-LL-3 116.73 106.49 907080000 43411000 2751100 3704900 90201000 69555000 27616000 274550000 199970000 11245000 47321000 36191000 66288000 22607000 11669000 0 23 84 23 266;267;268;269;270;271;272;273;274;275;276;277;278;279;280;281;282;283;284;285 150;151;152;153;154;155;156;157 157 8 AFGDFQKATPEER Unmodified 1494.7103 0.71030693 54 F4JBY2;Q8RWV0 At3g60750;TKL-1 Transketolase-1, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching 1 1 1 1 1 1 1 1 23.536 23.334 3 1.4027E-05 15896 22-052-Murphy-SHP20-PEI-LL-1 51.841 46.95 42303000 2242300 3499000 4317300 0 0 0 11713000 0 7119400 0 0 0 6544300 2126500 4740700 24 54 24 286;287;288;289;290;291;292;293 158 158 1 AFGDFQKATPEERNLR Unmodified 1877.9384 0.93840938 54 F4JBY2;Q8RWV0 At3g60750;TKL-1 Transketolase-1, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 24.666 24.516 3 6.3276E-22 16605 22-052-Murphy-SHP20-PEI-LL-2 87.498 87.498 50800000 2719100 2703600 6334800 0 0 0 13821000 15196000 5720100 0 0 0 0 4304900 0 25 54 25 294;295;296;297;298;299;300 159;160;161 161 3 AFIDPKKNFLAR Unmodified 1418.8034 0.80341945 224 Q9SUU5;F4JUC2 QCR7-1;At4g32470 Cytochrome b-c1 complex subunit 7-1;Cytochrome b-c1 complex subunit 7 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 2 2 2 2 2 1 2 2 2 2 2 1 2 29.182 29.039 3;4 1.4968E-05 21049 22-052-Murphy-SHP20-PEI-LL-3 53.751 51.042 225230000 14121000 12263000 13622000 6244700 6037700 1604000 50564000 41924000 40666000 0 5152400 21251000 3525100 0 8254800 26 224 26 301;302;303;304;305;306;307;308;309;310;311;312;313;314;315;316;317;318;319;320;321;322;323;324 162;163;164;165;166;167;168 168 7 AFLGGRPLPEEF Unmodified 1331.6874 0.68738664 164 Q8VY01 SCPL46 Serine carboxypeptidase-like 46 yes yes 0 0 1 By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 45.884 45.766 2 7.6146E-08 43972 22-052-Murphy-SHP20infil-3 62.546 41.04 33429000 0 0 0 2717500 0 0 2516100 0 2205400 0 0 20956000 0 2186200 2847700 27 164 27 325;326;327;328;329;330;331 169;170;171 169 2 AFLKQPKVFLSSK Unmodified 1491.8813 0.88133542 84 P16181;P42733;O65569 RPS11A;RPS11C;RPS11B 40S ribosomal protein S11-1;40S ribosomal protein S11-3;40S ribosomal protein S11-2 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.89 26.727 3 2.1729E-05 18789 22-052-Murphy-SHP20-PEI-LL-2 51.774 46.791 58603000 3207500 2731400 2815500 3557600 3712600 1576300 8921100 9566200 6895100 3770900 3527400 0 2960600 2740500 2620100 28 84 28 332;333;334;335;336;337;338;339;340;341;342;343;344;345 172;173;174;175;176 175 0 AFSLGKSLSTGNSKSFFVQQNK Unmodified 2374.2281 0.22810904 132 P61847 rpl32 50S ribosomal protein L32, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 2 2 2 1 1 2 2 2 1 2 1 35.17 35.046 3;4 5.7208E-51 28102 22-052-Murphy-SHP20-PEI-LL-1 79.013 79.013 250540000 24322000 31482000 62244000 6371200 3990400 0 58543000 23892000 27358000 0 3043200 0 0 5765700 3532500 29 132 29 346;347;348;349;350;351;352;353;354;355;356;357;358;359;360;361;362;363 177;178;179;180;181;182;183 180 7 AGAEVIGISGDDSASHKAFASK Unmodified 2117.0389 0.038911287 2 A0A1I9LR27;F4JBC9;Q9LU86 ATPRX Q;PRXQ Peroxiredoxin Q, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 25.128 24.953 3;4 6.2718E-10 16469 22-052-Murphy-SHP20-PEI-infil-1 49.528 40.274 290510000 11413000 10488000 11228000 24715000 15749000 3240000 27922000 29084000 22521000 16437000 27025000 47007000 19171000 8434300 16080000 30 2 30 364;365;366;367;368;369;370;371;372;373;374;375;376;377;378;379;380;381;382;383;384;385;386;387;388;389;390;391;392 184;185;186;187;188;189;190;191;192;193;194;195 190 12 AGFKAIALTVDTPR Unmodified 1458.8195 0.81946344 27 A8MS37;B3H4B8;Q9LRR9;Q2V3V9;F4JFV6;Q9LRS0 At3g14420;GLO1;At3g14415;GLO2 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1;Peroxisomal (S)-2-hydroxy-acid oxidase GLO2 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 34.973 34.887 3 2.1137E-14 27912 22-052-Murphy-SHP20-PEI-LL-1 58.172 45.79 28258000 1859100 3705200 3181600 1527400 0 0 8220400 4104200 5660100 0 0 0 0 0 0 31 27 31 393;394;395;396;397;398;399 196 196 1 AGGAYTMNTASAVTVR Oxidation (M) 1584.7566 0.75660519 162 Q8RXU5;Q9SRK6 RPL37AC;RPL37AB 60S ribosomal protein L37a-2;Putative 60S ribosomal protein L37a-1 yes no 0 1 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 22.214 22.07 2 2.2243E-33 14502 22-052-Murphy-SHP20-PEI-LL-1 96.143 81.171 49250000 0 0 0 5328100 0 0 15498000 11958000 8254000 1610900 0 6601300 0 0 0 32 162 32 400;401;402;403;404;405 197;198;199;200 198 31 4 AGIREVHFLPFNPVDKR Unmodified 1994.085 0.085014039 12 A0A1P8AYX4;F4JPJ7;P19456;P20649 HA2;AHA2;AHA1 ATPase 2, plasma membrane-type;ATPase 1, plasma membrane-type yes no 0 0 2 By matching By MS/MS 1 1 34.435 34.317 4 0.0031984 26606 22-052-Murphy-SHP20-PEI-LL-2 45.014 39.804 12204000 0 0 0 0 0 0 2774400 9430000 0 0 0 0 0 0 0 33 12 33 406;407 201 201 1 AGKGFTLEELK Unmodified 1191.6499 0.6499385 179 Q9FF90;Q9SMT4 RPL13D;RPL13C 60S ribosomal protein L13-3;Putative 60S ribosomal protein L13-2 yes no 0 0 1 By matching By MS/MS 1 1 27.076 26.925 3 0.029604 14652 22-052-Murphy-control-3 34.692 28.388 3458700 0 935810 2522900 0 0 0 0 0 0 0 0 0 0 0 0 34 179 34 408;409 202 202 1 AGLINKIGDALHIGGGNK Acetyl (Protein N-term) 1788.9846 0.98463129 217 Q9SLJ2 F20D21.23 yes yes 1 0 1 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 55.823 55.717 3 2.6071E-10 48637 22-052-Murphy-SHP20-PEI-LL-1 45.014 44.897 40006000 1842000 0 0 1610500 2457800 2523800 17496000 0 0 5442000 0 5844800 0 1117400 1672000 35 217 35 410;411;412;413;414;415;416;417;418 203 203 1 AGLQFPVGR Unmodified 943.52395 0.52395013 66 Q9S9K7;O04848;Q9LD28;O81826;Q9LHQ5;Q9C681;Q94F49;Q9C944;Q9FJE8 RAT5 Probable histone H2AXb;Probable histone H2AXa;Histone H2A.6;Probable histone H2A.3;Probable histone H2A.2;Probable histone H2A.1;Probable histone H2A.5;Probable histone H2A variant 3;Probable histone H2A.7 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 33.236 33.091 2 0.00013744 25620 22-052-Murphy-SHP20-LL-3 86.344 0 646770000 19475000 25231000 28901000 44748000 31585000 24457000 68538000 56923000 58868000 27811000 48422000 131480000 33025000 0 47306000 36 66 36 419;420;421;422;423;424;425;426;427;428;429;430;431;432 204;205;206;207;208;209;210;211;212;213;214;215 209 10 AGLQFPVGRIAR Unmodified 1283.7462 0.74623892 66 Q9S9K7;O04848;Q9LD28;O81826;Q9LHQ5;Q9C681;Q94F49 RAT5 Probable histone H2AXb;Probable histone H2AXa;Histone H2A.6;Probable histone H2A.3;Probable histone H2A.2;Probable histone H2A.1;Probable histone H2A.5 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 33.139 32.988 3 1.7684E-05 25874 22-052-Murphy-SHP20-PEI-LL-1 55.461 26.735 431210000 14518000 18771000 23130000 18509000 17638000 12711000 49097000 41592000 45018000 17902000 33416000 70505000 25659000 12336000 30406000 37 66 37 433;434;435;436;437;438;439;440;441;442;443;444;445;446;447 216;217;218;219;220;221 220 4 AGLQFPVGRIARFLK Unmodified 1671.9937 0.99367984 66 Q9S9K7;O04848;Q9LD28;O81826;Q9LHQ5;Q9C681 RAT5 Probable histone H2AXb;Probable histone H2AXa;Histone H2A.6;Probable histone H2A.3;Probable histone H2A.2;Probable histone H2A.1 yes no 0 0 2 By MS/MS By MS/MS By MS/MS 1 1 1 44.572 44.492 3 6.2121E-07 37608 22-052-Murphy-SHP20-PEI-LL-1 51.774 46.883 13483000 2047600 2361400 0 0 0 0 9074400 0 0 0 0 0 0 0 0 38 66 38 448;449;450 222 222 1 AGRPIPVPNSGIQISQLGHVK Unmodified 2167.2226 0.22257015 7 A0A1P8ATL2;Q9SA52 CSP41B Chloroplast stem-loop binding protein of 41 kDa b, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 34.258 34.163 4 0.00025124 27183 22-052-Murphy-SHP20-PEI-LL-1 38.824 38.824 17239000 0 0 0 0 0 0 7889800 4823100 4526300 0 0 0 0 0 0 39 7 39 451;452;453 223 223 0 AHFTASSSER Unmodified 1091.4996 0.49958587 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 0 By MS/MS 1 7.8854 7.6604 2 0.022917 2379 22-052-Murphy-SHP20-PEI-LL-1 56.122 49.298 4091200 0 0 0 0 0 0 4091200 0 0 0 0 0 0 0 0 40 111 40 454 224 224 1 AHGLAPEIPEDLYHLIK Unmodified 1915.0203 0.020348097 127 P59224;P59223 RPS13B;RPS13A 40S ribosomal protein S13-2;40S ribosomal protein S13-1 yes no 0 0 0 By matching By MS/MS By MS/MS By MS/MS 1 2 2 2 47.623 47.538 3;4 3.5329E-29 40081 22-052-Murphy-SHP20-PEI-LL-2 65.805 56.056 89466000 0 467290 0 0 0 0 37597000 24143000 27259000 0 0 0 0 0 0 41 127 41 455;456;457;458;459;460;461 225;226;227;228;229;230 229 6 AKANSLAQLGKYTGEGESEEAK Unmodified 2280.1234 0.1233692 42 F4IGL5;Q944G9;Q9SJU4 FBA1;FBA2 Fructose-bisphosphate aldolase;Probable fructose-bisphosphate aldolase 2, chloroplastic;Probable fructose-bisphosphate aldolase 1, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 2 2 2 2 2 2 2 1 24.036 23.925 3;4 7.8069E-67 16471 22-052-Murphy-SHP20-PEI-LL-1 85.808 77.719 253810000 23064000 22255000 47917000 13631000 0 0 63039000 37474000 37860000 0 0 8571700 0 0 0 42 42 42 462;463;464;465;466;467;468;469;470;471;472;473;474;475;476 231;232;233;234;235;236;237;238;239;240;241 236 11 AKDVEAVPGEGFQTR Acetyl (Protein N-term) 1644.8107 0.81074925 102 P43286 PIP2-1 Aquaporin PIP2-1;Aquaporin PIP2-1, N-terminally processed yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 32.914 32.766 2 4.9286E-70 25766 22-052-Murphy-SHP20-PEI-LL-1 140.17 125.48 325880000 7251200 6777600 0 18848000 19083000 0 42905000 0 35481000 24098000 37583000 62801000 31738000 14804000 24513000 43 102 43 477;478;479;480;481;482;483;484;485;486;487;488 242;243;244;245;246;247;248 248 7 AKDVEAVPGEGFQTR Unmodified 1602.8002 0.80018457 102 P43286 PIP2-1 Aquaporin PIP2-1;Aquaporin PIP2-1, N-terminally processed yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 22.378 22.194 2;3 3.3245E-68 18996 22-052-Murphy-SHP20infil-3 161.63 153.99 946410000 15377000 17207000 21307000 46951000 63417000 29128000 99817000 91640000 91456000 53693000 82347000 158210000 83181000 27428000 65245000 44 102 43 489;490;491;492;493;494;495;496;497;498;499;500;501;502;503;504;505;506;507;508;509;510;511;512;513;514;515;516;517;518 249;250;251;252;253;254;255;256;257;258;259;260;261;262;263;264;265;266;267;268 254 20 AKDVEGPEGFQTR Acetyl (Protein N-term) 1474.7052 0.70522155 103 P43287 PIP2-2 Aquaporin PIP2-2;Aquaporin PIP2-2, N-terminally processed yes yes 1 0 1 By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 26.981 26.848 2 7.5643E-22 19524 22-052-Murphy-SHP20-PEI-LL-1 90.629 70.842 42176000 1350900 1493900 1866100 3189900 2401000 0 6616300 0 4352900 0 7702300 13203000 0 0 0 45 103 44 519;520;521;522;523;524;525;526;527 269;270;271 271 3 AKDVEGPEGFQTR Unmodified 1432.6947 0.69465686 103 P43287 PIP2-2 Aquaporin PIP2-2;Aquaporin PIP2-2, N-terminally processed yes yes 0 0 1 By matching By matching By matching By MS/MS By MS/MS By matching By matching By matching 1 1 1 1 1 1 1 1 9.356 9.224 3 0.024165 4210 22-052-Murphy-SHP20-PEI-LL-3 35.774 31.229 42582000 0 0 2107100 2470200 0 0 5779800 8395200 7429300 3965600 6257000 0 6178100 0 0 46 103 44 528;529;530;531;532;533;534;535 272 272 1 ALGLPVSKL Unmodified 896.5695 0.56950333 175 Q9C9W5 HPR Glycerate dehydrogenase HPR, peroxisomal yes yes 0 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By matching By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 1 38.965 38.816 2 0.00027051 31948 22-052-Murphy-SHP20infil-1 75.311 58.384 130170000 0 0 0 9585700 6921200 4439500 12071000 10745000 10145000 9240200 12232000 25887000 12546000 7881400 8474300 47 175 45 536;537;538;539;540;541;542;543;544;545;546;547 273;274 273 1 ALLGKASFR Unmodified 961.5709 0.57090032 191 Q9LR64 PSB27-1 Photosystem II repair protein PSB27-H1, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 19.79 19.519 2 0.012415 11970 22-052-Murphy-SHP20-PEI-LL-1 60.788 35.789 61304000 0 0 0 0 0 0 12911000 9485900 11352000 0 0 0 10155000 6517700 10883000 48 191 46 548;549;550;551;552;553 275;276 275 2 ALLVEK Acetyl (Protein N-term) 713.43234 0.43234115 22 A8MQP1;F4JTV4;Q9LK36;O23255 MEE58;SAHH2;SAHH1 Adenosylhomocysteinase;Adenosylhomocysteinase 2;Adenosylhomocysteinase 1 yes no 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 39.452 39.303 1 3.4512E-06 34042 22-052-Murphy-SHP20infil-2 112.58 100.99 421910000 0 0 20770000 25611000 0 0 31544000 27756000 19846000 48002000 40357000 106980000 46687000 23988000 30372000 49 22 47 554;555;556;557;558;559;560;561;562;563;564 277;278;279;280;281;282 278 0 ALPTEKDVQPK Unmodified 1224.6714 0.67140222 112 P51418;A0A1P8AY36 RPL18AB 60S ribosomal protein L18a-2 yes no 0 0 1 By MS/MS By matching By matching 1 1 1 8.8923 8.7547 2 0.0066349 3705 22-052-Murphy-SHP20-PEI-LL-1 63.565 54.171 41970000 0 0 0 0 0 0 19908000 12366000 9695700 0 0 0 0 0 0 50 112 48 565;566;567 283 283 1 ALPTEKDVQPKIYR Unmodified 1656.9199 0.91990577 112 P51418;A0A1P8AY36 RPL18AB 60S ribosomal protein L18a-2 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching 2 2 1 2 2 2 1 1 1 23.612 23.466 3;4 9.5337E-36 15221 22-052-Murphy-SHP20-PEI-LL-3 90.146 83.417 138760000 4473400 4691000 6599700 0 0 0 49291000 32178000 33665000 3432800 0 0 0 1722300 2702300 51 112 49 568;569;570;571;572;573;574;575;576;577;578;579;580;581 284;285;286;287;288;289;290 290 7 ALSTSKPDPVVEDQA Unmodified 1555.773 0.77296676 109 P49688 RPS2C 40S ribosomal protein S2-3 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 24.204 24.007 2 5.2297E-06 15877 22-052-Murphy-SHP20-PEI-LL-3 62.303 46.412 251510000 12831000 19204000 41301000 0 0 0 65606000 39542000 39451000 4123400 5845300 6873100 6608200 2682300 7448000 52 109 50 582;583;584;585;586;587;588;589;590;591;592;593 291 291 1 ALTVAKSALEAIR Acetyl (Protein N-term) 1383.8086 0.80856441 48 F4IZR4;Q9M9M9 At3g03100 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 yes no 1 0 1 By matching By MS/MS By MS/MS 1 1 1 55.931 55.853 2 8.8654E-16 48867 22-052-Murphy-SHP20-PEI-LL-1 68.735 49.464 5799800 0 549270 0 0 0 0 3166800 0 2083700 0 0 0 0 0 0 53 48 51 594;595;596 292;293 292 2 ALTVVEKPVEEPAPAKPASASLDR Unmodified 2474.3381 0.33805342 197 Q9M2D8 Uncharacterized protein At3g61260 yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 27.908 27.799 4 3.1189E-10 20490 22-052-Murphy-SHP20-PEI-LL-1 46.833 44.109 24234000 0 0 2302600 1598700 2958100 0 7550700 7519000 2304400 0 0 0 0 0 0 54 197 52 597;598;599;600;601;602 294 294 1 ANPGREGVGLNMR Unmodified 1369.6885 0.68846605 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 9.5515 9.4561 3 0.013246 3210 22-052-Murphy-control-1 54.259 44.255 162590000 22351000 21237000 16317000 11891000 13614000 12688000 0 0 29081000 11769000 3937800 0 19701000 0 0 55 202;207 53 603;604;605;606;607;608;609;610;611;612 295;296 295 2 ANPGREGVGLNMR Oxidation (M) 1385.6834 0.68338067 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 1 1 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 1 1 8.3973 8.2138 2 1.2978E-08 3923 22-052-Murphy-SHP20infil-3 72.038 60.887 354630000 4504300 0 0 13915000 15592000 6506100 65399000 30369000 37441000 29081000 39552000 68257000 18948000 9052600 16008000 56 202;207 53 613;614;615;616;617;618;619;620;621;622;623;624;625 297;298;299 297 35 3 ANSLAQLGKYTGEGESEEAK Unmodified 2080.9913 0.99129239 42 F4IGL5;Q944G9;Q9SJU4 FBA1;FBA2 Fructose-bisphosphate aldolase;Probable fructose-bisphosphate aldolase 2, chloroplastic;Probable fructose-bisphosphate aldolase 1, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 29.032 28.942 3 1.4099E-09 13988 22-052-Murphy-control-1 55.864 51.83 76419000 7384800 8019700 15225000 5357300 0 0 16737000 10417000 13277000 0 0 0 0 0 0 57 42 54 626;627;628;629;630;631;632 300;301;302 300 2 APGVQTPVIVR Unmodified 1135.6713 0.67134264 10 B9DG18;A0A1P8B564;A0A1P8AWT7;Q42547;P25819;F4HUL6;F4JM86 CAT3;CAT2 Catalase-3;Catalase-2;Catalase yes no 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 28.644 28.482 2 7.7772E-10 20633 22-052-Murphy-SHP20-PEI-LL-3 86.953 75.442 81161000 1129900 1224100 0 3212600 2342200 1837900 12726000 12563000 9806400 3923500 4947700 9362100 8914000 3810100 5362100 58 10 55 633;634;635;636;637;638;639;640;641;642;643;644;645;646 303;304;305;306 306 3 APLGQNTVLLR Unmodified 1180.6928 0.69280637 100 Q940B0;P42791;A0A1P8BGQ0;A0A1I9LT16 RPL18C;RPL18B 60S ribosomal protein L18-3;60S ribosomal protein L18-2 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 32.175 32.014 2 1.2493E-23 24778 22-052-Murphy-SHP20-PEI-LL-1 100.45 69.377 337830000 3960300 7681700 16185000 0 4744900 0 118690000 72615000 74505000 5873900 8710200 5933400 7977300 3534400 7418100 59 100 56 647;648;649;650;651;652;653;654;655;656;657;658;659 307;308;309;310;311;312;313;314 311 8 APWLEPLRGPNGLDLSR Unmodified 1890.0112 0.011180394 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 1 By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 46.79 46.647 3 0.003797 41272 22-052-Murphy-SHP20-LL-1 55.213 43.012 37097000 0 0 0 0 0 0 0 2824800 3813700 3278900 4798200 6845300 7541000 4239700 3755500 60 121 57 660;661;662;663;664;665;666;667 315;316;317 315 3 ARIKVHELR Unmodified 1120.6829 0.68291038 3 A0A1I9LSB4;F4KDR2;Q9SF53;Q9M3D2;Q9LZ41;O80626 At5g02610;RPL35A;RPL35C;RPL35D;RPL35B 60S ribosomal protein L35-1;60S ribosomal protein L35-3;60S ribosomal protein L35-4;60S ribosomal protein L35-2 yes no 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 1 1 1 8.0351 7.8054 2;3 5.3517E-09 2425 22-052-Murphy-SHP20-PEI-LL-1 93.262 55.024 92331000 0 0 0 1876900 1000700 0 60436000 15118000 12436000 0 0 0 0 1463000 0 61 3 58 668;669;670;671;672;673;674 318;319 319 2 ARVYDDEVR Unmodified 1121.5465 0.54653606 47 F4IVZ7;P10896 RCA Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By matching By matching 1 1 1 1 8.2714 8.238 3 0.020584 2020 22-052-Murphy-control-1 52.716 30.63 52445000 8130700 9392600 0 19924000 0 0 0 14998000 0 0 0 0 0 0 0 62 47 59 675;676;677;678 320 320 1 ASFDEAPPGNAK Acetyl (Protein N-term) 1244.5673 0.56733108 29 B3H4Y9;O23138 CYTC-1 Cytochrome c-1 yes no 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 2 1 1 1 30.876 30.71 1;2 3.0587E-06 28480 22-052-Murphy-SHP20infil-3 77.046 72.473 328820000 5202200 0 5473700 11981000 10869000 14306000 31933000 34536000 25737000 22609000 30341000 76869000 25650000 10885000 22427000 63 29 60 679;680;681;682;683;684;685;686;687;688;689;690;691;692;693 321;322;323;324;325;326;327;328;329;330;331;332;333;334;335;336 325 16 ASFDEAPPGNAKAGEK Acetyl (Protein N-term) 1629.7635 0.76346471 29 B3H4Y9;O23138 CYTC-1 Cytochrome c-1 yes no 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 24.234 24.042 2 1.0719E-67 14067 22-052-Murphy-SHP20-PEI-infil-3 135.86 135.86 869130000 0 5920600 7570400 31371000 36136000 37975000 93574000 97103000 65273000 59556000 84582000 190800000 75755000 27601000 55915000 64 29 61 694;695;696;697;698;699;700;701;702;703;704;705;706;707 337;338;339;340;341;342;343;344;345;346;347;348;349;350;351;352;353;354;355;356;357;358;359 354 23 ASFDEAPPGNPK Acetyl (Protein N-term) 1270.583 0.58298115 229 Q9T0G2 CYTC-2 Cytochrome c-2 yes yes 1 0 0 By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 32.177 32.025 2 5.172E-07 29546 22-052-Murphy-SHP20infil-3 75.213 75.213 31334000 905920 0 1072800 0 0 4291400 8174000 0 0 0 0 16890000 0 0 0 65 229 62 708;709;710;711;712 360;361;362 360 2 ASFDEAPPGNPKAGEK Acetyl (Protein N-term) 1655.7791 0.77911477 229 Q9T0G2 CYTC-2 Cytochrome c-2 yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 25.645 25.473 2 7.1309E-44 22327 22-052-Murphy-SHP20infil-3 123.79 119.78 186850000 1896900 1841100 0 5961800 7965200 8351100 17442000 19238000 14965000 12530000 18235000 44878000 14912000 6165100 12467000 66 229 63 713;714;715;716;717;718;719;720;721;722;723;724;725;726 363;364;365;366;367;368;369;370;371;372;373 365 11 ASGDYAIVIAHNPDNDTSR Unmodified 2014.9344 0.93444622 147 Q42064 RPL8C 60S ribosomal protein L8-3 yes yes 0 0 0 By matching By matching By MS/MS 1 1 1 28.645 28.534 3 0.0010788 20771 22-052-Murphy-SHP20-PEI-LL-3 41.202 37.234 17246000 0 0 0 0 0 0 7192500 4369800 5684200 0 0 0 0 0 0 67 147 64 727;728;729 374 374 1 ASGDYAIVIAHNPDNDTSRIKLPSGSK Unmodified 2825.4308 0.43078461 147 Q42064 RPL8C 60S ribosomal protein L8-3 yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 32.618 32.515 5 0.0033529 25465 22-052-Murphy-SHP20-PEI-LL-1 32.264 25.312 30722000 0 1073600 0 0 0 0 12821000 10126000 6702200 0 0 0 0 0 0 68 147 65 730;731;732;733 375 375 1 ASGDYAIVIAHNPDSDTTR Unmodified 2001.9392 0.93919724 104 P46286 RPL8A 60S ribosomal protein L8-1 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 29.445 29.35 3 1.718E-66 21610 22-052-Murphy-SHP20-PEI-LL-2 96.666 87.008 140600000 2861600 5655300 6008500 9034400 6397500 0 47220000 32130000 31292000 0 0 0 0 0 0 69 104 66 734;735;736;737;738;739;740;741 376;377;378;379;380;381;382;383 382 7 ASGDYAIVIAHNPDSDTTRIK Unmodified 2243.1182 0.11822424 104 P46286 RPL8A 60S ribosomal protein L8-1 yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 29.006 28.896 4 1.0367E-05 21805 22-052-Murphy-SHP20-PEI-LL-1 48.288 41.035 61904000 0 2562900 0 0 0 0 22279000 15948000 21114000 0 0 0 0 0 0 70 104 67 742;743;744;745 384 384 1 ASGDYAIVIAHNPDSDTTRIKLPSGSK Unmodified 2812.4355 0.43553563 104 P46286 RPL8A 60S ribosomal protein L8-1 yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 2 2 3 3 3 2 2 2 2 1 2 33.542 33.395 3;4;5 4.5879E-83 26350 22-052-Murphy-SHP20-PEI-LL-1 92.336 89.96 555110000 2777500 8653500 12569000 9965100 10561000 8172800 129250000 117380000 128750000 18364000 28010000 27726000 24017000 8102500 20796000 71 104 68 746;747;748;749;750;751;752;753;754;755;756;757;758;759;760;761;762;763;764;765;766;767;768;769;770;771;772;773;774;775;776 385;386;387;388;389;390;391;392;393;394;395;396;397;398;399;400;401;402;403;404;405 398 21 ASGSLKSLISSAVGRGVTEAR Acetyl (Protein N-term) 2087.1335 0.13348037 158 Q8GXH5 yes yes 1 0 2 By matching By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 48.773 48.719 3 3.9955E-71 42085 22-052-Murphy-SHP20-PEI-LL-1 95.662 81.96 36240000 1715300 0 0 1900000 0 0 11232000 7288900 12452000 1651000 0 0 0 0 0 72 158 69 777;778;779;780;781;782 406;407;408;409 406 4 ASHIVGYPR Acetyl (Protein N-term) 1040.5403 0.54032847 72 Q9SRV5;O50008 MS2;MS1 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 2;5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 yes no 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.398 26.235 2 5.5704E-10 17486 22-052-Murphy-SHP20-PEI-infil-2 102.98 96.07 362550000 21452000 26113000 37265000 16576000 11019000 4339200 64957000 55399000 38092000 12118000 12271000 31880000 20954000 10112000 0 73 72 70 783;784;785;786;787;788;789;790;791;792;793;794;795;796 410;411;412;413;414;415;416;417;418;419;420;421;422;423;424;425;426;427 422 17 ASQLDVVVSNK Unmodified 1158.6245 0.62445203 180 Q9FHG2 RPL32B 60S ribosomal protein L32-2 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching 1 1 1 1 1 1 1 1 24.415 24.295 2 0.01482 16752 22-052-Murphy-SHP20-PEI-LL-1 58.981 34.058 50740000 1415000 1693600 3162700 3563500 0 0 12780000 13581000 12643000 0 1900900 0 0 0 0 74 180 71 797;798;799;800;801;802;803;804 428 428 1 ASQLDVVVSNKLGR Unmodified 1484.8311 0.83109076 180 Q9FHG2 RPL32B 60S ribosomal protein L32-2 yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 29.491 29.418 3 3.7145E-09 22182 22-052-Murphy-SHP20-PEI-LL-1 61.932 49.787 38955000 1007700 1315800 0 3027200 0 0 15981000 9297400 8326500 0 0 0 0 0 0 75 180 72 805;806;807;808;809;810 429;430 429 2 ASQLDVVVSNKLGRLR Unmodified 1754.0163 0.016265772 180 Q9FHG2 RPL32B 60S ribosomal protein L32-2 yes yes 0 0 2 By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 31.979 31.856 4 0.012691 24777 22-052-Murphy-SHP20-PEI-LL-1 38.028 31.996 44732000 0 0 4382900 0 0 0 21765000 10030000 8553500 0 0 0 0 0 0 76 180 73 811;812;813;814 431 431 1 ASQLDVVVTNR Unmodified 1200.6463 0.64625011 107 P49211 RPL32A 60S ribosomal protein L32-1 yes yes 0 0 0 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching 1 1 1 1 1 1 1 1 1 1 1 26.917 26.769 2 0.030212 19508 22-052-Murphy-SHP20-PEI-LL-1 56.81 40.666 48971000 932160 1414900 1322500 2580900 0 0 11343000 9613700 9270700 1689200 0 6194500 2217800 0 2391900 77 107 74 815;816;817;818;819;820;821;822;823;824;825 432 432 0 ASQLDVVVTNRLAR Unmodified 1540.8685 0.8685389 107 P49211 RPL32A 60S ribosomal protein L32-1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 1 1 1 1 1 1 1 30.813 30.706 3 1.9919E-13 22997 22-052-Murphy-SHP20-PEI-LL-3 71.176 58.816 362520000 9377000 10829000 23745000 12329000 0 0 153440000 74743000 67574000 0 0 10485000 0 0 0 78 107 75 826;827;828;829;830;831;832;833 433;434 434 1 ASREIFNISGEK Unmodified 1349.6939 0.69392858 7 A0A1P8ATL2;Q9SA52 CSP41B Chloroplast stem-loop binding protein of 41 kDa b, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 2 2 2 2 2 1 1 1 1 1 1 23.609 23.437 2;3 2.0318E-79 15323 22-052-Murphy-SHP20-PEI-LL-2 129.38 80.588 313430000 2942700 4793200 5851100 9309700 16981000 11144000 76119000 81931000 73786000 3433100 4677000 7556700 6869900 3439900 4594900 79 7 76 834;835;836;837;838;839;840;841;842;843;844;845;846;847;848;849;850;851;852;853 435;436;437;438;439;440;441;442;443;444;445;446;447;448;449;450 447 16 ASVGFKAGVK Unmodified 962.55492 0.5549159 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 2 1 8.4549 8.3008 2 8.7706E-13 2836 22-052-Murphy-SHP20-PEI-infil-2 73.637 43.025 675520000 0 0 0 21120000 0 0 29258000 31389000 24601000 62024000 127310000 211200000 107690000 0 60940000 80 64 77 854;855;856;857;858;859;860;861;862;863;864;865 451;452;453;454;455;456;457;458 456 7 ASVGFKAGVKEYK Unmodified 1382.7558 0.75580056 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 2 By matching By matching By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 2 2 2 2 2 2 2 1 1 9.3407 9.1788 2;3 4.5607E-26 3265 22-052-Murphy-SHP20-PEI-LL-1 87.308 68.037 549450000 4826800 8374700 9600000 18173000 14676000 12996000 37521000 62824000 50291000 31079000 56378000 65223000 89685000 27518000 60284000 81 64 78 866;867;868;869;870;871;872;873;874;875;876;877;878;879;880;881;882;883;884;885;886;887 459;460;461;462;463;464;465;466 464 7 ATATEVPSAVRRSSSSGK Unmodified 1789.9282 0.92823863 208 Q9SAJ6 GAPCP1 Glyceraldehyde-3-phosphate dehydrogenase GAPCP1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS 1 1 34.1 33.976 3 0.0074955 26471 22-052-Murphy-SHP20-LL-3 27.496 0 16752000 0 0 0 9201300 0 0 0 0 0 0 0 0 0 0 7550300 82 208 79 888;889 467;468 467 2 ATAYQPMKPGK Acetyl (Protein N-term);Oxidation (M) 1248.6173 0.61725816 105 P49200 RPS20A 40S ribosomal protein S20-1 yes yes 1 1 1 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 9.4247 9.3157 2 0.0020058 4264 22-052-Murphy-SHP20-PEI-LL-2 60.76 40.973 52865000 1000100 1019900 0 4116600 0 2336600 14987000 10680000 0 0 8810000 9915400 0 0 0 83 105 80 890;891;892;893;894;895;896;897 469;470 470 20 2 ATGGNKTKTPGPGAQSALR Unmodified 1810.965 0.96495848 98;176;213 P42036;Q9CAX6;Q9SIH0 RPS14C;RPS14B;RPS14A 40S ribosomal protein S14-3;40S ribosomal protein S14-2;40S ribosomal protein S14-1 no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching 1 2 2 2 1 1 3 2 2 1 1 8.1684 8.0264 2;3;4 2.4677E-99 2616 22-052-Murphy-SHP20-PEI-LL-1 131.72 121.06 795360000 6636200 21083000 29942000 21484000 6187700 16558000 199060000 253620000 237320000 2537800 0 0 0 924620 0 84 98;176;213 81 898;899;900;901;902;903;904;905;906;907;908;909;910;911;912;913;914;915 471;472;473;474;475;476;477;478;479;480;481 477 11 ATGKTVKDVSPHEFVK Acetyl (Protein N-term) 1783.9468 0.9468488 185 Q9FNP8 RPS19C 40S ribosomal protein S19-3 yes yes 1 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 22.512 22.33 3 9.9394E-40 14299 22-052-Murphy-SHP20-PEI-LL-2 86.944 68.806 65822000 3671400 3027800 5658700 0 0 1350600 17491000 16129000 12414000 0 0 5123600 0 956550 0 85 185 82 916;917;918;919;920;921;922;923;924 482;483;484 483 3 ATITVVKAR Acetyl (Protein N-term) 999.60768 0.60767976 88 P25696 ENO2 Bifunctional enolase 2/transcriptional activator yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 25.097 24.911 2 0.0001504 16311 22-052-Murphy-SHP20-PEI-infil-1 76.847 52.874 105620000 0 0 5458700 18650000 8112800 0 0 6478500 11087000 8247900 9143100 26348000 7831200 4258200 0 86 88 83 925;926;927;928;929;930;931;932;933;934 485;486;487;488;489;490;491;492;493;494 491 9 ATLVVGNVLPLR Unmodified 1250.7711 0.77105669 104;147 P46286;Q42064 RPL8A;RPL8C 60S ribosomal protein L8-1;60S ribosomal protein L8-3 no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 46.976 46.853 2 2.0375E-11 39987 22-052-Murphy-SHP20-PEI-LL-1 88.942 83.595 134300000 2022200 2759500 5382500 3283700 3000400 3867400 18680000 17468000 12679000 11971000 9344400 13800000 13034000 10762000 6244500 87 104;147 84 935;936;937;938;939;940;941;942;943;944;945;946;947;948;949 495;496;497;498;499;500;501;502;503;504;505;506;507;508 506 13 ATNGSASSAQLSQKEADVR Acetyl (Protein N-term) 1960.945 0.9450109 30 B9DG17;Q08682 P40;RPSaA 40S ribosomal protein SA;40S ribosomal protein Sa-1 yes no 1 0 1 By matching By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 23.017 22.929 2 1.8755E-83 15500 22-052-Murphy-SHP20-PEI-LL-1 132.76 127.16 29212000 1441700 2425200 0 1433100 0 0 10744000 5803100 7364800 0 0 0 0 0 0 88 30 85 950;951;952;953;954;955 509;510;511 509 3 ATQTVEDSSRSGPR Unmodified 1489.7121 0.71209784 122 P56780 psbH Photosystem II reaction center protein H yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 3 4 4 5 7 4 5 4 4 4 5 6 4 3 6 8.5456 8.3839 2;3 1.0779E-47 1852 22-052-Murphy-SHP20-LL-1 87.001 87.001 1081400000 1901200 3082000 8776100 51890000 38883000 21232000 176280000 39327000 35165000 38439000 142470000 296780000 106160000 5297800 115700000 89 122 86 956;957;958;959;960;961;962;963;964;965;966;967;968;969;970;971;972;973;974;975;976;977;978;979;980;981;982;983;984;985;986;987;988;989;990;991;992;993;994;995;996;997;998;999;1000;1001;1002;1003;1004;1005;1006;1007;1008;1009;1010;1011;1012;1013;1014;1015;1016;1017;1018;1019;1020;1021;1022;1023 512;513;514;515;516;517;518;519;520;521;522;523;524;525;526;527;528;529;530;531;532;533;534;535;536;537;538;539;540;541;542;543;544;545;546;547;548;549;550;551;552;553;554;555;556;557;558;559;560;561;562;563;564;565;566;567;568;569;570;571;572;573 537 60 ATQTVEDSSRSGPRSTTVGK Unmodified 2063.0243 0.024323855 122 P56780 psbH Photosystem II reaction center protein H yes yes 0 0 2 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 1 2 2 2 2 2 2 2 2 2 2 2 8.1176 7.9981 3;4 3.497E-86 2651 22-052-Murphy-SHP20-LL-3 110.38 92.56 1243700000 12223000 12881000 3921300 52514000 62145000 71876000 40761000 57832000 58081000 99683000 154200000 232950000 227210000 0 157400000 90 122 87 1024;1025;1026;1027;1028;1029;1030;1031;1032;1033;1034;1035;1036;1037;1038;1039;1040;1041;1042;1043;1044;1045;1046;1047;1048;1049;1050 574;575;576;577;578;579;580;581;582;583;584;585;586;587;588;589 584 16 ATSEGEISEK Unmodified 1049.4877 0.48768378 68 O22914 CP12-1 Calvin cycle protein CP12-1, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 8.1757 8.078 2 6.9375E-05 2603 22-052-Murphy-SHP20-PEI-infil-2 79.469 66.979 32322000 4159700 3311300 8286500 0 9405100 0 7159000 0 0 0 0 0 0 0 0 91 68 88 1051;1052;1053;1054;1055 590;591 591 2 ATSEGEISEKVEKSIQEAK Unmodified 2062.043 0.042993612 68 O22914 CP12-1 Calvin cycle protein CP12-1, chloroplastic yes yes 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 30.421 30.315 3 0.0020753 21925 22-052-Murphy-SHP20-PEI-infil-2 34.094 30.314 30115000 2184900 2459100 3041000 0 3800000 0 7383900 4431900 6814300 0 0 0 0 0 0 92 68 89 1056;1057;1058;1059;1060;1061;1062 592 592 1 ATSEILSPISGEIIEVNK Unmodified 1899.0201 0.020073325 89 P25855 GDH1 Glycine cleavage system H protein 1, mitochondrial yes yes 0 0 0 By matching By matching By MS/MS By MS/MS 1 1 1 1 50.204 50.089 2 0.0013708 33812 22-052-Murphy-control-3 22.198 8.7703 7190700 1242300 934620 2299600 0 0 2714200 0 0 0 0 0 0 0 0 0 93 89 90 1063;1064;1065;1066 593 593 1 ATTEVGEAPATTTEAETTELPEIVK Unmodified 2587.2752 0.27523797 160 Q8LCA1 CURT1B Protein CURVATURE THYLAKOID 1B, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 43.954 43.825 3 4.1412E-17 41881 22-052-Murphy-SHP20infil-3 53.342 46.148 80609000 0 0 0 0 0 0 21451000 13203000 9048500 0 0 24292000 0 0 12614000 94 160 91 1067;1068;1069;1070;1071 594;595;596;597;598;599 595 6 AVGNWFYGR Unmodified 1068.5141 0.51411372 58 F4JT64;Q940J8 At4g19410;PAE7 Pectin acetylesterase 7 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 36.834 36.719 2 4.3923E-07 31555 22-052-Murphy-SHP20infil-2 81.672 74.443 65435000 3645100 2861400 1358500 0 0 0 7269300 0 5584100 20228000 24489000 0 0 0 0 95 58 92 1072;1073;1074;1075;1076;1077;1078 600;601;602;603 603 4 AVILLQGRYAGKK Unmodified 1415.8613 0.86126868 26 A8MS28;Q8LCL3;P51419 At4g15000;RPL27B;RPL27C 60S ribosomal protein L27-2;60S ribosomal protein L27-3 yes no 0 0 2 By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 18.402 18.103 3 0.022651 11679 22-052-Murphy-SHP20-LL-1 39.917 32.715 16813000 0 0 0 655380 0 0 0 0 0 0 0 2853800 5609100 4785100 2910000 96 26 93 1079;1080;1081;1082;1083 604 604 1 AVTFSDLHTERGLK Acetyl (Protein N-term) 1614.8366 0.83657007 155 Q84WM9 Elongation factor 1-beta 1 yes yes 1 0 1 By MS/MS By MS/MS 1 1 33.641 33.562 3 6.4847E-14 26019 22-052-Murphy-SHP20-PEI-LL-2 57.802 51.073 11167000 0 0 0 0 0 0 0 5380200 5787100 0 0 0 0 0 0 97 155 94 1084;1085 605 605 1 AVVYALSPFQQK Unmodified 1349.7343 0.73433683 182 Q9SG91;Q9FLB7 T7M13.6;At5g05370 yes no 0 0 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 40.915 40.77 2 0.010862 33909 22-052-Murphy-SHP20-PEI-LL-1 66.073 61.29 59619000 0 0 1684200 0 0 0 19712000 15315000 10515000 2298800 3015100 4975900 0 0 2102600 98 182 95 1086;1087;1088;1089;1090;1091;1092;1093 606;607 606 2 AYGGVLSGSAVR Unmodified 1135.5986 0.59857163 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 no no 0 0 0 By MS/MS 1 25.904 25.904 2 0.024127 17406 22-052-Murphy-SHP20-PEI-infil-1 39.022 29.808 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 99 178 96 1094 608 608 1 DAFGNANSAR Unmodified 1021.4577 0.45772105 218 Q9SMU8;Q9LDN9;Q9LDA4 PER34;PER37;PER38 Peroxidase 34;Peroxidase 37;Peroxidase 38 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 8.8223 8.7025 2 0.01168 2458 22-052-Murphy-control-1 54.157 43.69 316970000 4089000 3798800 0 25541000 12798000 30156000 17520000 23929000 22728000 17026000 30364000 79006000 28272000 0 21746000 100 218 97 1095;1096;1097;1098;1099;1100;1101;1102;1103;1104;1105;1106;1107 609;610;611;612;613;614;615;616;617 609 8 DAFGNANSARGFPVIDR Unmodified 1805.8809 0.8808945 218 Q9SMU8 PER34 Peroxidase 34 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 1 2 2 4 2 1 3 3 3 2 3 2 37.448 37.29 2;3 4.2785E-54 34836 22-052-Murphy-SHP20infil-3 91.207 73.105 1541300000 17492000 12178000 12453000 87355000 47687000 47288000 142370000 153020000 113310000 92106000 173220000 347330000 123180000 60703000 111610000 101 218 98 1108;1109;1110;1111;1112;1113;1114;1115;1116;1117;1118;1119;1120;1121;1122;1123;1124;1125;1126;1127;1128;1129;1130;1131;1132;1133;1134;1135;1136;1137;1138;1139;1140 618;619;620;621;622;623;624;625;626;627;628;629;630;631;632;633;634;635;636;637;638;639;640;641;642;643;644;645 623 27 DAFGNANSARGFPVIDRMK Unmodified 2065.0163 0.016342126 218 Q9SMU8 PER34 Peroxidase 34 yes yes 0 0 2 By MS/MS By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 1 2 2 2 2 2 2 35.749 35.586 3;4 1.9075E-06 30296 22-052-Murphy-SHP20infil-2 60.489 55.78 151130000 2725800 0 0 2210100 0 0 9627100 13147000 4207000 11356000 19226000 41349000 26155000 11911000 9215500 102 218 99 1141;1142;1143;1144;1145;1146;1147;1148;1149;1150;1151;1152;1153;1154;1155;1156;1157;1158 646;647;648;649;650;651;652;653 647 7 DAPPGQKVGLIAAR Unmodified 1391.7885 0.78849767 104 P46286 RPL8A 60S ribosomal protein L8-1 yes yes 0 0 1 By MS/MS 1 23.332 23.228 3 2.1646E-06 15204 22-052-Murphy-SHP20-PEI-LL-3 44.299 38.113 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 103 104 100 1159 654 654 1 DAPPGQKVGLIAARR Unmodified 1547.8896 0.8896087 104 P46286 RPL8A 60S ribosomal protein L8-1 yes yes 0 0 2 By MS/MS By matching 1 1 18.116 17.797 4 0.027709 14232 22-052-Murphy-SHP20infil-3 28.976 24.346 10686000 0 0 0 0 0 0 0 0 0 0 0 8814500 0 0 1871200 104 104 101 1160;1161 655 655 1 DDEVQIVR Unmodified 972.48762 0.4876242 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 23.375 23.236 2 2.4704E-05 15161 22-052-Murphy-SHP20-PEI-LL-2 103.41 53.289 43709000 1884700 1793800 1337900 0 0 0 14446000 13457000 9261100 0 1527900 0 0 0 0 105 111 102 1162;1163;1164;1165;1166;1167;1168 656;657 657 2 DDEVQIVRGTYKGR Unmodified 1634.8376 0.8376327 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 20.394 20.201 3;4 3.7207E-45 11901 22-052-Murphy-SHP20-PEI-LL-3 112.86 112.86 321550000 6475400 5442300 12731000 18177000 10605000 4363400 72722000 51373000 47409000 10985000 10840000 27978000 16169000 6493900 19785000 106 111 103 1169;1170;1171;1172;1173;1174;1175;1176;1177;1178;1179;1180;1181;1182;1183;1184;1185;1186;1187;1188;1189;1190;1191;1192;1193;1194;1195;1196;1197 658;659;660;661;662;663;664;665;666;667;668 668 8 DFKNTQAGDLIDK Unmodified 1463.7256 0.72562264 152 Q680B7 At2g14690 yes yes 0 0 1 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 8.6522 8.5026 3 0.013514 2239 22-052-Murphy-control-1 38.021 6.5901 100150000 4673500 0 0 0 0 0 0 15886000 0 0 15237000 29999000 19467000 0 14892000 107 152 104 1198;1199;1200;1201;1202;1203 669 669 0 DGEEGEEAAVAAPEEVKKSNHLLR Unmodified 2577.2671 0.26707332 166 Q93VG5 RPS8A 40S ribosomal protein S8-1 yes yes 0 0 2 By MS/MS 1 28.073 27.928 4 9.7542E-09 20711 22-052-Murphy-SHP20-PEI-LL-1 40.012 37.288 12289000 0 0 0 0 0 0 12289000 0 0 0 0 0 0 0 0 108 166 105 1204 670 670 1 DGVYPEK Unmodified 806.38103 0.38103386 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 8.7277 8.6121 2 0.0022412 2532 22-052-Murphy-control-2 110.54 84.407 3642800000 148100000 152180000 163590000 247610000 370900000 351680000 0 0 0 253550000 487490000 840790000 345850000 0 281080000 109 202;207 106 1205;1206;1207;1208;1209;1210;1211;1212;1213;1214;1215 671;672;673;674;675;676;677 672 0 DGVYPEKANPGR Unmodified 1301.6364 0.6364137 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 4 2 4 4 4 3 9 4 9 2 4 3 4 2 5 8.442 8.2879 2;3 9.2112E-24 4063 22-052-Murphy-SHP20infil-3 98.997 98.47 5626200000 209340000 198300000 250350000 389150000 321670000 199090000 703150000 649630000 649300000 178910000 369390000 906030000 245120000 35974000 320780000 110 202;207 107 1216;1217;1218;1219;1220;1221;1222;1223;1224;1225;1226;1227;1228;1229;1230;1231;1232;1233;1234;1235;1236;1237;1238;1239;1240;1241;1242;1243;1244;1245;1246;1247;1248;1249;1250;1251;1252;1253;1254;1255;1256;1257;1258;1259;1260;1261;1262;1263;1264;1265;1266;1267;1268;1269;1270;1271;1272;1273;1274;1275;1276;1277;1278 678;679;680;681;682;683;684;685;686;687;688;689;690;691;692;693;694;695;696;697;698;699;700;701;702;703;704;705;706;707;708;709;710;711;712;713;714;715;716;717;718 689 38 DGVYPEKANPGREGVGLNMR Oxidation (M) 2174.0538 0.053849845 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 1 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 1 1 2 22.32 22.168 3;4 2.6998E-09 14343 22-052-Murphy-SHP20-PEI-LL-2 56.407 52.603 2566300000 41031000 0 0 0 292120000 0 0 1284100000 527580000 74814000 0 0 346660000 0 0 111 202;207 108 1279;1280;1281;1282;1283;1284;1285;1286 719;720;721;722;723;724 722 35 6 DGVYPEKANPGREGVGLNMR Unmodified 2158.0589 0.058935222 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 1 1 1 2 2 2 1 2 3 2 2 2 26.987 26.806 3;4 5.5907E-41 18796 22-052-Murphy-SHP20-PEI-LL-2 74.12 68.91 832320000 24246000 35117000 34096000 4437100 5402800 2792400 89027000 101200000 66108000 6263900 47896000 300620000 61843000 22726000 30551000 112 202;207 108 1287;1288;1289;1290;1291;1292;1293;1294;1295;1296;1297;1298;1299;1300;1301;1302;1303;1304;1305;1306;1307;1308;1309;1310;1311;1312;1313 725;726;727;728;729;730;731;732;733;734;735;736;737;738;739;740;741;742;743;744;745;746;747;748;749 746 24 DIALITGQKPIKTR Unmodified 1552.9301 0.93007653 65 O04603 RPL5 50S ribosomal protein L5, chloroplastic yes yes 0 0 2 By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 26.052 25.889 3 5.428E-17 18475 22-052-Murphy-SHP20-PEI-LL-1 70.963 57.284 70382000 1808700 1930600 0 5856000 3381100 2150900 8428100 7521100 8623700 4845800 6351500 12733000 4700300 2051300 0 113 65 109 1314;1315;1316;1317;1318;1319;1320;1321;1322;1323;1324;1325;1326 750;751;752;753;754;755 753 6 DIINVKPLIDR Unmodified 1294.7609 0.76088593 231 Q9XFT3 PSBQ1 Oxygen-evolving enhancer protein 3-1, chloroplastic yes yes 0 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 39.778 39.671 3 0.0021149 32764 22-052-Murphy-SHP20-PEI-LL-1 52.49 35.016 22032000 1089800 1748100 1122900 3372100 0 0 0 2520300 2302300 0 2757900 7119100 0 0 0 114 231 110 1327;1328;1329;1330;1331;1332;1333;1334;1335 756;757 757 2 DIINVKPLIDRK Unmodified 1422.8558 0.85584895 231 Q9XFT3 PSBQ1 Oxygen-evolving enhancer protein 3-1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 1 1 2 1 2 1 2 2 1 1 2 32.409 32.255 3;4 0.0064288 18010 22-052-Murphy-control-2 56.359 53.65 130810000 1853900 3372500 2694900 14080000 5130700 3158600 13147000 5389200 14730000 3287000 15921000 35642000 4208600 1994800 6202600 115 231 111 1336;1337;1338;1339;1340;1341;1342;1343;1344;1345;1346;1347;1348;1349;1350;1351;1352;1353;1354;1355;1356;1357;1358 758;759;760;761 758 4 DIQPWQERR Unmodified 1226.6156 0.61561868 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 19.511 19.319 3 0.0031538 15992 22-052-Murphy-SHP20infil-3 60.59 56.139 157750000 0 1357400 0 2424200 0 0 8176700 8838600 11122000 8202600 15438000 39046000 45580000 0 17568000 116 121 112 1359;1360;1361;1362;1363;1364;1365;1366;1367;1368 762;763;764 762 1 DITFQNTAGPSKHQAVALR Unmodified 2053.0705 0.070486187 71 O49006;Q42534 PME3;PME2 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3;Pectinesterase 2 yes no 0 0 1 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 2 2 2 1 25.615 25.452 3;4 2.3781E-56 22426 22-052-Murphy-SHP20infil-3 95.57 71.032 110960000 2023800 1248900 0 8143800 6003600 2817000 8035600 8250100 8813500 0 18472000 41938000 0 0 5213800 117 71 113 1369;1370;1371;1372;1373;1374;1375;1376;1377;1378;1379;1380;1381;1382 765;766;767;768;769;770;771;772 768 8 DLDQVAGRIAVEP Unmodified 1381.7201 0.72014333 210 Q9SGA6 RPS19A 40S ribosomal protein S19-1 yes yes 0 0 1 By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 43.378 43.26 2 6.1961E-34 35912 22-052-Murphy-SHP20-PEI-LL-2 101.65 97.397 74477000 6736300 5441700 9070900 0 0 362720 19248000 10854000 17901000 0 0 4861900 0 0 0 118 210 114 1383;1384;1385;1386;1387;1388;1389;1390 773;774;775;776 775 4 DLPQTYWPYGKSR Unmodified 1609.7889 0.7888916 189 Q9LJG3 ESM1 GDSL esterase/lipase ESM1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 36.52 36.342 3 0.0096366 28958 22-052-Murphy-SHP20-LL-3 51.841 38.124 46823000 0 0 0 0 0 0 7013400 0 4992100 2892300 9678100 12748000 5052400 1768100 2679000 119 189 115 1391;1392;1393;1394;1395;1396;1397;1398 777;778;779 777 1 DMRQTVAVGVIK Oxidation (M) 1331.7231 0.72312022 36 F4HUA0;Q8W4H7;Q8GTY0;Q0WL56;P0DH99 At1g07930;A2;A4;A3;A1 Elongation factor 1-alpha 2;Elongation factor 1-alpha 4;Elongation factor 1-alpha 3;Elongation factor 1-alpha 1 yes no 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 1 1 1 2 2 2 2 1 1 2 2 22.439 22.261 2;3 0.0026985 14235 22-052-Murphy-SHP20-LL-3 62.2 29.979 246800000 5758000 6443000 6912800 14755000 2857000 3914900 6695000 20909000 16655000 42965000 23376000 33700000 11718000 10461000 39684000 120 36 116 1399;1400;1401;1402;1403;1404;1405;1406;1407;1408;1409;1410;1411;1412;1413;1414;1415;1416;1417;1418;1419;1420;1421;1422;1423 780;781;782 782 5 3 DMRQTVAVGVIK Unmodified 1315.7282 0.7282056 36 F4HUA0;Q8W4H7;Q8GTY0;Q0WL56;P0DH99 At1g07930;A2;A4;A3;A1 Elongation factor 1-alpha 2;Elongation factor 1-alpha 4;Elongation factor 1-alpha 3;Elongation factor 1-alpha 1 yes no 0 0 1 By MS/MS 1 28.801 28.546 3 0.0082297 25803 22-052-Murphy-SHP20infil-3 46.64 27.033 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 121 36 116 1424 783 783 1 DNIQGITKPAIR Unmodified 1324.7463 0.7462985 129 P59259 Histone H4 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 2 2 2 1 1 2 1 1 2 23.768 23.573 2;3 0.0049096 20407 22-052-Murphy-SHP20infil-3 59.8 53.879 164720000 0 2012700 2768000 5783500 5221200 3389800 22853000 29728000 19553000 7314900 12208000 37764000 5567600 1915400 8636500 122 129 117 1425;1426;1427;1428;1429;1430;1431;1432;1433;1434;1435;1436;1437;1438;1439;1440;1441;1442;1443 784;785;786;787 784 4 DNIQGITKPAIRR Unmodified 1480.8474 0.84740953 129 P59259 Histone H4 yes yes 0 0 2 By matching By matching By matching By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 12.345 12.189 3 0.0083795 14263 22-052-Murphy-SHP20infil-3 40.577 28.519 70404000 3792400 3110800 1565300 9701100 3361900 0 18859000 9346600 336840 0 0 18177000 0 2152400 0 123 129 118 1444;1445;1446;1447;1448;1449;1450;1451;1452;1453 788;789 788 2 DRFYIQPLSPTEAAARAK Unmodified 2033.0694 0.069423554 145 Q41932 PSBQ2 Oxygen-evolving enhancer protein 3-2, chloroplastic yes yes 0 0 2 By matching By matching By MS/MS By MS/MS By matching By MS/MS By matching 2 1 2 2 1 2 1 33.048 32.936 3;4 5.2133E-29 25897 22-052-Murphy-SHP20-PEI-LL-1 68.944 59.897 38302000 3718300 2493500 4908000 0 0 0 10479000 3549700 11093000 0 0 0 0 0 2060600 124 145 119 1454;1455;1456;1457;1458;1459;1460;1461;1462;1463;1464 790;791;792;793 791 4 DRFYLQPLPPTEAAARAK Unmodified 2043.0902 0.090158996 231 Q9XFT3 PSBQ1 Oxygen-evolving enhancer protein 3-1, chloroplastic yes yes 0 0 2 By MS/MS By matching By matching By matching By MS/MS By MS/MS By matching By MS/MS 1 1 2 1 2 2 1 1 32.931 32.798 3;4 7.7861E-05 30173 22-052-Murphy-SHP20infil-3 51.695 34.617 59370000 2437400 2438900 3660100 0 1234100 0 14884000 0 14743000 0 5970000 14003000 0 0 0 125 231 120 1465;1466;1467;1468;1469;1470;1471;1472;1473;1474;1475 794;795;796;797;798 795 5 DSHGIPQVKSVTGSK Unmodified 1538.8053 0.80526994 127 P59224;P59223 RPS13B;RPS13A 40S ribosomal protein S13-2;40S ribosomal protein S13-1 yes no 0 0 1 By matching By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 9.332 9.247 3 0.0060689 4242 22-052-Murphy-SHP20-PEI-LL-1 44.44 39.286 93374000 898090 1959400 1528600 2140700 2668300 0 18977000 34664000 30538000 0 0 0 0 0 0 126 127 121 1476;1477;1478;1479;1480;1481;1482;1483 799 799 1 DSPAAAAAPDGATATKPKPPPIGPK Unmodified 2325.2329 0.23286007 205 Q9S831 PSAE1 Photosystem I reaction center subunit IV A, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 3 3 2 3 3 3 2 2 2 3 3 3 4 2 2 23.727 23.547 3;4 0 20465 22-052-Murphy-SHP20infil-3 164.02 164.02 4391600000 106300000 74065000 121650000 257340000 243800000 110830000 521270000 442350000 406360000 164240000 332660000 942300000 288500000 83044000 296890000 127 205 122 1484;1485;1486;1487;1488;1489;1490;1491;1492;1493;1494;1495;1496;1497;1498;1499;1500;1501;1502;1503;1504;1505;1506;1507;1508;1509;1510;1511;1512;1513;1514;1515;1516;1517;1518;1519;1520;1521;1522;1523 800;801;802;803;804;805;806;807;808;809;810;811;812;813;814;815;816;817;818;819;820;821;822;823;824;825;826;827;828;829;830;831;832;833;834;835;836;837;838;839;840;841;842;843;844;845;846;847;848;849;850;851;852;853;854;855;856;857;858;859;860;861;862;863;864;865 825 66 DVSPHDFVKAYASHLKR Unmodified 1969.017 0.016994053 210 Q9SGA6;Q9LF30 RPS19A;RPS19B 40S ribosomal protein S19-1;40S ribosomal protein S19-2 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 29.693 29.591 4 2.9115E-18 22489 22-052-Murphy-SHP20-PEI-LL-1 63.709 53.05 20038000 2072800 1834200 3095400 0 0 0 7237100 0 5798700 0 0 0 0 0 0 128 210 123 1524;1525;1526;1527;1528 866;867;868;869;870 869 5 DYLHFVKKYQR Unmodified 1495.7936 0.79358305 84 P16181 RPS11A 40S ribosomal protein S11-1 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS 1 1 1 23.711 23.576 4 2.9065E-05 15585 22-052-Murphy-SHP20-PEI-LL-2 69.954 64.569 14825000 0 0 0 0 0 0 5951200 4918400 3955800 0 0 0 0 0 0 129 84 124 1529;1530;1531 871;872;873;874 873 4 EAAAPAIGDTAQFPSLG Unmodified 1614.789 0.78895118 193 Q9LVT8 At5g47210 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS 1 1 1 53.47 53.378 2 2.2758E-14 51683 22-052-Murphy-SHP20infil-3 73.327 66.794 33137000 0 0 0 8012800 1906900 0 0 0 0 0 0 23218000 0 0 0 130 193 125 1532;1533;1534 875 875 1 EAGGAVVLTA Unmodified 886.476 0.47599688 108 Q9LR33;P49637 RPL27AB;RPL27AC 60S ribosomal protein L27a-2;60S ribosomal protein L27a-3 yes no 0 0 0 By MS/MS 1 33.039 32.845 2 1.1791E-08 20402 22-052-Murphy-control-3 29.149 25.029 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 131 108 126 1535 876 876 1 EALGALPLYQR Unmodified 1229.6768 0.67682195 224 Q9SUU5;F4JWS9;F4JWS8 QCR7-1;At5g25450;QCR7-2 Cytochrome b-c1 complex subunit 7-1;Cytochrome b-c1 complex subunit 7;Cytochrome b-c1 complex subunit 7-2 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 39.709 39.568 2 1.2837E-24 30532 22-052-Murphy-SHP20-PEI-infil-2 70.268 65.302 123180000 3629300 2978900 3297800 11328000 6889700 3932100 21094000 12985000 11770000 0 7596300 20027000 5430400 3495700 8724300 132 224 127 1536;1537;1538;1539;1540;1541;1542;1543;1544;1545;1546;1547;1548;1549 877;878;879;880;881;882;883;884;885;886 883 10 EALGALPLYQRTLP Unmodified 1540.8613 0.86132826 224 Q9SUU5 QCR7-1 Cytochrome b-c1 complex subunit 7-1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 1 1 1 2 1 1 1 1 1 1 1 2 1 49.077 48.96 2 4.4837E-284 42610 22-052-Murphy-SHP20-PEI-LL-1 162.88 0 267200000 6636000 4449900 6382300 13334000 10783000 5829300 44743000 30585000 25905000 9511500 17689000 43121000 17490000 11969000 18772000 133 224 128 1550;1551;1552;1553;1554;1555;1556;1557;1558;1559;1560;1561;1562;1563;1564;1565;1566;1567 887;888;889;890;891;892;893;894;895;896;897;898;899;900;901;902;903;904;905;906;907 902 20 EAPQGEKPEPVRTHLR Unmodified 1842.97 0.97004386 39 F4I472;Q08112 RPS15;RPS15A 40S ribosomal protein S15-1 yes no 0 0 2 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 2 1 2 1 8.3061 8.0982 3;4 0.00072563 2737 22-052-Murphy-SHP20-PEI-LL-1 45.434 42.097 187520000 0 6665500 10322000 0 6838700 0 48653000 51264000 62668000 0 0 0 0 1109700 0 134 39 129 1568;1569;1570;1571;1572;1573;1574;1575;1576 908;909 908 2 EAPVGFTPPQLDPNTPSPIFAGSTGGLLR Unmodified 2935.508 0.5079723 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 63.384 63.249 3 0.022503 49728 22-052-Murphy-SHP20-PEI-LL-3 22.456 20.081 27879000 0 0 1325900 0 0 0 0 0 9625400 6275500 1110300 0 3393700 5203100 944750 135 202;207 130 1577;1578;1579;1580;1581;1582;1583 910;911 911 2 EAPVGFTPPQLDPNTPSPIFAGSTGGLLRK Unmodified 3063.6029 0.60293531 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 1 1 2 3 3 2 2 2 3 1 2 55.18 55.067 3;4 4.6251E-05 46755 22-052-Murphy-SHP20infil-1 29.736 29.736 353170000 900280 3050100 2964600 5696800 4853000 1513600 40207000 48073000 54288000 37989000 45836000 68118000 24295000 2463200 12923000 136 202;207 131 1584;1585;1586;1587;1588;1589;1590;1591;1592;1593;1594;1595;1596;1597;1598;1599;1600;1601;1602;1603;1604;1605;1606;1607;1608;1609;1610;1611;1612 912;913;914;915;916;917;918;919;920;921;922 914 11 EEAEKEIAEYK Unmodified 1337.6351 0.6350763 78 O82628 VHA-G1 V-type proton ATPase subunit G1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 9.5755 9.5091 2 7.3657E-23 3302 22-052-Murphy-control-1 73.26 46.006 33836000 9394400 8194300 6632500 0 0 0 0 0 9614900 0 0 0 0 0 0 137 78 132 1613;1614;1615;1616 923;924;925 923 3 EEPKTVVAAVPVDKLPLESK Unmodified 2148.2042 0.2041857 187 Q9LER7 PSRP5 50S ribosomal protein 5, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 1 2 2 2 1 2 1 2 2 2 2 2 2 36.571 36.423 3;4 2.2001E-05 29591 22-052-Murphy-SHP20-PEI-LL-1 46.663 45.053 233180000 5175900 3585900 3074800 18111000 11517000 5120600 11632000 22586000 8334300 17053000 29637000 65919000 12390000 8438500 10602000 138 187 133 1617;1618;1619;1620;1621;1622;1623;1624;1625;1626;1627;1628;1629;1630;1631;1632;1633;1634;1635;1636;1637;1638;1639;1640;1641;1642;1643 926;927;928;929;930;931;932 930 5 EETGRQLGQRISFSGQVR Unmodified 2047.0559 0.055898755 6 A0A1P8ASL8;Q9C7N4 GDSL esterase/lipase At1g29670 yes no 0 0 2 By matching By matching By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 24.552 24.382 4 4.0357E-05 18746 22-052-Murphy-SHP20infil-2 39.143 30.434 71455000 1579600 0 0 4348300 5189200 3116900 7720100 10693000 4304700 0 9479300 13522000 5875000 0 5626900 139 6 134 1644;1645;1646;1647;1648;1649;1650;1651;1652;1653;1654 933;934;935;936;937;938 933 6 EGAIQQLENAR Unmodified 1227.6208 0.62076364 116 P56759 atpF ATP synthase subunit b, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 28.236 28.095 2 1.5519E-22 20101 22-052-Murphy-SHP20-PEI-LL-3 95.909 73.418 118130000 6475300 7244400 5731200 10445000 4512100 0 0 15444000 22738000 0 8580400 31143000 0 0 5812800 140 116 135 1655;1656;1657;1658;1659;1660;1661;1662;1663;1664;1665 939;940;941;942;943;944;945;946;947;948 948 10 EGAIQQLENARAR Unmodified 1454.759 0.75898845 116 P56759 atpF ATP synthase subunit b, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 2 1 2 2 2 1 2 2 1 2 23.936 23.765 2;3 1.582E-09 15557 22-052-Murphy-SHP20-PEI-LL-3 49.448 43.262 652640000 14356000 12047000 13213000 45997000 34718000 12770000 125630000 90208000 103500000 15843000 40849000 118820000 0 4871700 19819000 141 116 136 1666;1667;1668;1669;1670;1671;1672;1673;1674;1675;1676;1677;1678;1679;1680;1681;1682;1683;1684;1685;1686;1687 949;950;951;952;953;954;955;956;957;958 957 8 EGALASSTTSKPLPEVGQR Unmodified 1927.0011 0.0010692176 45 F4IJM1;Q8LBP4 ALB3 Inner membrane protein ALBINO3, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 24.887 24.725 3 3.9676E-72 17206 22-052-Murphy-SHP20-PEI-LL-1 86.378 76.72 132980000 6437900 4178300 7177000 8765800 9130600 7988200 14335000 14362000 13191000 7743800 10147000 18351000 5494800 0 5681300 142 45 137 1688;1689;1690;1691;1692;1693;1694;1695;1696;1697;1698;1699;1700;1701 959;960;961;962;963;964;965;966;967;968;969 967 11 EGLLTRDARVVER Unmodified 1512.8372 0.83723877 232 Q9XJ27 RPS9 30S ribosomal protein S9, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 2 2 2 2 1 2 2 2 2 2 1 2 2 20.767 20.602 3;4 0.011429 8383 22-052-Murphy-control-3 42.095 18.346 118940000 6306600 6966700 15829000 6166100 1669200 0 17247000 13082000 13292000 8475800 8221400 6754100 8625400 0 6305500 143 232 138 1702;1703;1704;1705;1706;1707;1708;1709;1710;1711;1712;1713;1714;1715;1716;1717;1718;1719;1720;1721;1722;1723;1724;1725 970;971;972 971 3 EGNDLYMEMK 2 Oxidation (M) 1260.5002 0.50023907 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 2 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 9.3445 9.2258 2 3.0741E-05 4053 22-052-Murphy-SHP20-LL-3 53.166 33.389 244800000 3365100 5699400 10574000 12917000 0 0 60314000 38083000 37533000 0 12241000 38028000 0 0 26047000 144 86 139 1726;1727;1728;1729;1730;1731;1732;1733;1734;1735 973;974;975;976 973 11;12 4 EGPNLLK Unmodified 769.4334 0.43340378 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 18.701 18.509 2 0.0074503 6133 22-052-Murphy-control-2 59.89 12.846 4403100000 103130000 104250000 166600000 181850000 157010000 50280000 860720000 604010000 686070000 155090000 280560000 600260000 188550000 56817000 207960000 145 202;207 140 1736;1737;1738;1739;1740;1741;1742;1743;1744;1745;1746;1747;1748;1749;1750 977;978;979;980;981;982;983;984;985 977 0 EGPNLLKLAR Unmodified 1109.6557 0.65569258 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 29.105 28.943 2;3 5.5101E-06 14067 22-052-Murphy-control-1 86.113 75.928 3701200000 137480000 143230000 172570000 293570000 231330000 50381000 616440000 409670000 411490000 103420000 187980000 517650000 144730000 62369000 218900000 146 202;207 141 1751;1752;1753;1754;1755;1756;1757;1758;1759;1760;1761;1762;1763;1764;1765;1766;1767;1768;1769;1770;1771;1772;1773;1774;1775;1776;1777;1778;1779;1780 986;987;988;989;990;991;992 986 0 EGPNLLKLARK Unmodified 1237.7507 0.7506556 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21.916 21.73 3 0.010243 14028 22-052-Murphy-SHP20-PEI-LL-1 47.603 40.34 136170000 4770900 4965800 5885500 9584900 9871500 3005100 19794000 15430000 16293000 5426900 7753600 15173000 6653500 3272900 8289100 147 202;207 142 1781;1782;1783;1784;1785;1786;1787;1788;1789;1790;1791;1792;1793;1794;1795 993;994;995 995 3 EGPPVFEQPEMTYEK Oxidation (M) 1795.7975 0.79746695 47 F4IVZ7;P10896 RCA Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic yes no 0 1 0 By MS/MS By matching By MS/MS 1 1 1 33.628 33.532 2 0.00013501 26519 22-052-Murphy-SHP20-PEI-LL-1 51.927 42.494 21484000 0 0 0 0 0 0 10347000 5316300 5820100 0 0 0 0 0 0 148 47 143 1796;1797;1798 996 996 7 1 EGVGLNMR Unmodified 874.43309 0.43308621 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 22.013 21.845 2 8.1054E-06 13638 22-052-Murphy-SHP20-PEI-LL-3 74.849 46.32 128750000 6395400 6120500 5712100 6430400 4695600 2366800 11961000 11674000 9243900 3603400 9854200 37256000 5642300 0 7791000 149 202;207 144 1799;1800;1801;1802;1803;1804;1805;1806;1807;1808;1809;1810;1811;1812 997;998;999;1000 1000 4 EGVGLNMRSIGKNVSPIEVK Oxidation (M) 2142.1467 0.1466876 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 1 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 28.679 28.502 3 1.4184E-32 22977 22-052-Murphy-SHP20infil-2 44.998 35.524 143280000 2831700 2742500 6590600 0 7586300 3441500 35498000 17085000 0 8454500 19251000 0 12784000 12956000 14062000 150 202;207 145 1813;1814;1815;1816;1817;1818;1819;1820;1821;1822;1823;1824 1001;1002;1003;1004 1001 35 4 EILMRDSNR Oxidation (M) 1148.5608 0.56080592 174 Q9C9H9 PCMP-H70 Pentatricopeptide repeat-containing protein At1g71420 yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 1 1 1 1 1 1 21.957 21.808 2 0.029327 9680 22-052-Murphy-control-3 50.966 12.174 71207000 4796600 6135700 12008000 0 0 0 17634000 14713000 14007000 0 0 0 1912500 0 0 151 174 146 1825;1826;1827;1828;1829;1830;1831 1005 1005 34 0 EIVPENPNSYRAR Unmodified 1543.7743 0.77430417 183 Q9FLN4 RPL27 50S ribosomal protein L27, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 3 2 2 2 2 2 2 21.455 21.269 2;3 7.9743E-06 13973 22-052-Murphy-SHP20infil-1 52.928 30.73 947800000 24392000 27680000 31999000 99228000 39995000 18648000 133040000 102480000 90680000 52725000 54674000 164620000 41118000 14302000 52223000 152 183 147 1832;1833;1834;1835;1836;1837;1838;1839;1840;1841;1842;1843;1844;1845;1846;1847;1848;1849;1850;1851;1852;1853;1854;1855;1856;1857;1858;1859;1860;1861 1006;1007;1008;1009;1010;1011;1012;1013;1014;1015;1016;1017;1018;1019;1020;1021 1009 13 EIVPENPNSYRARK Unmodified 1671.8693 0.86926718 183 Q9FLN4 RPL27 50S ribosomal protein L27, chloroplastic yes yes 0 0 2 By matching By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 8.74 8.6252 3 0.018196 4847 22-052-Murphy-SHP20infil-3 50.207 32.112 209200000 4036700 10325000 4126300 10768000 9557400 0 0 15960000 14255000 20901000 27558000 50079000 22216000 0 19417000 153 183 148 1862;1863;1864;1865;1866;1867;1868;1869;1870;1871;1872;1873 1022 1022 1 EKVNGTTVNVGIQPSK Unmodified 1669.8999 0.89989861 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 1 2 2 2 2 2 2 2 2 2 2 1 2 21.383 21.197 2;3 1.2375E-220 17956 22-052-Murphy-SHP20infil-3 153.12 136.49 1085400000 13588000 21573000 19304000 52618000 37284000 22682000 206080000 170870000 138410000 56320000 67514000 103640000 79553000 25115000 70855000 154 111 149 1874;1875;1876;1877;1878;1879;1880;1881;1882;1883;1884;1885;1886;1887;1888;1889;1890;1891;1892;1893;1894;1895;1896;1897;1898;1899;1900 1023;1024;1025;1026;1027;1028;1029;1030;1031;1032;1033;1034;1035;1036;1037;1038;1039;1040;1041 1027 19 ELIEGLPKKFK Unmodified 1300.7755 0.77547336 97 P36212;P36210 RPL12C;RPL12A 50S ribosomal protein L12-3, chloroplastic;50S ribosomal protein L12-1, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 26.23 26.155 3 0.011236 14017 22-052-Murphy-control-3 54.982 47.071 18551000 3535500 3983700 4748100 6283600 0 0 0 0 0 0 0 0 0 0 0 155 97 150 1901;1902;1903;1904 1042;1043 1043 2 EMPIVGGSGLFRFAR Oxidation (M) 1651.8504 0.850446 173 Q9C891 DIR20 Dirigent protein 20 yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 41.641 41.533 3 2.6965E-07 34693 22-052-Murphy-SHP20-PEI-LL-1 60.628 9.4172 100580000 3069400 4041000 7096500 7809000 5096200 3076800 18553000 16708000 8809000 5319800 0 20998000 0 0 0 156 173 151 1905;1906;1907;1908;1909;1910;1911;1912;1913;1914;1915 1044;1045;1046;1047 1045 33 4 ENVKNTAASVGEITLK Unmodified 1672.8996 0.89956426 87;206 P23321;Q9S841 PSBO1;PSBO2 Oxygen-evolving enhancer protein 1-1, chloroplastic;Oxygen-evolving enhancer protein 1-2, chloroplastic no no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 1 1 2 2 2 1 1 2 1 1 2 27.917 27.762 2;3 1.1327E-43 20458 22-052-Murphy-SHP20-PEI-LL-1 109.42 94.729 320620000 10367000 8822400 10635000 17001000 6416900 2241600 59539000 59924000 53826000 7839000 11769000 34535000 13530000 4877500 19300000 157 87;206 152 1916;1917;1918;1919;1920;1921;1922;1923;1924;1925;1926;1927;1928;1929;1930;1931;1932;1933;1934;1935;1936;1937;1938 1048;1049;1050;1051;1052;1053;1054;1055;1056;1057;1058 1056 11 EQIFEMPTGGAAIMR 2 Oxidation (M) 1681.7804 0.7803771 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 2 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 33.289 33.157 2 3.522E-21 26133 22-052-Murphy-SHP20-PEI-LL-1 90.906 83.019 96196000 2025200 4110900 3713700 11147000 6038900 0 24208000 15096000 16974000 0 5965400 0 0 1957100 4959600 158 202;207 153 1939;1940;1941;1942;1943;1944;1945;1946;1947;1948;1949 1059 1059 36;37 1 EQPPQVGKVIGK Unmodified 1278.7296 0.7295858 204 Q9S7Y7 XYL1 Alpha-xylosidase 1 yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 2 1 1 1 1 2 2 1 1 2 18.263 18.066 2;3 1.6064E-05 14932 22-052-Murphy-SHP20infil-3 52.79 43.601 122740000 1080300 2330600 3209700 7880700 7400500 0 8337800 9085600 5515500 6082100 13569000 43697000 6003000 1717500 6832300 159 204 154 1950;1951;1952;1953;1954;1955;1956;1957;1958;1959;1960;1961;1962;1963;1964;1965;1966;1967;1968 1060;1061;1062;1063;1064;1065;1066 1062 6 ESAGASSSSVAEFSMFIKK Unmodified 1961.9404 0.9404428 150 Q5PNU4 B3 domain-containing protein At2g35310 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 38.598 38.455 3 0.00092368 33048 22-052-Murphy-SHP20-LL-1 41.871 23.954 184130000 0 0 0 8621700 6605900 4649900 18602000 25438000 9266100 18687000 38734000 0 22931000 9928200 20665000 160 150 155 1969;1970;1971;1972;1973;1974;1975;1976;1977;1978;1979 1067;1068;1069;1070;1071 1067 5 EVAGMAPYEK Oxidation (M) 1109.5063 0.50631073 77 O80929 RPL36A 60S ribosomal protein L36-1 yes yes 0 1 0 By matching By MS/MS By matching By matching 1 1 1 1 8.6068 8.4802 2 1.926E-05 3310 22-052-Murphy-SHP20-PEI-LL-1 71.342 52.612 29702000 0 0 0 0 2863000 0 11692000 8652800 6493400 0 0 0 0 0 0 161 77 156 1980;1981;1982;1983 1072 1072 9 1 FAAYEKKYPEEASELK Unmodified 1901.9411 0.94109472 54 F4JBY2;Q8RWV0 At3g60750;TKL-1 Transketolase-1, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By matching 1 1 1 23.037 22.902 4 0.018935 10668 22-052-Murphy-control-3 28.812 25.092 11224000 0 2311000 5522800 0 0 0 0 3389900 0 0 0 0 0 0 0 162 54 157 1984;1985;1986 1073 1073 1 FALSKGWVIEK Unmodified 1276.718 0.71795849 204 Q9S7Y7 XYL1 Alpha-xylosidase 1 yes yes 0 0 1 By matching By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 36.189 36.02 3 0.021777 33658 22-052-Murphy-SHP20infil-3 53.317 43.995 21810000 690170 502830 0 0 0 1102100 0 0 0 3883400 3021900 7425700 3686800 1496700 0 163 204 158 1987;1988;1989;1990;1991;1992;1993;1994 1074 1074 1 FFETFAAPFTK Unmodified 1304.6441 0.64412484 223 Q9SUI7;Q9SUI6 PSAH1;PSAH2 Photosystem I reaction center subunit VI-1, chloroplastic;Photosystem I reaction center subunit VI-2, chloroplastic yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 51.022 50.919 2 7.7335E-06 44268 22-052-Murphy-SHP20-PEI-LL-1 72.485 47.562 15138000 0 0 0 0 0 0 5247100 4068200 3672000 0 0 0 0 0 2150500 164 223 159 1995;1996;1997;1998 1075;1076 1075 0 FFETFAAPFTKR Unmodified 1460.7452 0.74523587 223 Q9SUI7;Q9SUI6 PSAH1;PSAH2 Photosystem I reaction center subunit VI-1, chloroplastic;Photosystem I reaction center subunit VI-2, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 43.082 42.998 3 0.0014111 36156 22-052-Murphy-SHP20-PEI-LL-1 58.676 44.713 21103000 0 0 0 0 0 0 9519700 6647700 4935900 0 0 0 0 0 0 165 223 160 1999;2000;2001 1077;1078;1079 1077 3 FFETFAAPFTKRGLLLK Unmodified 1985.1139 0.11385455 223 Q9SUI7;Q9SUI6 PSAH1;PSAH2 Photosystem I reaction center subunit VI-1, chloroplastic;Photosystem I reaction center subunit VI-2, chloroplastic yes no 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 3 2 2 1 2 49.184 49.071 3;4 7.5117E-22 41094 22-052-Murphy-SHP20-PEI-LL-2 68.972 63.868 453760000 778010 1591100 2255500 0 0 0 367520000 25418000 32818000 0 0 0 2541300 0 20839000 166 223 161 2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014 1080;1081;1082;1083;1084 1083 5 FGLAPSANR Unmodified 931.48756 0.48756462 222 Q9SUI5 PSAK Photosystem I reaction center subunit psaK, chloroplastic yes yes 0 0 0 By matching By MS/MS By matching By MS/MS 1 1 1 1 21.828 21.756 2 0.015738 13111 22-052-Murphy-SHP20-PEI-infil-1 60.788 25.682 9363900 873080 1818000 1380000 5292800 0 0 0 0 0 0 0 0 0 0 0 167 222 162 2015;2016;2017;2018 1085 1085 0 FGLAPSANRKATAGLR Unmodified 1628.9111 0.91107242 222 Q9SUI5 PSAK Photosystem I reaction center subunit psaK, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 2 1 1 1 1 1 1 19.028 18.863 4 0.016547 11429 22-052-Murphy-SHP20-PEI-LL-1 38.511 29.69 194440000 3193300 4717200 4189700 10547000 7553600 2295200 46588000 42868000 33724000 3996800 7127700 15659000 3922800 0 8060500 168 222 163 2019;2020;2021;2022;2023;2024;2025;2026;2027;2028;2029;2030;2031;2032;2033 1086;1087;1088 1087 3 FGQTFMGKNFRV Unmodified 1430.7129 0.71288988 144 Q38865 EXPA6 Expansin-A6 yes yes 0 0 2 By matching By MS/MS By matching 1 1 1 35.742 35.62 3 0.026147 22982 22-052-Murphy-control-3 31.431 28.48 4592700 0 1700800 1679600 0 0 0 0 0 1212200 0 0 0 0 0 0 169 144 164 2034;2035;2036 1089 1089 0 FGQTFMGKNFRV Oxidation (M) 1446.7078 0.70780451 144 Q38865 EXPA6 Expansin-A6 yes yes 0 1 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 29.458 29.311 3 0.0047278 21382 22-052-Murphy-SHP20-PEI-LL-3 54.066 39.808 177370000 7342500 9183000 16725000 8879700 8745700 2171500 42851000 13985000 25683000 5111400 6154100 15386000 5315900 2569300 7265700 170 144 164 2037;2038;2039;2040;2041;2042;2043;2044;2045;2046;2047;2048;2049;2050;2051;2052;2053;2054;2055;2056 1090;1091;1092;1093;1094;1095 1095 30 6 FIDTASIFGHGRFQTSLEK Unmodified 2153.0906 0.090552927 23 A8MQQ1;P17094 RP1;ARP1 60S ribosomal protein L3-1 yes no 0 0 1 By MS/MS By matching By MS/MS 1 1 1 41.475 41.388 4 0.00091758 34603 22-052-Murphy-SHP20-PEI-LL-1 33.307 15.818 13358000 0 0 0 0 0 0 6913600 3703000 2740900 0 0 0 0 0 0 171 23 165 2057;2058;2059 1096 1096 1 FLVPSYRGSSFLDPKGR Unmodified 1925.0159 0.015931421 87;206 P23321;Q9S841 PSBO1;PSBO2 Oxygen-evolving enhancer protein 1-1, chloroplastic;Oxygen-evolving enhancer protein 1-2, chloroplastic no no 0 0 2 By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 37.914 37.767 4 4.8717E-06 35672 22-052-Murphy-SHP20infil-3 57.159 46.674 68552000 0 824020 1309600 3207000 3907300 2449800 8902300 8458500 8470700 5575900 7980200 8565100 5681200 0 3220200 172 87;206 166 2060;2061;2062;2063;2064;2065;2066;2067;2068;2069;2070;2071;2072 1097;1098;1099;1100;1101;1102;1103 1098 7 FSLAPLVPR Unmodified 998.5913 0.59130141 37 F4I3L1;P50318 At1g56190 Phosphoglycerate kinase;Phosphoglycerate kinase 2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 45.237 45.111 2 7.145E-09 37605 22-052-Murphy-SHP20-PEI-LL-2 106.29 106.29 95050000 11428000 12100000 9883200 5643900 2531300 1641700 10444000 8065600 5708900 2912700 4124700 8452500 5195000 3299600 3618200 173 37 167 2073;2074;2075;2076;2077;2078;2079;2080;2081;2082;2083;2084;2085;2086;2087;2088;2089 1104;1105;1106;1107;1108;1109;1110;1111 1111 5 FSRSPYQEHTDFLASK Unmodified 1911.9115 0.91152593 109 P49688 RPS2C 40S ribosomal protein S2-3 yes yes 0 0 1 By matching By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 24.767 24.654 4 9.6216E-25 16710 22-052-Murphy-SHP20-PEI-LL-3 65.956 59.688 58634000 2401400 3705400 4017700 0 0 0 18523000 13029000 16957000 0 0 0 0 0 0 174 109 168 2090;2091;2092;2093;2094;2095 1112;1113 1113 2 FTGKQSYDL Unmodified 1057.508 0.50802529 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 22.987 22.805 2 3.4339E-60 8895 22-052-Murphy-control-1 135.6 129.94 393970000 35998000 41429000 62625000 13900000 5826800 0 80168000 38761000 45438000 5272000 9436400 22447000 10395000 3412500 18856000 175 202;207 169 2096;2097;2098;2099;2100;2101;2102;2103;2104;2105;2106;2107;2108;2109 1114;1115 1114 0 FVESLGVEK Unmodified 1006.5335 0.53351176 47 F4IVZ7;P10896 RCA Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic yes no 0 0 0 By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 2 2 1 1 1 1 26.796 26.607 2 0.0017028 18825 22-052-Murphy-SHP20-PEI-LL-2 80.462 12.064 83609000 0 3060900 4019900 6342700 0 0 15700000 9296700 11669000 0 7651800 10816000 6342900 2497400 6211400 176 47 170 2110;2111;2112;2113;2114;2115;2116;2117;2118;2119;2120;2121;2122 1116;1117;1118;1119;1120;1121 1120 6 FYLQPLPPTEAAARAKESAK Unmodified 2187.1688 0.16880325 231 Q9XFT3 PSBQ1 Oxygen-evolving enhancer protein 3-1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 2 2 1 1 1 1 2 31.789 31.668 3;4 1.8361E-32 24600 22-052-Murphy-SHP20-PEI-LL-1 65.716 56.897 149370000 2151500 0 3878800 22058000 0 0 23584000 9974000 12135000 6920000 15153000 53514000 0 0 0 177 231 171 2123;2124;2125;2126;2127;2128;2129;2130;2131;2132;2133;2134 1122;1123;1124;1125;1126;1127;1128;1129;1130 1127 9 GAFRFHQYQVVGR Unmodified 1563.8059 0.80587907 112 P51418 RPL18AB 60S ribosomal protein L18a-2 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS 2 2 2 2 2 5 3 4 2 2 1 2 2 2 24.311 24.143 2;3;4 1.3286E-32 16012 22-052-Murphy-SHP20-PEI-LL-3 91.041 81.853 937640000 11708000 21506000 39694000 12051000 9183900 0 320290000 227300000 202750000 9361600 13746000 14137000 21187000 9300100 25430000 178 112 172 2135;2136;2137;2138;2139;2140;2141;2142;2143;2144;2145;2146;2147;2148;2149;2150;2151;2152;2153;2154;2155;2156;2157;2158;2159;2160;2161;2162;2163;2164;2165;2166;2167 1131;1132;1133;1134;1135;1136;1137;1138;1139;1140;1141;1142;1143;1144;1145 1145 15 GAFRFHQYQVVGRALPTEK Unmodified 2203.1651 0.16505527 112 P51418 RPL18AB 60S ribosomal protein L18a-2 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 3 3 3 3 1 1 28.97 28.831 3;4;5 4.7959E-39 21497 22-052-Murphy-SHP20-PEI-LL-1 71.08 58.952 440950000 6775000 9765300 32906000 0 0 0 128840000 129540000 123440000 0 0 0 2275900 7411700 0 179 112 173 2168;2169;2170;2171;2172;2173;2174;2175;2176;2177;2178;2179;2180;2181;2182;2183 1146;1147;1148;1149;1150;1151;1152;1153;1154;1155;1156 1151 10 GALDGGLDIPHSDKR Unmodified 1549.7849 0.78486885 53 F4J912;Q8LBI1;P49227 ATL5;RPL5B 60S ribosomal protein L5-1;60S ribosomal protein L5-2 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 3 2 3 2 2 2 2 2 2 24.42 24.244 2;3;4 0.0055215 16360 22-052-Murphy-SHP20-PEI-LL-2 48.14 48.14 478760000 4123900 7219100 9719200 13166000 9045500 5575300 137910000 59687000 70930000 16327000 21417000 33537000 42325000 15720000 32061000 180 53 174 2184;2185;2186;2187;2188;2189;2190;2191;2192;2193;2194;2195;2196;2197;2198;2199;2200;2201;2202;2203;2204;2205;2206;2207;2208;2209;2210;2211;2212;2213;2214;2215 1157;1158;1159;1160;1161;1162;1163;1164;1165 1164 9 GALPGKPGNLLR Unmodified 1191.7088 0.70879078 215 Q9SKX4 RPL3A 50S ribosomal protein L3-1, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 21.94 21.753 2 0.0098939 14169 22-052-Murphy-SHP20-PEI-LL-1 32.61 24.191 20082000 0 0 0 0 0 0 6168000 6071300 6286900 0 0 0 0 0 1555700 181 215 175 2216;2217;2218;2219 1166 1166 1 GARKFVESAATSFSVA Unmodified 1626.8366 0.83657007 146 Q42029 PSBP1 Oxygen-evolving enhancer protein 2-1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 33.091 32.99 2 0.010118 25961 22-052-Murphy-SHP20-PEI-LL-1 51.436 50.396 49693000 5381900 3880500 7470500 0 0 0 13677000 7370200 11913000 0 0 0 0 0 0 182 146 176 2220;2221;2222;2223;2224;2225 1167;1168 1167 2 GFGFVTFKDEK Unmodified 1273.6343 0.63428844 43 F4JVC0;F4JVB9;F4JVC1;F4IHK9;Q03251;Q03250 CCR1;CCR2;RBG8;RBG7 Glycine-rich RNA-binding protein 8;Glycine-rich RNA-binding protein 7 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 33.988 33.878 3 0.0090188 17883 22-052-Murphy-control-1 52.79 45.661 28349000 5690400 5147000 7719400 0 0 0 4622000 5169900 0 0 0 0 0 0 0 183 43 177 2226;2227;2228;2229;2230 1169;1170 1169 2 GGFRFHQYQVVGR Unmodified 1549.7902 0.790229 192 Q9LUD4 RPL18AC 60S ribosomal protein L18a-3 yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 1 2 1 24.024 23.887 3;4 7.0864E-33 15870 22-052-Murphy-SHP20-PEI-LL-2 70.17 63.04 40635000 0 0 1938900 0 0 0 10971000 19833000 7892000 0 0 0 0 0 0 184 192 178 2231;2232;2233;2234;2235 1171;1172;1173;1174 1172 3 GGLGVGAFRR Unmodified 988.55665 0.55664724 210;185 Q9SGA6;Q9LF30;Q9FNP8 RPS19A;RPS19B;RPS19C 40S ribosomal protein S19-1;40S ribosomal protein S19-2;40S ribosomal protein S19-3 no no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 20.4 20.246 2 0.013828 11893 22-052-Murphy-SHP20-PEI-LL-3 44.531 0.90502 155240000 0 0 0 0 0 0 58251000 46836000 50150000 0 0 0 0 0 0 185 210;185 179 2236;2237;2238 1175 1175 1 GGVISFSKTAAR Unmodified 1192.6564 0.65642086 94 P33207 3-oxoacyl-[acyl-carrier-protein] reductase, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 2 2 2 1 2 1 2 2 1 2 2 1 1 2 17.799 17.609 2;3 0.0031486 14556 22-052-Murphy-SHP20infil-3 65.246 59.587 138660000 0 2356200 3446400 12051000 4801200 5309000 9728000 15325000 8880700 4424200 12774000 45580000 2780500 1403800 9800700 186 94 180 2239;2240;2241;2242;2243;2244;2245;2246;2247;2248;2249;2250;2251;2252;2253;2254;2255;2256;2257;2258;2259;2260;2261 1176;1177;1178 1177 3 GIDLIAGGK Unmodified 842.48617 0.48616764 100 Q940B0;P42791;O22254 RPL18C;RPL18B;RPL18A 60S ribosomal protein L18-3;60S ribosomal protein L18-2;Putative 60S ribosomal protein L18-1 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 28.278 28.084 2 0.0067197 20484 22-052-Murphy-SHP20-LL-3 72.021 7.4579 91699000 0 0 0 4127700 4119000 3582900 0 7842500 0 9867300 9693500 16244000 17093000 6657400 12473000 187 100 181 2262;2263;2264;2265;2266;2267;2268;2269;2270;2271 1179;1180;1181 1179 3 GIVYGKPTNQGVTQLK Unmodified 1701.9414 0.94136949 69 Q8VYF1;O23515 RPL15B;RPL15A 60S ribosomal protein L15-2;60S ribosomal protein L15-1 yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 2 1 1 1 1 1 1 1 23.131 22.954 3 1.1174E-38 14933 22-052-Murphy-SHP20-PEI-LL-3 87.498 87.498 175180000 1542300 2511100 3778300 5745600 4244100 0 52665000 27558000 32559000 6193500 5296300 10002000 9766100 3842900 9473000 188 69 182 2272;2273;2274;2275;2276;2277;2278;2279;2280;2281;2282;2283;2284;2285;2286 1182;1183;1184;1185;1186 1186 5 GIYPAVDPLDSTSTMLQPR Oxidation (M) 2076.0198 0.019755749 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 1 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 2 2 1 1 2 2 47.341 47.227 2;3 1.9871E-21 40426 22-052-Murphy-SHP20-PEI-LL-1 69.01 69.01 69837000 2043200 2139300 0 2534600 2304200 0 8614800 11905000 12205000 0 6599400 9064300 7952600 4474400 0 189 86 183 2287;2288;2289;2290;2291;2292;2293;2294;2295;2296;2297;2298;2299;2300;2301 1187;1188 1188 13 2 GLAAKGIYPAVDPLDSTSTMLQPR Oxidation (M) 2516.2945 0.29447405 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 43.886 43.783 3 3.7997E-53 38143 22-052-Murphy-SHP20-LL-1 63.488 60.765 48956000 4806200 8564000 12311000 2127300 9665500 581650 10900000 0 0 0 0 0 0 0 0 190 86 184 2302;2303;2304;2305;2306;2307;2308;2309;2310 1189;1190;1191;1192 1192 13 4 GLAAKGIYPAVDPLDSTSTMLQPR Unmodified 2500.2996 0.29955942 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 0 1 By matching By MS/MS By matching 1 1 1 48.712 48.638 3 2.483E-27 40995 22-052-Murphy-SHP20-PEI-LL-3 63.578 60.816 13449000 0 0 0 1753100 0 0 0 0 5715400 0 0 0 5980900 0 0 191 86 184 2311;2312;2313 1193 1193 1 GLAGSGNPAYPGGPFFNPLGFGKDEK Unmodified 2593.2601 0.26013745 225 Q9SY97 T25B24.12 yes yes 0 0 1 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 51.916 51.8 3 0.0090135 44249 22-052-Murphy-SHP20-PEI-LL-2 25.604 18.411 72633000 0 0 0 1665700 1373700 0 12431000 9874700 6863800 3561300 6420500 6563700 9587700 6838300 7452800 192 225 185 2314;2315;2316;2317;2318;2319;2320;2321;2322;2323;2324 1194 1194 1 GLDEKELAALASVGELK Unmodified 1741.9462 0.9461801 230 Q9XFI1 Thioredoxin-like 1-2, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 2 2 2 1 1 2 1 1 2 1 2 24.146 23.977 3 0.013517 11170 22-052-Murphy-SHP20infil-1 28.089 16.321 1667200000 24379000 20488000 38096000 44691000 41314000 22528000 318760000 122080000 95661000 147780000 107320000 122440000 355670000 27008000 178940000 193 230 186 2325;2326;2327;2328;2329;2330;2331;2332;2333;2334;2335;2336;2337;2338;2339;2340;2341;2342;2343;2344;2345;2346;2347;2348 1195;1196 1195 2 GLLSLCNELR Unmodified 1116.5961 0.59612879 1 A0A1I9LNY1;Q6NLP7 GDSL esterase/lipase At3g62280 yes no 0 0 0 By MS/MS 1 8.1756 7.9506 2 0.00028067 2683 22-052-Murphy-SHP20-PEI-LL-1 67.032 14.349 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 194 1 187 2349 1197 1197 1 GPAKFRSLDFGER Unmodified 1478.763 0.7630112 104;147 P46286;Q42064 RPL8A;RPL8C 60S ribosomal protein L8-1;60S ribosomal protein L8-3 no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 23.217 23.1 3 1.4826E-31 15685 22-052-Murphy-SHP20-PEI-LL-1 84.479 71.279 147370000 11493000 10629000 25975000 0 0 0 44812000 31018000 23448000 0 0 0 0 0 0 195 104;147 188 2350;2351;2352;2353;2354;2355 1198;1199;1200;1201 1200 4 GPAPLSLALAHADIDEAGK Unmodified 1844.9632 0.96322715 233 Q9ZR03 petC Cytochrome b6-f complex iron-sulfur subunit, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 42.611 42.481 3 0.0054513 28680 22-052-Murphy-control-3 31.801 27.766 12808000 2310600 2908300 5386600 0 0 0 0 0 0 0 0 0 0 0 2202300 196 233 189 2356;2357;2358;2359 1202 1202 1 GPGGDVAPVAAPAPAATPAPTAAVPKKK Unmodified 2506.3908 0.39075769 221 Q9SRX2 RPL19A 60S ribosomal protein L19-1 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 1 1 1 1 1 26.149 26.008 4 0.020403 18239 22-052-Murphy-SHP20-PEI-LL-3 21.667 21.667 39153000 0 0 0 2474200 0 3063500 11055000 7186400 8277800 0 0 7096700 0 0 0 197 221 190 2360;2361;2362;2363;2364;2365 1203 1203 1 GPNGLDLSRLK Unmodified 1168.6564 0.65642086 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 1 1 1 1 2 2 3 2 2 2 2 2 2 27.635 27.463 2;3 2.3149E-07 19453 22-052-Murphy-SHP20-PEI-LL-2 84.213 84.213 377880000 5168500 4559100 4077000 8522500 5051900 2622100 61127000 67929000 76976000 13357000 19724000 34610000 32893000 13160000 28099000 198 121 191 2366;2367;2368;2369;2370;2371;2372;2373;2374;2375;2376;2377;2378;2379;2380;2381;2382;2383;2384;2385;2386;2387;2388;2389;2390;2391 1204;1205;1206;1207;1208;1209;1210;1211;1212;1213 1209 10 GPNGLDLSRLKK Unmodified 1296.7514 0.75138388 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 20.94 20.723 3 2.5541E-09 12471 22-052-Murphy-SHP20-PEI-LL-2 83.499 57.454 223720000 0 0 0 5007800 4203700 0 37725000 39583000 39786000 6204100 13875000 18936000 25474000 8883400 24046000 199 121 192 2392;2393;2394;2395;2396;2397;2398;2399;2400;2401;2402 1214;1215;1216 1216 3 GPQEPPKLGPR Unmodified 1174.6459 0.64585618 223 Q9SUI7;Q9SUI6 PSAH1;PSAH2 Photosystem I reaction center subunit VI-1, chloroplastic;Photosystem I reaction center subunit VI-2, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 8.4094 8.2614 3 0.0088869 3147 22-052-Murphy-SHP20-PEI-LL-1 35.511 26.253 246950000 0 0 0 0 20681000 13584000 26218000 1034100 43291000 0 31446000 84093000 0 0 26600000 200 223 193 2403;2404;2405;2406;2407;2408;2409;2410 1217;1218;1219;1220;1221;1222 1221 6 GPSGSPWYGSDR Unmodified 1264.5473 0.54726434 80 Q39141;Q8VZ87;P0CJ48;P04778 Lhb1B2;LHCB1.2;LHCB1.1;LHCB1.3 Chlorophyll a-b binding protein 3, chloroplastic;Chlorophyll a-b binding protein 2, chloroplastic;Chlorophyll a-b binding protein 1, chloroplastic yes no 0 0 0 By MS/MS By MS/MS 1 1 23.724 23.441 2 0.0074326 17656 22-052-Murphy-SHP20infil-2 55.37 45.459 18915000 0 0 0 0 0 0 0 0 0 0 3582200 15332000 0 0 0 201 80 194 2411;2412 1223 1223 1 GQKINPLGFR Unmodified 1128.6404 0.64037687 125 P56798 rps3 30S ribosomal protein S3, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching 1 1 1 1 1 1 1 1 1 1 1 1 24.346 24.175 3 0.003123 16666 22-052-Murphy-SHP20-PEI-LL-1 50.607 42.386 67090000 3559000 4165300 4995300 5170400 0 1260400 14686000 7677600 10744000 0 2767200 5784400 3363900 0 2916500 202 125 195 2413;2414;2415;2416;2417;2418;2419;2420;2421;2422;2423;2424 1224;1225 1225 1 GQSPLTSLTQRMEKICDVTR Unmodified 2262.146 0.14603567 52 F4J405 At3g17140 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 8.8369 8.7484 4 0.004696 2393 22-052-Murphy-control-1 4.1063 0 168830000 34265000 30307000 34308000 0 0 0 0 52801000 6773900 0 0 0 0 0 10377000 203 52 196 2425;2426;2427;2428;2429;2430 1226 1226 1 GRLPDGTLIAVK Unmodified 1238.7347 0.73467118 9 A0A1P8AUL0;A0A1P8AUP1;F4I336;A0A1P8AUL5 At1g29730 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 24.502 24.321 2 0.00011172 17226 22-052-Murphy-SHP20infil-1 60.59 29.516 74236000 2255400 2214400 3373800 5051700 0 0 11665000 9674400 8152800 3265900 5045600 11528000 5532800 2679600 3796200 204 9 197 2431;2432;2433;2434;2435;2436;2437;2438;2439;2440;2441;2442;2443 1227;1228;1229;1230;1231 1227 3 GVTKKPDLNDPVLR Unmodified 1550.878 0.87804096 120 P56774 petD Cytochrome b6-f complex subunit 4 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 1 1 2 2 2 2 1 1 1 1 1 19.108 18.941 3;4 1.6446E-13 11418 22-052-Murphy-SHP20-PEI-LL-1 53.967 53.335 364560000 6955400 12482000 26736000 22421000 11478000 4965500 35695000 79189000 72087000 24484000 17704000 25546000 11759000 3112500 9946800 205 120 198 2444;2445;2446;2447;2448;2449;2450;2451;2452;2453;2454;2455;2456;2457;2458;2459;2460;2461;2462;2463;2464;2465 1232;1233;1234;1235;1236;1237 1236 4 GVVTEIIHDPGRGAPLAR Unmodified 1857.0221 0.022079431 104;147 P46286;Q42064 RPL8A;RPL8C 60S ribosomal protein L8-1;60S ribosomal protein L8-3 no no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 2 2 2 1 1 1 2 1 1 1 31.405 31.289 3;4 2.9942E-29 23497 22-052-Murphy-SHP20-PEI-LL-2 72.898 64.984 155990000 3735800 5434100 10500000 2345700 0 0 40870000 28242000 55217000 3373400 0 0 0 3491700 2784400 206 104;147 199 2466;2467;2468;2469;2470;2471;2472;2473;2474;2475;2476;2477;2478;2479 1238;1239;1240;1241;1242;1243;1244 1242 7 HAVSEGTKAVTKFTSS Unmodified 1648.842 0.84204938 70 Q9LZT0;P40283;O23629;Q9FFC0;Q9LQQ4;Q9SI96;Q9SF55;Q9LZ45;Q9LFF6 H2B Histone H2B.7;Histone H2B.11;Histone H2B.6;Histone H2B.10;Histone H2B.1;Histone H2B.3;Histone H2B.5;Histone H2B.9;Histone H2B.8 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 3 3 2 2 2 2 3 3 3 3 2 3 8.7932 8.67 2;3 0 2753 22-052-Murphy-control-3 164.43 139.57 4137100000 206950000 209660000 408330000 160230000 166640000 60807000 903600000 689140000 663450000 42176000 94952000 361280000 64121000 0 105740000 207 70 200 2480;2481;2482;2483;2484;2485;2486;2487;2488;2489;2490;2491;2492;2493;2494;2495;2496;2497;2498;2499;2500;2501;2502;2503;2504;2505;2506;2507;2508;2509;2510;2511;2512;2513;2514 1245;1246;1247;1248;1249;1250;1251;1252;1253;1254;1255;1256;1257;1258;1259;1260;1261;1262;1263;1264;1265 1249 21 HIEEELHHTK Unmodified 1271.6258 0.62584901 14 A0A1P8B3P8;F4JW21;A0A1P8B3N6;F4JW20 At4g39420 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 27.109 26.949 2 0.003062 19858 22-052-Murphy-SHP20-PEI-LL-1 55.717 55.717 148800000 5988200 9456500 6604300 12157000 10066000 4233500 61749000 0 0 9519000 7793000 16530000 0 4699600 0 208 14 201 2515;2516;2517;2518;2519;2520;2521;2522;2523;2524;2525 1266;1267;1268;1269;1270;1271;1272 1272 4 IAAISVAQR Unmodified 927.55016 0.55016488 41 F4I9Q5 At1g58060 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS 1 1 1 8.1994 8.0626 2 0.00042295 2964 22-052-Murphy-SHP20-PEI-LL-3 64.776 21.71 240630000 0 0 0 0 0 0 94576000 80338000 65715000 0 0 0 0 0 0 209 41 202 2526;2527;2528 1273;1274 1274 2 IAIQAGAAGIIVSNHGAR Unmodified 1717.9588 0.95875089 27 A8MS37;B3H4B8;Q9LRR9;F4JFV6;Q9LRS0 At3g14420;GLO1;At3g14415;GLO2 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1;Peroxisomal (S)-2-hydroxy-acid oxidase GLO2 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 33.346 33.176 3 0.0065497 30713 22-052-Murphy-SHP20infil-3 28.549 17.761 54588000 0 2562800 0 3990600 0 1849000 11064000 5883200 0 0 5422400 15418000 4154700 0 4243200 210 27 203 2529;2530;2531;2532;2533;2534;2535;2536;2537 1275 1275 1 IDISGVNTEK Unmodified 1074.5557 0.55570376 186 Q9FZ76 RPL6A 60S ribosomal protein L6-1 yes yes 0 0 0 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 23.994 23.726 2 0.0044027 17649 22-052-Murphy-SHP20-LL-1 63.565 26.544 76648000 0 0 0 0 0 3471200 0 0 0 10180000 9872600 16309000 18316000 4952900 13547000 211 186 204 2538;2539;2540;2541;2542;2543;2544 1276;1277 1277 1 IDMTTTVLGFK Oxidation (M) 1240.6373 0.6373249 27 A8MS37;B3H4B8;Q9LRR9;Q2V3V9 At3g14420;GLO1 Peroxisomal (S)-2-hydroxy-acid oxidase GLO1 yes no 0 1 0 By MS/MS 1 37.308 37.092 2 2.035E-08 34950 22-052-Murphy-SHP20infil-3 67.981 51.205 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 212 27 205 2545 1278 1278 2 1 IFPDKPVTVRPAETR Unmodified 1724.9574 0.95735391 124 P56793 rpl16 50S ribosomal protein L16, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 1 2 2 1 1 2 2 1 1 2 1 2 1 22.069 21.895 3;4 5.5237E-15 16034 22-052-Murphy-SHP20infil-2 69.602 64.971 417270000 10578000 14762000 13558000 16492000 17723000 4404700 66262000 84367000 74758000 9897400 14047000 52120000 14828000 7014400 16456000 213 124 206 2546;2547;2548;2549;2550;2551;2552;2553;2554;2555;2556;2557;2558;2559;2560;2561;2562;2563;2564;2565;2566;2567;2568 1279;1280;1281;1282;1283;1284;1285;1286;1287;1288;1289;1290;1291;1292;1293;1294 1283 11 IFPRPTSGPLRPVVHGQTLK Unmodified 2199.264 0.26404104 21;179 P41127;A8MQA1;F4IWP7;Q9FF90 RPL13B;BBC1;RPL13D 60S ribosomal protein L13-1;60S ribosomal protein L13;60S ribosomal protein L13-3 no no 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 25.985 25.826 5 0.0040703 17712 22-052-Murphy-SHP20-PEI-LL-3 31.514 23.227 65595000 0 2460300 575720 0 0 0 20709000 21948000 14714000 0 0 0 0 0 5188200 214 21;179 207 2569;2570;2571;2572;2573;2574 1295 1295 1 IGATSDLQSVK Unmodified 1117.5979 0.59790293 71 O49006 PME3 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21.152 20.963 2 0.012445 12228 22-052-Murphy-SHP20-PEI-infil-1 70.919 53.533 189630000 5531700 4577500 4234800 14655000 9556800 0 7547900 10456000 5704000 13791000 24171000 68867000 9507000 1849800 9182400 215 71 208 2575;2576;2577;2578;2579;2580;2581;2582;2583;2584;2585;2586;2587;2588 1296 1296 1 IGEITSGGFSPNLK Unmodified 1418.7405 0.74054442 19 A0A2H1ZEA9;O65396 GDCST Aminomethyltransferase, mitochondrial yes no 0 0 0 By MS/MS 1 37.37 37.175 2 0.029134 26084 22-052-Murphy-SHP20-PEI-infil-3 35.944 7.5451 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 216 19 209 2589 1297 1297 1 IGEITSGGFSPNLKK Unmodified 1546.8355 0.83550744 19 A0A2H1ZEA9;O65396 GDCST Aminomethyltransferase, mitochondrial yes no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 29.345 29.151 3 2.026E-08 26420 22-052-Murphy-SHP20infil-3 49.929 38.489 39148000 0 0 0 0 8776800 6095200 0 0 0 0 0 24276000 0 0 0 217 19 210 2590;2591;2592 1298;1299 1298 2 IGEITSGGFSPNLKKNIAMGYVK Unmodified 2423.2883 0.28826646 19 A0A2H1ZEA9;O65396 GDCST Aminomethyltransferase, mitochondrial yes no 0 0 2 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 38.352 38.284 4 0.0081115 31470 22-052-Murphy-SHP20-PEI-LL-1 31.753 28.952 15754000 2417000 0 0 0 0 0 5715800 5254900 2366100 0 0 0 0 0 0 218 19 211 2593;2594;2595;2596 1300 1300 1 IGEVTKIFTHNSTIVIK Unmodified 1899.0829 0.082948354 136 P92959 RPL24 50S ribosomal protein L24, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 35.714 35.568 3;4 2.352E-11 27888 22-052-Murphy-SHP20-PEI-LL-3 71.344 55.5 623120000 15097000 19715000 15321000 28741000 14822000 5052100 164460000 94442000 85019000 25628000 28833000 45445000 32083000 16849000 31612000 219 136 212 2597;2598;2599;2600;2601;2602;2603;2604;2605;2606;2607;2608;2609;2610;2611;2612;2613;2614;2615;2616;2617;2618;2619;2620;2621;2622;2623;2624;2625;2626 1301;1302;1303;1304;1305;1306 1306 5 IGGIGTVPVGR Unmodified 1024.6029 0.60292873 36 F4HUA0;Q8W4H7;Q8GTY0;Q0WL56;P0DH99 At1g07930;A2;A4;A3;A1 Elongation factor 1-alpha 2;Elongation factor 1-alpha 4;Elongation factor 1-alpha 3;Elongation factor 1-alpha 1 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 29.101 28.926 2 1.1238E-06 26067 22-052-Murphy-SHP20infil-3 67.032 48.301 113030000 1755800 3890500 4119200 18739000 6228500 3670900 0 0 0 7681600 10841000 42260000 6840600 2122800 4878200 220 36 213 2627;2628;2629;2630;2631;2632;2633;2634;2635;2636;2637;2638 1307;1308;1309;1310 1308 1 IGINGFGR Unmodified 832.45554 0.45553621 34 F4HQT1;Q9FX54;P25858 GAPC2;GAPC1 Glyceraldehyde-3-phosphate dehydrogenase GAPC2, cytosolic;Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 29.102 28.932 2 1.8624E-05 16828 22-052-Murphy-control-3 93.595 15.594 316050000 18432000 21370000 31588000 24985000 4881600 0 85138000 31623000 0 0 18502000 27726000 19538000 7090100 25179000 221 34 214 2639;2640;2641;2642;2643;2644;2645;2646;2647;2648;2649;2650 1311;1312;1313;1314;1315 1314 5 IGINGFGRIGR Unmodified 1158.6622 0.66217494 34 F4HQT1;Q9FX54;P25858 GAPC2;GAPC1 Glyceraldehyde-3-phosphate dehydrogenase GAPC2, cytosolic;Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 1 1 1 1 1 1 1 30.598 30.42 3 0.028299 24735 22-052-Murphy-SHP20-LL-1 27.329 8.0862 34681000 0 0 0 0 0 1218300 4450500 7262600 5748000 3078300 4510300 0 6478000 1934500 0 222 34 215 2651;2652;2653;2654;2655;2656;2657;2658 1316 1316 1 IGLFGGAGVGK Unmodified 974.55492 0.5549159 86 P19366;P83484;P83483;Q9C5A9 atpB ATP synthase subunit beta, chloroplastic;ATP synthase subunit beta-2, mitochondrial;ATP synthase subunit beta-1, mitochondrial;ATP synthase subunit beta-3, mitochondrial yes no 0 0 0 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 35.313 35.166 2 2.1383E-23 29691 22-052-Murphy-SHP20-LL-1 86.113 61.114 148390000 2708600 2562700 2324700 7106600 5854500 6597900 14051000 14030000 13592000 7017500 9655800 25328000 15478000 7052300 15033000 223 86 216 2659;2660;2661;2662;2663;2664;2665;2666;2667;2668;2669;2670;2671;2672;2673 1317;1318;1319;1320;1321;1322;1323;1324 1319 7 IGQMVQIER Oxidation (M) 1088.5648 0.56482866 18 Q8W112;A0A1P8BG25 At5g20950 yes no 0 1 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 1 2 2 19.241 19.047 2 4.5288E-07 9541 22-052-Murphy-SHP20-PEI-infil-1 74.415 51.396 319500000 3324400 0 4188000 23444000 14397000 10696000 37881000 32857000 25044000 9947800 35220000 96917000 7035000 6777400 11772000 224 18 217 2674;2675;2676;2677;2678;2679;2680;2681;2682;2683;2684;2685;2686;2687;2688;2689;2690;2691;2692;2693;2694;2695;2696;2697;2698;2699;2700 1325;1326;1327;1328;1329;1330;1331;1332 1327 1 6 IGQMVQIER Unmodified 1072.5699 0.56991404 18 Q8W112;A0A1P8BG25 At5g20950 yes no 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 26.205 25.968 2 0.0028085 23217 22-052-Murphy-SHP20infil-3 72.138 46.402 109370000 0 0 0 0 0 975950 0 0 0 789340 0 70730000 20392000 0 16477000 225 18 217 2701;2702;2703;2704;2705 1333 1333 1 IGRIEDVTPIPTDSTR Unmodified 1768.9319 0.93192702 98;176;213 P42036;Q9CAX6;Q9SIH0 RPS14C;RPS14B;RPS14A 40S ribosomal protein S14-3;40S ribosomal protein S14-2;40S ribosomal protein S14-1 no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 32.775 32.666 3 1.0171E-17 24333 22-052-Murphy-SHP20-PEI-infil-1 67.964 56.525 52397000 2317600 3217500 0 4784100 3710000 3907300 8642100 11400000 7476600 0 0 6941600 0 0 0 226 98;176;213 218 2706;2707;2708;2709;2710;2711;2712;2713;2714 1334;1335;1336;1337;1338;1339;1340 1335 7 IGRIEDVTPIPTDSTRR Unmodified 1925.033 0.033038048 98;176;213 P42036;Q9CAX6;Q9SIH0 RPS14C;RPS14B;RPS14A 40S ribosomal protein S14-3;40S ribosomal protein S14-2;40S ribosomal protein S14-1 no no 0 0 2 By MS/MS By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 28.131 28.024 4 0.0085086 20154 22-052-Murphy-SHP20-PEI-LL-3 31.319 25.539 28555000 0 0 1998000 2986200 2206400 0 6932000 8223700 6208200 0 0 0 0 0 0 227 98;176;213 219 2715;2716;2717;2718;2719;2720 1341;1342 1342 2 IIGTWLGLCIQDK Unmodified 1458.7905 0.7904715 138 Q0WPH4 At2g21840 yes yes 0 0 0 By MS/MS 1 46.366 46.343 2 0.01389 38774 22-052-Murphy-SHP20-PEI-LL-3 49.813 22.071 1095400 0 0 0 0 0 0 0 0 1095400 0 0 0 0 0 0 228 138 220 2721 1343 1343 0 IINSDEIQSVVNPIKK Unmodified 1796.0044 0.0043636815 141 Q2V3X4;Q9SF40 At3g09630;RPL4A 60S ribosomal protein L4-1 yes no 0 0 1 By MS/MS By MS/MS By matching 1 1 1 37.194 37.116 3 0.0093445 30219 22-052-Murphy-SHP20-PEI-LL-1 53.754 47.974 11521000 0 0 0 1855600 0 0 5612800 4052300 0 0 0 0 0 0 0 229 141 221 2722;2723;2724 1344 1344 1 IINSDEIQSVVNPIKKDAK Unmodified 2110.1634 0.16338352 141 Q2V3X4;Q9SF40 At3g09630;RPL4A 60S ribosomal protein L4-1 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 34.485 34.359 4 0.00082802 27288 22-052-Murphy-SHP20-PEI-LL-1 33.872 29.838 41879000 0 0 0 2052200 0 0 21121000 6248000 5730700 0 0 4520100 0 0 2207100 230 141 222 2725;2726;2727;2728;2729;2730 1345;1346 1345 2 IINSDEVQSVVNPIKDGSK Unmodified 2041.0691 0.069148783 63 F4KDU5;P49691 At5g02870;RPL4D 60S ribosomal protein L4-2 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 35.695 35.591 3 0.0028453 28771 22-052-Murphy-SHP20-PEI-LL-1 35.64 32.091 25575000 0 0 0 3042300 0 0 9520600 5568200 4222100 0 0 0 0 0 3222300 231 63 223 2731;2732;2733;2734;2735 1347;1348 1347 2 IIRSPEPEVK Acetyl (Protein N-term) 1208.6765 0.6764876 118 P56766 psaA Photosystem I P700 chlorophyll a apoprotein A1 yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 3 1 1 1 2 2 1 1 1 1 2 2 3 2 2 31.953 31.787 2 2.8716E-119 27971 22-052-Murphy-SHP20infil-3 124.83 89.539 7214300000 116440000 173620000 117770000 430280000 332130000 246630000 308060000 388990000 361200000 639730000 863380000 1694400000 769860000 303750000 468080000 232 118 224 2736;2737;2738;2739;2740;2741;2742;2743;2744;2745;2746;2747;2748;2749;2750;2751;2752;2753;2754;2755;2756;2757;2758;2759;2760 1349;1350;1351;1352;1353;1354;1355;1356;1357;1358;1359;1360;1361;1362;1363;1364;1365;1366;1367;1368;1369;1370;1371;1372;1373;1374;1375;1376;1377;1378;1379;1380;1381;1382;1383;1384;1385;1386;1387;1388;1389;1390;1391;1392;1393;1394;1395;1396 1362 48 ILSLLPFLNNQK Unmodified 1398.8235 0.82348619 126 P56807 rps18 30S ribosomal protein S18, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By matching 1 1 1 59.014 58.939 2 0.0093235 48967 22-052-Murphy-SHP20-PEI-LL-2 54.549 32.463 6935700 0 0 0 0 0 0 3917200 1557800 1460700 0 0 0 0 0 0 233 126 225 2761;2762;2763 1397 1397 1 ILSLLPFLNNQKQFER Unmodified 1959.0942 0.094181742 126 P56807 rps18 30S ribosomal protein S18, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 53.355 53.265 3 2.8678E-60 45609 22-052-Murphy-SHP20-PEI-LL-2 105.03 99.924 193240000 8954000 10051000 21527000 4161700 1749200 0 72223000 34696000 36794000 0 0 0 0 0 3080400 234 126 226 2764;2765;2766;2767;2768;2769;2770;2771;2772 1398;1399;1400;1401;1402 1401 5 ILSLLPFLNNQKQFERSESTPR Unmodified 2616.4024 0.40238501 126 P56807 rps18 30S ribosomal protein S18, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS 1 1 1 47.078 46.935 4 0.0045194 31901 22-052-Murphy-control-3 39.385 32.587 13270000 0 3246800 6308000 0 0 0 3715500 0 0 0 0 0 0 0 0 235 126 227 2773;2774;2775 1403 1403 1 ILVDRDPIK Unmodified 1067.6339 0.63389451 118 P56766 psaA Photosystem I P700 chlorophyll a apoprotein A1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 21.63 21.42 2 1.6522E-15 13209 22-052-Murphy-SHP20-PEI-LL-2 110.61 74.426 103470000 0 0 0 4605300 2229000 1413300 8013100 11946000 6972300 8145900 10840000 22057000 10442000 6622000 10181000 236 118 228 2776;2777;2778;2779;2780;2781;2782;2783;2784;2785;2786;2787 1404;1405;1406;1407 1407 2 IPPAYTKTFQGPPHGIQVER Unmodified 2235.18 0.18003664 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 30.168 29.991 4 1.0789E-50 22792 22-052-Murphy-SHP20-PEI-LL-1 85.563 73.607 116560000 0 0 1382000 4249100 3047000 0 24763000 23987000 18202000 0 8775700 12776000 6449500 4321300 8605500 237 64 229 2788;2789;2790;2791;2792;2793;2794;2795;2796;2797;2798 1408;1409;1410 1408 3 IQGIPHLRPTEYKR Unmodified 1706.958 0.95802261 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS 1 2 1 20.552 20.407 4 0.00017149 12773 22-052-Murphy-SHP20-PEI-LL-1 47.712 40.983 35951000 0 0 0 0 0 0 11727000 15100000 9123900 0 0 0 0 0 0 238 178 230 2799;2800;2801;2802 1411;1412 1411 2 IQKGPVRGISLK Unmodified 1294.8085 0.80850483 106 Q9SQZ1;Q9SJ36;Q9LZ17;P49205 RPS17C;RPS17B;RPS17D;RPS17A 40S ribosomal protein S17-3;40S ribosomal protein S17-2;40S ribosomal protein S17-4;40S ribosomal protein S17-1 yes no 0 0 2 By matching By matching By matching By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 2 1 1 8.7164 8.6161 2;3 0.0082055 3432 22-052-Murphy-SHP20-PEI-LL-3 39.625 27.706 96882000 3682700 4063800 4782700 4479500 4596900 0 26723000 23324000 25230000 0 0 0 0 0 0 239 106 231 2803;2804;2805;2806;2807;2808;2809;2810;2811 1413;1414 1414 2 IRIGINGFGR Unmodified 1101.6407 0.64071122 34 F4HQT1;Q9FX54;P25858 GAPC2;GAPC1 Glyceraldehyde-3-phosphate dehydrogenase GAPC2, cytosolic;Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic yes no 0 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 31.554 31.452 3 0.0012748 23809 22-052-Murphy-SHP20-PEI-LL-2 45.68 36.323 21218000 983780 1751500 973360 0 0 0 5456300 4851400 7201600 0 0 0 0 0 0 240 34 232 2812;2813;2814;2815;2816;2817 1415;1416 1415 2 ISDFLSPK Unmodified 905.48583 0.48583328 81 P0DKC4;P0DKC3 PGLP1B;PGLP1A Phosphoglycolate phosphatase 1B, chloroplastic;Phosphoglycolate phosphatase 1A, chloroplastic yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 29.504 29.395 2 3.1575E-08 17124 22-052-Murphy-control-3 114.54 47.546 21398000 4303300 4830000 6823900 1685200 0 0 0 0 2663800 0 0 0 0 1092200 0 241 81 233 2818;2819;2820;2821;2822;2823 1417 1417 0 ISLIQSAPQTNK Unmodified 1298.7194 0.71941505 199 Q9M3D6 ABCG19 ABC transporter G family member 19 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 2 2 1 2 2 2 2 2 2 2 3 29.399 29.225 2 0.00038452 21745 22-052-Murphy-SHP20infil-2 71.379 33.904 1081900000 6871600 6128500 6669200 36602000 23152000 13061000 106970000 143320000 122040000 61957000 106580000 156270000 127120000 46201000 118970000 242 199 234 2824;2825;2826;2827;2828;2829;2830;2831;2832;2833;2834;2835;2836;2837;2838;2839;2840;2841;2842;2843;2844;2845;2846;2847;2848;2849;2850 1418;1419 1418 2 ISQLVNTAPGIPR Unmodified 1364.7776 0.77759863 211 Q9SGZ5 BXL7 Probable beta-D-xylosidase 7 yes yes 0 0 0 By MS/MS By MS/MS 1 1 33.897 33.683 2 0.0024066 31309 22-052-Murphy-SHP20infil-3 65.224 47.405 9187500 0 0 0 0 0 2145500 0 0 0 0 0 7042000 0 0 0 243 211 235 2851;2852 1420 1420 0 ISVYPREIVPENPNSYRAR Unmodified 2259.176 0.17601389 183 Q9FLN4 RPL27 50S ribosomal protein L27, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 31.346 31.237 4 0.0028081 18804 22-052-Murphy-control-3 33.697 25.705 10008000 2484800 2359700 3289500 0 1873800 0 0 0 0 0 0 0 0 0 0 244 183 236 2853;2854;2855;2856 1421 1421 1 ITLDPEDPAAVK Unmodified 1267.666 0.66598249 44 F4III4;Q9SJ12 MGP1 Probable ATP synthase 24 kDa subunit, mitochondrial yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 33.763 33.62 2 8.8661E-06 31340 22-052-Murphy-SHP20infil-3 60.973 26.165 55298000 0 0 0 3552000 3928200 2734300 7314100 6302400 4896700 2792000 7905500 13363000 0 0 2510300 245 44 237 2857;2858;2859;2860;2861;2862;2863;2864;2865;2866 1422;1423;1424 1422 1 ITLDPEDPAAVKQYANVMK Oxidation (M) 2118.0667 0.066705942 44 F4III4;Q9SJ12 MGP1 Probable ATP synthase 24 kDa subunit, mitochondrial yes no 0 1 1 By matching By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 37.169 37.028 3 1.2071E-29 29317 22-052-Murphy-SHP20-PEI-LL-3 71.344 57.512 190100000 2528900 4740600 6890600 6843500 0 0 39719000 34060000 31971000 7391600 12078000 17831000 12178000 6281000 7588700 246 44 238 2867;2868;2869;2870;2871;2872;2873;2874;2875;2876;2877;2878;2879 1425;1426 1426 6 2 ITPAKIVGVNIPK Unmodified 1348.8442 0.84422163 215 Q9SKX4 RPL3A 50S ribosomal protein L3-1, chloroplastic yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 31.888 31.813 3 0.014632 24026 22-052-Murphy-SHP20-PEI-LL-3 57.348 54.639 56326000 0 0 0 3863400 0 0 17991000 20228000 14243000 0 0 0 0 0 0 247 215 239 2880;2881;2882;2883 1427 1427 1 ITPAKIVGVNIPKN Unmodified 1462.8871 0.88714908 215 Q9SKX4 RPL3A 50S ribosomal protein L3-1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 30.912 30.756 2;3 2.3E-16 23278 22-052-Murphy-SHP20-PEI-LL-2 91.853 82.895 1847300000 25814000 43322000 66222000 48859000 30112000 7432600 425410000 326270000 313280000 77445000 113120000 129220000 95395000 50861000 94482000 248 215 240 2884;2885;2886;2887;2888;2889;2890;2891;2892;2893;2894;2895;2896;2897;2898;2899;2900;2901;2902;2903;2904;2905;2906;2907;2908;2909;2910;2911;2912 1428;1429;1430;1431;1432;1433;1434;1435;1436;1437;1438;1439;1440;1441;1442;1443;1444 1442 12 ITREKVNGTTVNVGIQPSK Unmodified 2040.1328 0.13275209 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 2 2 2 3 3 3 2 3 3 3 3 3 18.768 18.551 2;3;4 4.1005E-73 11293 22-052-Murphy-SHP20-PEI-LL-1 115.8 115.8 2278000000 15437000 1038100 19775000 41035000 38107000 17843000 460930000 326110000 249000000 120300000 182570000 255180000 231170000 157420000 162110000 249 111 241 2913;2914;2915;2916;2917;2918;2919;2920;2921;2922;2923;2924;2925;2926;2927;2928;2929;2930;2931;2932;2933;2934;2935;2936;2937;2938;2939;2940;2941;2942;2943;2944;2945;2946;2947;2948 1445;1446;1447;1448;1449;1450;1451;1452;1453;1454;1455;1456;1457;1458;1459;1460;1461;1462;1463;1464;1465;1466;1467;1468;1469;1470;1471;1472;1473 1466 25 IVGVNIPKN Unmodified 952.57057 0.57056597 215 Q9SKX4 RPL3A 50S ribosomal protein L3-1, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.609 26.439 2 0.0013816 14450 22-052-Murphy-control-3 65.331 48.404 833830000 9275600 13654000 22269000 22473000 20036000 11551000 66280000 57633000 52395000 80591000 95181000 133690000 116740000 53040000 79013000 250 215 242 2949;2950;2951;2952;2953;2954;2955;2956;2957;2958;2959;2960;2961;2962;2963 1474;1475;1476;1477;1478;1479;1480;1481;1482;1483;1484;1485 1474 9 IWDAKPLVNGREIMQIAELK Unmodified 2323.2722 0.27222246 8 F4I2Y2;Q94K06;A0A1P8AU61 At1g22660;T22J18.17 yes no 0 0 2 By matching By matching By MS/MS By MS/MS 1 1 1 1 19.814 19.656 6 0.010707 11420 22-052-Murphy-SHP20-PEI-LL-3 15.09 8.3666 14433000 0 0 1269700 0 0 0 6100700 3379400 3682900 0 0 0 0 0 0 251 8 243 2964;2965;2966;2967 1486;1487 1487 2 KATLVVGNVLPLR Unmodified 1378.866 0.86601971 104;147 P46286;Q42064 RPL8A;RPL8C 60S ribosomal protein L8-1;60S ribosomal protein L8-3 no no 0 0 1 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 37.674 37.571 3 4.1204E-13 30557 22-052-Murphy-SHP20-PEI-LL-1 72.652 72.652 21727000 909720 1537500 2921000 0 1187100 0 6204300 3926500 5041100 0 0 0 0 0 0 252 104;147 244 2968;2969;2970;2971;2972;2973;2974 1488;1489;1490;1491 1489 4 KDAATALFNLSIHQENK Unmodified 1898.985 0.98502522 11 A0A1P8AYN7;F4ILG6;O22193 At2g23140;PUB4 U-box domain-containing protein 4 yes no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 9.3621 9.2686 3 0.0095985 4233 22-052-Murphy-SHP20-PEI-LL-2 17.489 4.9965 322130000 0 0 0 0 6868800 0 0 160820000 154440000 0 0 0 0 0 0 253 11 245 2975;2976;2977 1492 1492 1 KFVESAATSFSVA Unmodified 1342.6769 0.67688153 146 Q42029 PSBP1 Oxygen-evolving enhancer protein 2-1, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 35.489 35.389 2 0.023764 27795 22-052-Murphy-SHP20-PEI-LL-3 36.693 24.468 41188000 5263900 6202500 11317000 0 0 0 8363600 2868400 7173100 0 0 0 0 0 0 254 146 246 2978;2979;2980;2981;2982;2983 1493;1494 1494 2 KGLTPSQIGVILR Unmodified 1380.8453 0.84528426 127 P59224;P59223 RPS13B;RPS13A 40S ribosomal protein S13-2;40S ribosomal protein S13-1 yes no 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 35.673 35.53 3 0.01459 28016 22-052-Murphy-SHP20-PEI-LL-2 54.198 48.714 18846000 0 0 5108700 0 0 0 8991000 4746100 0 0 0 0 0 0 0 255 127 247 2984;2985;2986 1495;1496;1497 1497 3 KGPLVVFGTEGAK Unmodified 1301.7343 0.73433683 63 F4KDU5;P49691 At5g02870;RPL4D 60S ribosomal protein L4-2 yes no 0 0 1 By matching By MS/MS By MS/MS 1 1 1 26.39 26.27 3 4.2657E-06 19039 22-052-Murphy-SHP20-PEI-LL-1 48.188 37.43 33158000 0 1168600 0 0 0 0 18956000 0 13033000 0 0 0 0 0 0 256 63 248 2987;2988;2989 1498;1499 1498 1 KGPLVVFGTEGAKIVK Unmodified 1641.9818 0.98177775 63 F4KDU5;P49691 At5g02870;RPL4D 60S ribosomal protein L4-2 yes no 0 0 2 By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 30.743 30.643 3 0.027805 23373 22-052-Murphy-SHP20-PEI-LL-1 41.996 37.753 39528000 0 0 2634800 1833700 0 0 16588000 9293400 9178300 0 0 0 0 0 0 257 63 249 2990;2991;2992;2993;2994 1500 1500 1 KGPLVVYGTEGSK Unmodified 1333.7242 0.72416608 141 Q2V3X4;Q9SF40 At3g09630;RPL4A 60S ribosomal protein L4-1 yes no 0 0 1 By matching By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 2 1 1 1 2 2 1 2 17.186 17.002 2;3 1.4032E-05 9983 22-052-Murphy-SHP20-PEI-LL-1 70.816 66.033 77576000 0 915050 2754900 587900 1011500 0 15638000 26689000 22616000 0 0 0 0 1430100 5933000 258 141 250 2995;2996;2997;2998;2999;3000;3001;3002;3003;3004;3005;3006;3007 1501;1502;1503 1501 1 KGVTTIIGGGDSVAAVEK Unmodified 1700.9309 0.93086439 37 F4I3L1;P50318 At1g56190 Phosphoglycerate kinase;Phosphoglycerate kinase 2, chloroplastic yes no 0 0 1 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 29.594 29.482 3 2.6291E-14 17180 22-052-Murphy-control-3 48.216 35.116 16901000 2784000 3333600 6849800 0 0 0 3933400 0 0 0 0 0 0 0 0 259 37 251 3008;3009;3010;3011 1504;1505;1506 1506 3 KSEGGFGGLGSLFKK Unmodified 1510.8144 0.81437807 209 Q9SD66 F13I12.120 yes yes 0 0 2 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 33.045 32.88 3 3.6577E-05 25077 22-052-Murphy-SHP20-PEI-LL-3 58.487 50.182 84752000 0 0 0 13700000 4786900 1370700 14516000 0 12263000 0 10454000 20557000 2402200 0 4701000 260 209 252 3012;3013;3014;3015;3016;3017;3018;3019;3020 1507;1508;1509 1509 3 LAEDQRNLLQTQAQTKAQNLR Unmodified 2438.299 0.29898257 57 F4JQE9 At4g36580 yes yes 0 0 2 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 8.8267 8.7116 3 0.0086639 3899 22-052-Murphy-SHP20-PEI-LL-1 30.956 17.084 177150000 3411700 3171500 9253600 11012000 9105000 0 92113000 0 0 6737000 12774000 29574000 0 0 0 261 57 253 3021;3022;3023;3024;3025;3026;3027;3028;3029 1510 1510 1 LAFVSSAGAFEK Unmodified 1225.6343 0.63428844 15 A0A1P8B5H3;O22773 Thylakoid lumenal 16.5 kDa protein, chloroplastic yes no 0 0 0 By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 37.557 37.434 2 3.9263E-26 27183 22-052-Murphy-SHP20-LL-2 89.355 56.884 57885000 3050400 2245000 0 1405600 0 0 17302000 0 10253000 1816200 0 4665400 15963000 0 1183400 262 15 254 3030;3031;3032;3033;3034;3035;3036;3037;3038;3039;3040 1511;1512;1513;1514;1515;1516 1513 6 LAKGPGGDVAPVAAPAPAATPAPTAAVPK Unmodified 2562.417 0.41697244 221 Q9SRX2 RPL19A 60S ribosomal protein L19-1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 33.201 33.111 3 3.2869E-18 25498 22-052-Murphy-SHP20-PEI-LL-3 43.895 40.301 70693000 0 0 0 4832700 5204700 0 26268000 14853000 15010000 4524600 0 0 0 0 0 263 221 255 3041;3042;3043;3044;3045;3046 1517;1518;1519;1520 1520 4 LAPNLYPKFRP Unmodified 1314.7448 0.74484194 170 Q949U1 CYP79F1 Dihomomethionine N-hydroxylase yes yes 0 0 2 By matching By matching By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 32.578 32.435 3 5.7966E-07 25356 22-052-Murphy-SHP20-PEI-LL-1 57.598 57.598 36022000 832900 990320 1101900 470550 1839300 0 4471900 3018500 4839200 1472200 0 7616500 4415700 1895900 3056900 264 170 256 3047;3048;3049;3050;3051;3052;3053;3054;3055;3056;3057;3058;3059;3060 1521;1522;1523;1524 1523 4 LASRLNVRPSI Unmodified 1224.7303 0.73025451 10 B9DG18;A0A1P8B564;A0A1P8AWT7;Q42547;P25819;Q2V4M4 CAT3;CAT2 Catalase-3;Catalase-2 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 24.97 24.793 3 0.029262 16717 22-052-Murphy-SHP20-PEI-LL-2 42.802 29.846 173960000 2956200 4141000 4443400 7045300 7015000 2758800 11747000 18844000 15256000 9068100 16474000 19450000 28395000 8576400 17793000 265 10 257 3061;3062;3063;3064;3065;3066;3067;3068;3069;3070;3071;3072;3073;3074;3075 1525 1525 1 LASVPSGGGGGVAVASATSGGGGGGGAPAAESK Unmodified 2597.2681 0.26813595 13 A0A1P8B2C7;F4IGR5;F4IGR4;P51407 At2g27720;RPP2A 60S acidic ribosomal protein P2-1 yes no 0 0 0 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 29.418 29.286 3 4.3182E-50 22021 22-052-Murphy-SHP20-PEI-LL-1 67.911 67.911 38406000 0 0 1441900 3353200 3810500 0 11213000 8540400 8533300 0 0 0 0 1513900 0 266 13 258 3076;3077;3078;3079;3080;3081;3082 1526;1527;1528 1526 3 LASVPSGGGGGVAVASATSGGGGGGGAPAAESKK Unmodified 2725.3631 0.36309897 13 A0A1P8B2C7;F4IGR5;F4IGR4;P51407 At2g27720;RPP2A 60S acidic ribosomal protein P2-1 yes no 0 0 1 By matching By matching By MS/MS By matching By matching By MS/MS By matching By matching 1 1 1 1 1 1 1 1 24.925 24.786 3 0.0039346 14541 22-052-Murphy-SHP20-PEI-infil-3 26.995 24.382 66097000 0 0 0 5296300 5502100 5291800 15761000 12456000 7461400 3229900 0 11099000 0 0 0 267 13 259 3083;3084;3085;3086;3087;3088;3089;3090 1529;1530 1529 2 LASVPSGGGGGVAVASATSGGGGGGGAPAAESKKEEK Unmodified 3111.5432 0.54324818 13 A0A1P8B2C7;F4IGR5;F4IGR4;P51407 At2g27720;RPP2A 60S acidic ribosomal protein P2-1 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 22.225 22.054 3;4 0 18771 22-052-Murphy-SHP20infil-3 163.73 161.75 504470000 6168400 4908600 7371300 33332000 36095000 23820000 102510000 98733000 53395000 18206000 16734000 64988000 18347000 6563300 13304000 268 13 260 3091;3092;3093;3094;3095;3096;3097;3098;3099;3100;3101;3102;3103;3104;3105;3106;3107 1531;1532;1533;1534;1535;1536;1537;1538;1539;1540;1541;1542;1543;1544;1545 1535 15 LASVPSGGGGGVAVASATSGGGGGGGASAAESK Unmodified 2587.2474 0.24740051 216 Q9SLF7 RPP2B 60S acidic ribosomal protein P2-2 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 28.552 28.379 3 2.897E-115 20539 22-052-Murphy-SHP20-PEI-LL-2 94.275 87.771 122120000 0 0 0 5784700 5377100 4155500 26772000 24032000 18476000 6640400 0 17906000 5457900 3379100 4135800 269 216 261 3108;3109;3110;3111;3112;3113;3114;3115;3116;3117;3118 1546;1547;1548;1549;1550;1551;1552 1551 7 LASVPSGGGGGVAVASATSGGGGGGGASAAESKK Unmodified 2715.3424 0.34236353 216 Q9SLF7 RPP2B 60S acidic ribosomal protein P2-2 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 24.174 24.034 3 1.9653E-113 16008 22-052-Murphy-SHP20-PEI-LL-3 71.608 64.075 99969000 0 0 0 8722200 7594800 5802200 27257000 21239000 11719000 3149800 0 14485000 0 0 0 270 216 262 3119;3120;3121;3122;3123;3124;3125;3126 1553;1554;1555;1556;1557;1558 1558 6 LASVPSGGGGGVAVASATSGGGGGGGASAAESKKEEK Unmodified 3101.5225 0.52251274 216 Q9SLF7 RPP2B 60S acidic ribosomal protein P2-2 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 2 1 2 2 2 1 1 2 1 1 1 21.405 21.219 3;4 1.8305E-262 12922 22-052-Murphy-SHP20-PEI-LL-2 148.3 146.3 663790000 8384600 4195200 9257200 41273000 46447000 32630000 135330000 128790000 81062000 17597000 22000000 98776000 14763000 5679600 17610000 271 216 263 3127;3128;3129;3130;3131;3132;3133;3134;3135;3136;3137;3138;3139;3140;3141;3142;3143;3144;3145;3146 1559;1560;1561;1562;1563;1564;1565;1566;1567;1568;1569;1570;1571;1572;1573 1571 15 LATSGANFAR Unmodified 1006.5196 0.51959303 61 F4KC80;P49107 PSAN Photosystem I reaction center subunit N, chloroplastic yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 2 1 1 17.002 16.83 2 1.3802E-83 4886 22-052-Murphy-control-1 142.11 113.6 1093500000 26478000 41611000 66549000 99009000 59272000 24571000 143360000 102030000 80974000 42039000 72048000 251050000 35953000 0 48587000 272 61 264 3147;3148;3149;3150;3151;3152;3153;3154;3155;3156;3157;3158;3159;3160;3161 1574;1575;1576;1577;1578;1579;1580;1581;1582;1583;1584;1585;1586;1587;1588;1589;1590;1591;1592;1593 1574 20 LDFDWIGKEELEEQSLPISR Unmodified 2403.1958 0.19580586 238 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 3 1 1 1 2 3 1 4 1 1 34.036 33.851 3 0.0077201 27302 22-052-Murphy-SHP20infil-1 35.64 27.928 + 382790000 0 0 0 5233600 4545100 10053000 12423000 18817000 8439100 49812000 84420000 52488000 99463000 18997000 18099000 273 238 265 3162;3163;3164;3165;3166;3167;3168;3169;3170;3171;3172;3173;3174;3175;3176;3177;3178;3179;3180;3181 1594;1595;1596 1594 3 LDTKPVSRPVASEPVDR Unmodified 1865.0007 0.0006752871 172 Q96500 CCL yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 2 2 2 2 1 2 2 2 2 1 9.1805 9.0471 3;4 3.5276E-30 5189 22-052-Murphy-SHP20infil-3 80.706 63.304 277330000 3002100 2345500 3043400 3345100 17627000 10828000 31401000 31214000 9256400 19550000 27555000 82469000 28127000 0 7564200 274 172 266 3182;3183;3184;3185;3186;3187;3188;3189;3190;3191;3192;3193;3194;3195;3196;3197;3198;3199;3200;3201;3202;3203 1597;1598;1599;1600;1601;1602;1603;1604;1605;1606 1599 10 LEDLRIPPAYTKTFQGPPHGIQVER Unmodified 2861.5188 0.51881175 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 38.777 38.621 4 0.0070424 31742 22-052-Murphy-SHP20-PEI-LL-1 32.337 25.973 19910000 0 0 0 0 0 0 5490400 0 4754500 0 0 0 5379500 4285900 0 275 64 267 3204;3205;3206;3207 1607;1608;1609 1608 3 LFGGTTPGTITNK Unmodified 1305.6929 0.69286595 143 Q38842 ATOZI1 yes yes 0 0 0 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 29.435 29.237 2 0.010015 23699 22-052-Murphy-SHP20infil-2 57.598 37.812 41881000 0 0 0 0 2342800 2805100 0 0 3765700 6451700 7463400 12003000 4460700 0 2589000 276 143 268 3208;3209;3210;3211;3212;3213;3214;3215 1610;1611 1610 2 LGANVGSAQGPTGLGK Unmodified 1425.7576 0.75759147 121 P56778 psbC Photosystem II CP43 reaction center protein yes yes 0 0 0 By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 25.367 25.115 2 8.462E-21 17369 22-052-Murphy-SHP20-LL-3 72.643 61.05 32681000 0 0 0 2707900 0 0 0 0 0 0 5014200 10251000 6061600 2201800 6445000 277 121 269 3216;3217;3218;3219;3220;3221 1612;1613 1613 2 LGDIMGLLNKK Oxidation (M) 1216.6849 0.6849438 163 Q8RXX5 50S ribosomal protein L19-2, chloroplastic yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 30.437 30.276 3 4.2079E-07 23047 22-052-Murphy-SHP20-PEI-LL-1 70.256 67.218 40614000 0 1920300 3030200 2990900 2507400 0 8992600 0 7395800 0 0 0 5664500 2206000 5906500 278 163 270 3222;3223;3224;3225;3226;3227;3228;3229;3230 1614 1614 32 1 LGEHNIDVLEGNEQFINAAK Unmodified 2210.0968 0.096760517 32 CON__P00761 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 42.101 41.984 3 2.8638E-05 40036 22-052-Murphy-SHP20infil-3 47.223 44.032 + 50980000 5559600 2537000 4337100 3494300 5602900 2364400 6143000 3468300 0 0 0 17473000 0 0 0 279 32 271 3231;3232;3233;3234;3235;3236;3237;3238;3239 1615;1616 1616 2 LGLSAKNYGR Unmodified 1077.5931 0.59309232 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 1 2 2 2 9.2055 9.0898 2;3 0.006006 4247 22-052-Murphy-SHP20-PEI-LL-1 76.847 53.827 224980000 6502200 11849000 18062000 16274000 12195000 5396800 30045000 24559000 17604000 3344000 0 32067000 28781000 0 18301000 280 64 272 3240;3241;3242;3243;3244;3245;3246;3247;3248;3249;3250;3251;3252;3253;3254;3255;3256;3257;3258;3259;3260;3261;3262;3263;3264 1617;1618;1619;1620;1621;1622 1620 6 LGLVFNPYGGK Unmodified 1163.6339 0.63389451 190 Q9LPC3 F22M8.11 yes yes 0 0 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 42.454 42.31 2 4.7924E-05 40371 22-052-Murphy-SHP20infil-3 62.714 0 20300000 0 0 0 1208700 0 2234000 0 0 0 2717500 3056100 9749100 0 0 1334700 281 190 273 3265;3266;3267;3268;3269;3270 1623;1624 1624 2 LGPTSQPQRVKYTQLLR Unmodified 1984.1218 0.12179348 59 F4K5B9 At5g07030 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 27.101 27.007 3;4 0.0013617 14705 22-052-Murphy-control-3 58.831 55.312 97944000 4354700 7430900 12010000 4728400 0 0 30797000 22404000 16218000 0 0 0 0 0 0 282 59 274 3271;3272;3273;3274;3275;3276;3277;3278;3279;3280;3281;3282;3283;3284 1625;1626;1627;1628;1629;1630;1631;1632 1627 8 LGSQLDVLAPVK Unmodified 1238.7234 0.72343779 55 F4JD96;Q9SVR0;Q9SFU1 At3g07110;RPL13AC;RPL13AA 60S ribosomal protein L13a-3;60S ribosomal protein L13a-1 yes no 0 0 0 By MS/MS By MS/MS 1 1 40.214 40.101 2 0.0044896 33286 22-052-Murphy-SHP20-PEI-LL-1 75.109 75.109 7441300 0 0 0 0 0 0 4177500 3263800 0 0 0 0 0 0 0 283 55 275 3285;3286 1633;1634 1633 0 LGSQLDVLAPVKY Unmodified 1401.7868 0.78676633 55 F4JD96;Q9SVR0;Q9SFU1 At3g07110;RPL13AC;RPL13AA 60S ribosomal protein L13a-3;60S ribosomal protein L13a-1 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 46.359 46.237 2 6.7451E-33 31477 22-052-Murphy-control-3 139.19 119.92 215220000 2399600 4328500 10243000 9960700 3020700 0 86242000 35852000 31954000 4622200 5740000 9618500 4185700 2353600 4698300 284 55 276 3287;3288;3289;3290;3291;3292;3293;3294;3295;3296;3297;3298;3299;3300 1635;1636;1637;1638 1635 2 LGVKIYGDQVAKPGAIIVR Unmodified 1996.1833 0.1833311 183 Q9FLN4 RPL27 50S ribosomal protein L27, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 34.769 34.621 3;4 4.5457E-19 27572 22-052-Murphy-SHP20-PEI-LL-1 62.377 62.341 334480000 11537000 10316000 19488000 24851000 15469000 7799800 63203000 26994000 18522000 23708000 19990000 50230000 16236000 10132000 16005000 285 183 277 3301;3302;3303;3304;3305;3306;3307;3308;3309;3310;3311;3312;3313;3314;3315;3316;3317;3318;3319;3320;3321;3322;3323;3324;3325;3326;3327;3328;3329;3330 1639;1640;1641;1642;1643;1644;1645;1646;1647;1648;1649;1650;1651 1649 12 LIESPAPGIISR Unmodified 1251.7187 0.71868677 115 P56757 atpA ATP synthase subunit alpha, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 2 1 1 1 1 1 1 1 2 34.644 34.492 2 1.7646E-18 31865 22-052-Murphy-SHP20infil-3 98.392 86.545 350550000 2918800 6232500 5096100 37186000 18939000 12080000 30369000 22021000 20784000 10235000 24216000 119040000 16642000 5496100 19299000 286 115 278 3331;3332;3333;3334;3335;3336;3337;3338;3339;3340;3341;3342;3343;3344;3345;3346;3347 1652;1653;1654;1655;1656;1657;1658;1659;1660;1661;1662;1663;1664 1657 12 LIESPAPGIISRR Unmodified 1407.8198 0.8197978 115 P56757 atpA ATP synthase subunit alpha, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 2 1 1 2 1 1 1 27.909 27.743 3 1.669E-15 20502 22-052-Murphy-SHP20-PEI-LL-1 67.153 26.564 236880000 3501600 6779100 3945700 23446000 12644000 8579900 20730000 12439000 17900000 8571700 15178000 65436000 16877000 6005300 14848000 287 115 279 3348;3349;3350;3351;3352;3353;3354;3355;3356;3357;3358;3359;3360;3361;3362;3363;3364 1665;1666;1667;1668;1669;1670;1671;1672;1673;1674;1675;1676 1674 11 LIIQGKNLELSEPIKQHVEEK Unmodified 2444.3639 0.36387424 171 Q94K97 At5g24490 yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching 1 1 1 1 1 1 1 1 30.999 30.874 4 1.0733E-20 23673 22-052-Murphy-SHP20-PEI-LL-1 63.337 55.625 56643000 2529600 4301300 9295200 0 0 0 15349000 8317000 8611000 4683000 0 0 0 0 3556700 288 171 280 3365;3366;3367;3368;3369;3370;3371;3372 1677;1678;1679 1678 3 LIVAGASAYAR Unmodified 1090.6135 0.61349341 227 Q9SZJ5;Q94C74 SHM1;SHM2 Serine hydroxymethyltransferase 1, mitochondrial;Serine hydroxymethyltransferase 2, mitochondrial yes no 0 0 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 27.186 27.095 2 4.9338E-07 19826 22-052-Murphy-SHP20-PEI-LL-1 61.999 29.159 37175000 0 2868500 0 5718200 0 0 11808000 8442800 8337100 0 0 0 0 0 0 289 227 281 3373;3374;3375;3376;3377 1680;1681 1680 2 LLGEDEPEK Unmodified 1028.5026 0.50260556 53 F4J912;Q8LBI1;P49227 ATL5;RPL5B 60S ribosomal protein L5-1;60S ribosomal protein L5-2 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 17.71 17.505 2 0.00029028 9074 22-052-Murphy-SHP20-PEI-LL-3 83.377 74.432 174170000 0 1494500 2867600 4595100 4792200 2538100 25177000 17631000 16247000 9622000 11080000 23975000 26698000 10679000 16772000 290 53 282 3378;3379;3380;3381;3382;3383;3384;3385;3386;3387;3388;3389;3390;3391 1682;1683;1684;1685 1685 2 LLGPGLNK Unmodified 810.49634 0.49633839 128 P59230;Q8VZB9;P59231 RPL10AB;RPL10AA;RPL10AC 60S ribosomal protein L10a-2;60S ribosomal protein L10a-1;60S ribosomal protein L10a-3 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 21.708 21.543 2 0.022545 13306 22-052-Murphy-SHP20-PEI-LL-2 70.49 39.749 93977000 0 1300300 1561800 5312700 3643700 2422300 28146000 21545000 19615000 0 0 0 3996000 0 6433700 291 128 283 3392;3393;3394;3395;3396;3397;3398;3399;3400;3401 1686 1686 1 LLGSVTIANGGVLPNIHQTLLPSK Unmodified 2441.4006 0.4005941 66 Q9S9K7;O04848 Probable histone H2AXb;Probable histone H2AXa yes no 0 0 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 51.269 51.137 3 0.01984 49400 22-052-Murphy-SHP20infil-3 20.891 17.087 42584000 0 0 0 0 0 0 3606100 4339500 2786100 3845500 9512500 7454100 6030200 2236900 2773300 292 66 284 3402;3403;3404;3405;3406;3407;3408;3409;3410 1687 1687 1 LQDSEESIEKPTTE Unmodified 1604.7417 0.74172621 157 Q8GWP4 At2g21530 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 21.851 21.704 2 1.0049E-21 13645 22-052-Murphy-SHP20-PEI-LL-3 87.328 71.437 39559000 1742900 2116700 3921800 0 0 0 10379000 7182300 8457300 0 0 5758700 0 0 0 293 157 285 3411;3412;3413;3414;3415;3416;3417 1688;1689 1689 2 LQGNAAVPLIPK Unmodified 1219.7289 0.72885752 214 Q9SKC9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 34.051 33.901 2 1.9005E-08 26381 22-052-Murphy-SHP20-LL-3 83.614 75.394 242910000 2073300 1900100 2162600 9069400 14184000 9670900 24437000 21289000 20984000 18203000 27361000 38022000 23985000 12293000 17278000 294 214 286 3418;3419;3420;3421;3422;3423;3424;3425;3426;3427;3428;3429;3430;3431;3432 1690;1691;1692;1693;1694 1690 1 LQGNAAVPLIPKTANA Unmodified 1576.8937 0.89369102 214 Q9SKC9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 yes yes 0 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 35.751 35.603 2 0.023181 28680 22-052-Murphy-SHP20-PEI-LL-1 81.338 74.648 71979000 1513500 0 1515200 1881500 0 0 14294000 12362000 11137000 0 4218700 7996100 8512600 2974200 5575100 295 214 287 3433;3434;3435;3436;3437;3438;3439;3440;3441;3442;3443 1695 1695 0 LSGGDHIHAGTVVGKLEGDR Unmodified 2017.0341 0.03410068 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 1 By MS/MS By MS/MS By matching By matching By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 23.131 22.942 4 0.0002161 10678 22-052-Murphy-control-3 41.348 31.248 62125000 0 0 2801600 5670800 2434500 1595100 10472000 10714000 7398000 0 7512100 10180000 0 3346700 0 296 64 288 3444;3445;3446;3447;3448;3449;3450;3451;3452;3453 1696;1697 1696 2 LSSPATLNSR Unmodified 1044.5564 0.55637247 32 CON__P00761 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 16.729 16.558 2 8.1719E-21 8024 22-052-Murphy-SHP20-PEI-LL-3 101.33 61.664 + 635150000 6561500 11971000 31431000 30526000 14527000 0 137070000 67157000 45211000 15487000 34258000 154530000 28147000 14668000 43600000 297 32 289 3454;3455;3456;3457;3458;3459;3460;3461;3462;3463;3464;3465;3466;3467;3468;3469;3470;3471 1698;1699;1700;1701;1702;1703;1704;1705;1706;1707;1708;1709;1710;1711;1712;1713;1714;1715;1716;1717;1718;1719;1720;1721;1722;1723;1724;1725;1726;1727;1728;1729;1730;1731;1732;1733;1734;1735;1736;1737 1736 40 LTELLK Unmodified 715.44799 0.44799122 49 F4J0F5;Q9LK19 At3g28870;At3g24260 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 21.615 21.474 2 9.7768E-55 13321 22-052-Murphy-SHP20-PEI-LL-3 130.16 0 150060000 0 4224300 13311000 10631000 5889600 0 46814000 27891000 26847000 4922400 0 0 0 0 9525700 298 49 290 3472;3473;3474;3475;3476;3477;3478;3479;3480 1738 1738 0 LTLGIISEPISEINKSWLVLSTICPPVHRK Unmodified 3342.8738 0.87375421 239 yes yes 0 0 2 By MS/MS By matching By MS/MS 2 1 2 43.836 43.757 4 0.010712 36965 22-052-Murphy-SHP20-PEI-LL-1 21.255 19.251 + 100150000 0 0 0 0 0 0 58719000 10739000 30689000 0 0 0 0 0 0 299 239 291 3481;3482;3483;3484;3485 1739;1740 1739 2 LVLTPAAVEFLNAR Unmodified 1512.8664 0.86641364 73 Q2V4Q4;Q3EDH2;O50061 RPL4 50S ribosomal protein L4, chloroplastic yes no 0 0 0 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 55.005 54.904 2 3.5997E-14 48006 22-052-Murphy-SHP20-PEI-LL-1 87.308 72.042 11127000 602890 819810 1357000 0 0 0 3305900 2086500 1654900 0 0 0 0 0 1299700 300 73 292 3486;3487;3488;3489;3490;3491;3492 1741 1741 1 MDGIKYAVFTDK Oxidation (M) 1402.6803 0.68025235 131 P61845 rpl23-A 50S ribosomal protein L23, chloroplastic yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 1 2 2 2 1 1 2 2 2 2 29.127 28.961 2;3 1.0168E-31 21147 22-052-Murphy-SHP20-PEI-LL-2 128.38 126.34 433540000 9769400 11165000 28288000 11183000 0 0 117290000 78679000 64382000 7739000 11750000 28643000 20139000 10992000 33516000 301 131 293 3493;3494;3495;3496;3497;3498;3499;3500;3501;3502;3503;3504;3505;3506;3507;3508;3509;3510;3511;3512;3513;3514;3515 1742;1743;1744;1745;1746;1747;1748;1749;1750;1751;1752;1753;1754;1755;1756;1757;1758;1759 1757 26 15 MDSQIKHAVVVKVMGR Acetyl (Protein N-term) 1838.9859 0.98589362 96 Q9SR73;P34789 RPS28A;RPS28C 40S ribosomal protein S28-1;40S ribosomal protein S28-2 yes no 1 0 2 By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching 2 1 1 1 1 1 1 35.24 35.165 3;4 1.2541E-21 18796 22-052-Murphy-control-1 74.46 70.426 25012000 7724900 2018800 2624700 1796700 0 0 3312200 4947500 2586800 0 0 0 0 0 0 302 96 294 3516;3517;3518;3519;3520;3521;3522;3523 1760;1761;1762 1761 3 MDSQIKHAVVVKVMGR Acetyl (Protein N-term);Oxidation (M) 1854.9808 0.98080824 96 Q9SR73;P34789 RPS28A;RPS28C 40S ribosomal protein S28-1;40S ribosomal protein S28-2 yes no 1 1 2 By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 2 2 2 2 1 3 2 2 1 1 1 28.406 28.29 3;4 1.3104E-29 20417 22-052-Murphy-SHP20-PEI-LL-2 84.169 73.83 166980000 6549500 4002700 9503800 10168000 2090400 0 40328000 44298000 28925000 4111900 0 14701000 0 0 2302600 303 96 294 3524;3525;3526;3527;3528;3529;3530;3531;3532;3533;3534;3535;3536;3537;3538;3539;3540;3541;3542 1763;1764;1765;1766;1767;1768;1769;1770 1769 18;19 8 MDSQIKHAVVVKVMGR Acetyl (Protein N-term);2 Oxidation (M) 1870.9757 0.97572286 96 Q9SR73;P34789 RPS28A;RPS28C 40S ribosomal protein S28-1;40S ribosomal protein S28-2 yes no 1 2 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 1 1 1 1 1 1 1 22.988 22.823 3 1.3391E-40 14314 22-052-Murphy-SHP20-PEI-LL-2 91.202 91.202 211460000 5705800 0 0 0 0 0 64818000 60383000 49977000 6961300 0 17854000 0 0 5764900 304 96 294 3543;3544;3545;3546;3547;3548;3549 1771;1772;1773;1774;1775 1773 18;19 5 MEETAKPLGFNVR Unmodified 1490.7551 0.75514863 200 Q9MAM1 CIPK9 CBL-interacting serine/threonine-protein kinase 9 yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 8.981 8.8435 3 0.00012964 3594 22-052-Murphy-SHP20-PEI-LL-2 58.676 36.202 43636000 0 0 0 0 0 0 8046400 21587000 14002000 0 0 0 0 0 0 305 200 295 3550;3551;3552;3553 1776;1777;1778 1777 3 METPSSAKRVTR Unmodified 1361.7085 0.70853279 154 Q6DYC8 At3g51230 yes yes 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 2 2 1 2 2 2 2 1 1 2 2 8.2909 8.1687 2;3 0.00027029 2889 22-052-Murphy-SHP20-LL-3 70.919 46.764 1625000000 97031000 77538000 156590000 55519000 43589000 22225000 121490000 232270000 142690000 18861000 36383000 182550000 254350000 0 183910000 306 154 296 3554;3555;3556;3557;3558;3559;3560;3561;3562;3563;3564;3565;3566;3567;3568;3569;3570;3571;3572;3573;3574;3575;3576 1779;1780;1781;1782;1783;1784;1785;1786;1787;1788;1789 1786 10 MEVPGSSKKMIATQEEMSAAK Acetyl (Protein N-term);3 Oxidation (M) 2342.0804 0.08038345 214 Q9SKC9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 yes yes 1 3 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 9.433 9.3204 3 2.0581E-08 4324 22-052-Murphy-SHP20-PEI-LL-3 52.814 48.375 160330000 4319900 3780600 0 13040000 9755900 2913000 0 0 55319000 0 10991000 15421000 18548000 0 26244000 307 214 297 3577;3578;3579;3580;3581;3582;3583;3584;3585;3586 1790 1790 38;39;40 1 MGNITPTTGTQGQIR Oxidation (M) 1589.7832 0.78315429 218 Q9SMU8;P24101 PER34;PER33 Peroxidase 34;Peroxidase 33 yes no 0 1 0 By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 19.681 19.504 2 2.8005E-44 16307 22-052-Murphy-SHP20infil-3 103.55 90.757 48014000 0 0 0 3510800 3221900 4044000 3867300 6821600 3834100 3218100 4495800 12765000 0 0 2234900 308 218 298 3587;3588;3589;3590;3591;3592;3593;3594;3595;3596 1791;1792 1791 41 2 MLTETPFRPR Oxidation (M) 1262.6441 0.64414162 28 A8MSE0;Q944S8 At4g21105 yes no 0 1 1 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 20.865 20.653 3 0.02243 12964 22-052-Murphy-SHP20-PEI-LL-1 46.158 46.158 95860000 1345800 1245700 1635600 0 0 0 29957000 23350000 0 0 12692000 23317000 0 2318200 0 309 28 299 3597;3598;3599;3600;3601;3602;3603;3604 1793;1794 1793 3 0 MPIKTQFIISE Oxidation (M) 1321.6952 0.69517413 124 P56793 rpl16 50S ribosomal protein L16, chloroplastic yes yes 0 1 1 By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 36.835 36.688 2 0.0003483 29040 22-052-Murphy-SHP20-PEI-LL-3 50.878 39.285 75112000 1349900 1635000 3355600 0 0 0 25921000 13240000 9862700 2604100 4378600 0 4594600 3535100 4636100 310 124 300 3605;3606;3607;3608;3609;3610;3611;3612;3613;3614;3615 1795 1795 24 0 NALETYVYNMK Oxidation (M) 1360.6333 0.63330216 17 F4K007;A0A1P8BF32;Q39043;Q9LKR3 BIP2;MED37F;MED37A Mediator of RNA polymerase II transcription subunit 37f;Mediator of RNA polymerase II transcription subunit 37a yes no 0 1 0 By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 32.003 31.881 2 0.017203 24254 22-052-Murphy-SHP20-PEI-LL-3 63.148 44.365 22347000 0 0 3239800 0 0 0 6644000 6242300 6220600 0 0 0 0 0 0 311 17 301 3616;3617;3618;3619 1796 1796 0 1 NAPPDFQNTK Unmodified 1130.5356 0.53563702 206 Q9S841 PSBO2 Oxygen-evolving enhancer protein 1-2, chloroplastic yes yes 0 0 0 By matching By matching By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 9.0758 9.0181 2 0.0017024 4058 22-052-Murphy-SHP20-PEI-LL-3 65.038 65.038 20349000 1814600 1159900 0 2494900 3069400 1958100 0 4831000 5021000 0 0 0 0 0 0 312 206 302 3620;3621;3622;3623;3624;3625;3626 1797 1797 1 NIGLGFKTPR Unmodified 1101.6295 0.62947783 84 P16181;P42733;O65569 RPS11A;RPS11C;RPS11B 40S ribosomal protein S11-1;40S ribosomal protein S11-3;40S ribosomal protein S11-2 yes no 0 0 1 By matching By MS/MS By matching By matching By matching 1 1 1 1 1 25.779 25.646 3 0.030081 13567 22-052-Murphy-control-3 47.198 38.665 13038000 0 958340 2334400 0 0 0 4350900 2639100 2754900 0 0 0 0 0 0 313 84 303 3627;3628;3629;3630;3631 1798 1798 1 NIIAAPMTDFIK Unmodified 1332.7112 0.71115855 92 P30187 CML10 Calmodulin-like protein 10 yes yes 0 0 0 By MS/MS 1 43.444 43.246 2 0.011241 41364 22-052-Murphy-SHP20infil-3 51.995 21.425 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 314 92 304 3632 1799 1799 1 NILVIGPVPGQK Unmodified 1233.7445 0.74450759 119 P56771 petA Cytochrome f yes yes 0 0 0 By matching By matching By matching By MS/MS By matching By matching By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 39.732 39.568 2 0.00081259 32743 22-052-Murphy-SHP20infil-1 67.757 54.704 41186000 0 0 0 1626300 0 1501500 0 2249400 0 5412200 7960500 7828500 6599300 4424400 3583900 315 119 305 3633;3634;3635;3636;3637;3638;3639;3640;3641 1800 1800 1 NMVTAQGRTDPNQNTGIVIQK Oxidation (M) 2300.1543 0.15429217 71 O49006 PME3 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3 yes yes 0 1 1 By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 21.87 21.722 3 2.6919E-09 18570 22-052-Murphy-SHP20infil-3 56.215 47.214 67197000 1126400 1758200 0 6498400 3870900 5106600 6965800 7317700 0 5786400 0 25171000 0 0 3595900 316 71 306 3642;3643;3644;3645;3646;3647;3648;3649;3650;3651 1801 1801 8 1 NMVTAQGRTDPNQNTGIVIQK Unmodified 2284.1594 0.15937755 71 O49006 PME3 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3 yes yes 0 0 1 By MS/MS 1 26.065 25.791 3 5.7316E-09 22807 22-052-Murphy-SHP20infil-3 57.499 41.377 14218000 0 0 0 0 0 0 0 0 0 0 0 14218000 0 0 0 317 71 306 3652 1802 1802 1 NTAASVGEITLK Unmodified 1202.6507 0.65066678 87;206 P23321;Q9S841 PSBO1;PSBO2 Oxygen-evolving enhancer protein 1-1, chloroplastic;Oxygen-evolving enhancer protein 1-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 29.031 28.868 2 3.69E-09 23368 22-052-Murphy-SHP20infil-2 93.551 66.026 213470000 4478600 4116900 4633300 11597000 5192300 2082800 29611000 36149000 27644000 10296000 15144000 27720000 14765000 5205100 14839000 318 87;206 307 3653;3654;3655;3656;3657;3658;3659;3660;3661;3662;3663;3664;3665;3666;3667 1803;1804;1805;1806;1807;1808;1809;1810;1811;1812;1813;1814;1815;1816;1817 1805 13 NVETEADKFR Unmodified 1207.5833 0.5833155 116 P56759 atpF ATP synthase subunit b, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 17.351 17.15 3 4.2801E-06 9894 22-052-Murphy-SHP20-PEI-LL-1 67.993 61.69 12138000 0 0 0 0 0 0 6270500 2198600 1911300 0 0 0 1757300 0 0 319 116 308 3668;3669;3670;3671 1818;1819 1818 2 NVGSVVAVDQDPK Unmodified 1326.6779 0.67794416 205;201 Q9S714;Q9S831 PSAE2;PSAE1 Photosystem I reaction center subunit IV B, chloroplastic;Photosystem I reaction center subunit IV A, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 23.484 23.342 2 1.023E-32 15322 22-052-Murphy-SHP20-PEI-LL-2 118.26 113.65 174370000 8054600 9135500 11267000 10360000 5372000 0 53063000 26811000 26931000 0 0 14621000 0 0 8757300 320 201;205 309 3672;3673;3674;3675;3676;3677;3678;3679;3680;3681 1820;1821;1822;1823;1824;1825 1825 5 NVGSVVAVDQDPKTR Unmodified 1583.8267 0.82673367 205;201 Q9S714;Q9S831 PSAE2;PSAE1 Photosystem I reaction center subunit IV B, chloroplastic;Photosystem I reaction center subunit IV A, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 19.095 18.883 3 0.0074101 10367 22-052-Murphy-SHP20-PEI-LL-3 50.563 38.647 141140000 0 0 1577600 6340100 5233200 2679500 15582000 15503000 13597000 10652000 11277000 34897000 10416000 2599500 10791000 321 201;205 310 3682;3683;3684;3685;3686;3687;3688;3689;3690;3691;3692;3693;3694 1826;1827 1827 1 NVGSVVAVDQDPKTRYPVVVR Unmodified 2297.2492 0.24917883 205;201 Q9S714;Q9S831 PSAE2;PSAE1 Photosystem I reaction center subunit IV B, chloroplastic;Photosystem I reaction center subunit IV A, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 17 12 14 21 16 9 30 33 33 11 20 20 15 11 26 38.825 38.693 2;3;4 2.1659E-118 23656 22-052-Murphy-SHP20-PEI-LL-2 125.52 118.25 21412000000 264740000 305760000 352330000 831990000 692660000 231910000 4648400000 3759400000 3030300000 891780000 1403100000 2190900000 1157400000 497440000 1153700000 322 201;205 311 3695;3696;3697;3698;3699;3700;3701;3702;3703;3704;3705;3706;3707;3708;3709;3710;3711;3712;3713;3714;3715;3716;3717;3718;3719;3720;3721;3722;3723;3724;3725;3726;3727;3728;3729;3730;3731;3732;3733;3734;3735;3736;3737;3738;3739;3740;3741;3742;3743;3744;3745;3746;3747;3748;3749;3750;3751;3752;3753;3754;3755;3756;3757;3758;3759;3760;3761;3762;3763;3764;3765;3766;3767;3768;3769;3770;3771;3772;3773;3774;3775;3776;3777;3778;3779;3780;3781;3782;3783;3784;3785;3786;3787;3788;3789;3790;3791;3792;3793;3794;3795;3796;3797;3798;3799;3800;3801;3802;3803;3804;3805;3806;3807;3808;3809;3810;3811;3812;3813;3814;3815;3816;3817;3818;3819;3820;3821;3822;3823;3824;3825;3826;3827;3828;3829;3830;3831;3832;3833;3834;3835;3836;3837;3838;3839;3840;3841;3842;3843;3844;3845;3846;3847;3848;3849;3850;3851;3852;3853;3854;3855;3856;3857;3858;3859;3860;3861;3862;3863;3864;3865;3866;3867;3868;3869;3870;3871;3872;3873;3874;3875;3876;3877;3878;3879;3880;3881;3882;3883;3884;3885;3886;3887;3888;3889;3890;3891;3892;3893;3894;3895;3896;3897;3898;3899;3900;3901;3902;3903;3904;3905;3906;3907;3908;3909;3910;3911;3912;3913;3914;3915;3916;3917;3918;3919;3920;3921;3922;3923;3924;3925;3926;3927;3928;3929;3930;3931;3932;3933;3934;3935;3936;3937;3938;3939;3940;3941;3942;3943;3944;3945;3946;3947;3948;3949;3950;3951;3952;3953;3954;3955;3956;3957;3958;3959;3960;3961;3962;3963;3964;3965;3966;3967;3968;3969;3970;3971;3972;3973;3974;3975;3976;3977;3978;3979;3980;3981;3982 1828;1829;1830;1831;1832;1833;1834;1835;1836;1837;1838;1839;1840;1841;1842;1843;1844;1845;1846;1847;1848;1849;1850;1851;1852;1853;1854;1855;1856;1857;1858;1859;1860;1861;1862;1863;1864;1865;1866;1867;1868;1869;1870;1871;1872;1873;1874;1875;1876;1877;1878;1879;1880;1881;1882;1883;1884;1885;1886;1887;1888;1889;1890;1891;1892;1893;1894;1895;1896;1897;1898;1899;1900;1901;1902;1903;1904;1905;1906;1907;1908;1909;1910;1911;1912;1913;1914;1915;1916;1917;1918;1919;1920;1921;1922;1923;1924;1925;1926;1927;1928;1929;1930;1931;1932;1933;1934;1935;1936;1937;1938;1939;1940;1941;1942;1943;1944;1945;1946;1947;1948;1949;1950;1951;1952;1953;1954;1955;1956;1957;1958;1959;1960;1961;1962;1963;1964;1965;1966;1967;1968;1969;1970;1971;1972;1973;1974;1975;1976;1977;1978;1979;1980;1981;1982;1983;1984;1985;1986;1987;1988;1989;1990;1991;1992;1993;1994;1995;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023;2024;2025;2026;2027;2028;2029;2030;2031;2032;2033;2034;2035;2036;2037;2038;2039;2040;2041;2042;2043 1976 197 NVSPIEVK Unmodified 884.49673 0.49673232 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 19.431 19.262 2 0.01058 16068 22-052-Murphy-SHP20infil-3 92.692 76.138 258090000 3373600 4702400 7046200 17197000 14199000 6932400 16377000 15087000 13010000 19489000 24577000 68349000 26409000 0 21341000 323 202;207 312 3983;3984;3985;3986;3987;3988;3989;3990;3991;3992;3993;3994;3995;3996 2044 2044 0 NVSPIEVKFTGK Unmodified 1317.7293 0.72925145 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By matching By MS/MS By matching By matching 1 1 1 1 1 28.203 28.081 3 0.0011001 20274 22-052-Murphy-SHP20-PEI-LL-2 63.624 57.965 20317000 0 0 0 3173200 0 0 4914600 5557300 3827300 0 0 0 0 0 2845100 324 202;207 313 3997;3998;3999;4000;4001 2045 2045 1 NVVDGSTTFHSATVAAVGER Unmodified 2016.9865 0.98648179 71 O49006;Q42534 PME3;PME2 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3;Pectinesterase 2 yes no 0 0 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 1 1 1 1 1 31.493 31.347 3 6.4299E-86 23692 22-052-Murphy-SHP20-PEI-LL-2 108.34 108.22 99358000 2308600 2312000 2516100 8964700 6501200 3809400 12963000 9919700 6302300 5694000 11306000 17764000 0 3107200 5889200 325 71 314 4002;4003;4004;4005;4006;4007;4008;4009;4010;4011;4012;4013;4014;4015 2046;2047;2048;2049;2050;2051;2052 2052 7 PAAYDGTIR Unmodified 962.48214 0.48214489 50 F4J1N5 TIF3C2 Eukaryotic translation initiation factor 3 subunit C yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 9.7464 9.6481 2 0.0089358 4597 22-052-Murphy-SHP20-PEI-LL-3 72.021 51.739 170140000 0 0 11715000 23970000 0 0 0 60839000 67434000 0 0 0 0 0 6187100 326 50 315 4016;4017;4018;4019;4020 2053 2053 1 PPSFTG Unmodified 604.28568 0.28567691 82 P10795 RBCS-1A Ribulose bisphosphate carboxylase small chain 1A, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 32.368 32.257 1 1.0015E-70 19745 22-052-Murphy-control-3 126.25 126.25 17041000 2560900 0 4626100 0 0 0 5217100 0 0 4636600 0 0 0 0 0 327 82 316 4021;4022;4023;4024 2054;2055;2056;2057 2055 3 PPTSPIPNSTTSVSPAK Unmodified 1679.873 0.87301516 159 Q8H0U5 TIC62 Protein TIC 62, chloroplastic yes yes 0 0 0 By matching By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 26.857 26.615 2 5.7909E-21 23697 22-052-Murphy-SHP20infil-3 94.692 85.26 44581000 0 0 0 0 2011100 0 0 0 0 6599500 6423000 13383000 8202900 3578900 4382900 328 159 317 4025;4026;4027;4028;4029;4030;4031 2058;2059;2060 2058 3 PPTSPLPSPVTNH Unmodified 1342.6881 0.68811492 159 Q8H0U5 TIC62 Protein TIC 62, chloroplastic yes yes 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 29.934 29.774 2 7.6512E-66 27122 22-052-Murphy-SHP20infil-3 107.15 92.947 147520000 1879900 1621500 3810000 6052900 8834200 8596400 5544000 5411900 4430900 25306000 18797000 41178000 7103500 3983900 4969700 329 159 318 4032;4033;4034;4035;4036;4037;4038;4039;4040;4041;4042;4043;4044;4045;4046 2061;2062;2063;2064;2065;2066 2063 6 PTIKQLIR Unmodified 967.61785 0.61785051 135 P62126 rps12-A 30S ribosomal protein S12, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 20.751 20.511 2 0.002157 11694 22-052-Murphy-SHP20-PEI-infil-1 103.41 82.255 119720000 0 0 0 9736800 0 0 22039000 21512000 21799000 0 6714900 20919000 6615800 3291400 7092700 330 135 319 4047;4048;4049;4050;4051;4052;4053;4054;4055 2067;2068;2069;2070 2068 3 QGPGEQAAGSASEAK Unmodified 1386.6375 0.63753591 235 Q9ZUX4 Uncharacterized protein At2g27730, mitochondrial yes yes 0 0 0 By matching By matching By MS/MS By MS/MS By matching By MS/MS By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 8.1841 8.0485 2 0 2701 22-052-Murphy-SHP20-PEI-LL-1 123.86 106.43 132330000 0 2604800 6171100 9552700 11667000 6037100 21035000 0 0 6958100 15007000 30116000 10676000 0 12509000 331 235 320 4056;4057;4058;4059;4060;4061;4062;4063;4064;4065;4066 2071;2072;2073 2073 3 QGPGEQAAGSASEAKVAGATASASAESGPK Unmodified 2671.2685 0.26852989 235 Q9ZUX4 Uncharacterized protein At2g27730, mitochondrial yes yes 0 0 1 By matching By MS/MS By matching By matching By MS/MS 1 1 1 1 1 24.314 24.138 3 0.00014313 13838 22-052-Murphy-SHP20-PEI-infil-3 29.736 27.263 40120000 0 0 0 2463900 0 3676400 0 0 0 5755600 11874000 16349000 0 0 0 332 235 321 4067;4068;4069;4070;4071 2074 2074 1 QGPNLNGLFGR Unmodified 1171.6098 0.60980502 29;229 B3H4Y9;O23138;Q9T0G2 CYTC-1;CYTC-2 Cytochrome c-1;Cytochrome c-2 no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 40.101 39.957 2 0.022056 38106 22-052-Murphy-SHP20infil-3 47.067 47.067 24581000 0 0 0 0 0 0 4509600 2785300 2178000 0 3240900 11053000 0 814440 0 333 29;229 322 4072;4073;4074;4075;4076;4077 2075 2075 0 QGRTLYGFGG Unmodified 1054.5196 0.51959303 129 P59259;A8MRV1 At1g07660 Histone H4 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 29.807 29.648 2 0.0001182 17154 22-052-Murphy-control-3 84.244 73.37 762100000 18524000 20038000 41426000 40276000 29459000 16526000 132820000 98138000 86346000 29998000 50738000 116820000 32539000 9818800 38638000 334 129 323 4078;4079;4080;4081;4082;4083;4084;4085;4086;4087;4088;4089;4090;4091;4092 2076;2077;2078;2079;2080;2081;2082;2083;2084 2077 0 QIGAYDDAEK Unmodified 1108.5037 0.50366819 141;63 F4KDU5;P49691;Q2V3X4;Q9SF40 At5g02870;RPL4D;At3g09630;RPL4A 60S ribosomal protein L4-2;60S ribosomal protein L4-1 no no 0 0 0 By matching By matching By matching By MS/MS By MS/MS 1 1 1 1 1 9.2411 9.1327 2 0.0014625 4045 22-052-Murphy-SHP20-PEI-LL-2 47.082 28.299 29294000 770120 0 1262900 0 0 0 9657600 9632600 7970400 0 0 0 0 0 0 335 63;141 324 4093;4094;4095;4096;4097 2085;2086 2085 2 QIGAYDDAEKAK Unmodified 1307.6357 0.635745 141;63 F4KDU5;P49691;Q2V3X4;Q9SF40 At5g02870;RPL4D;At3g09630;RPL4A 60S ribosomal protein L4-2;60S ribosomal protein L4-1 no no 0 0 1 By MS/MS By MS/MS By matching 2 2 1 8.3809 8.2357 2;3 0 2949 22-052-Murphy-SHP20-PEI-LL-1 103.83 84.562 129970000 0 0 0 0 0 0 60366000 41949000 27658000 0 0 0 0 0 0 336 63;141 325 4098;4099;4100;4101;4102 2087;2088;2089 2088 3 QILSGVNYASAAAGIR Unmodified 1589.8526 0.85255449 6 A0A1P8ASL8;Q9C7N4 GDSL esterase/lipase At1g29670 yes no 0 0 0 By MS/MS By matching 1 1 41.122 41.02 2 0.0052743 32510 22-052-Murphy-SHP20-PEI-infil-1 51.927 24.185 10685000 0 0 0 2469400 0 0 0 0 0 0 0 8216100 0 0 0 337 6 326 4103;4104 2090 2090 1 QLDASGKPDSFTGK Unmodified 1449.71 0.70997257 87 P23321 PSBO1 Oxygen-evolving enhancer protein 1-1, chloroplastic yes yes 0 0 1 By MS/MS 1 17.673 17.08 3 0.014453 7456 22-052-Murphy-SHP20-LL-2 33.782 33.782 3980300 0 0 0 0 0 0 0 0 0 0 0 0 0 3980300 0 338 87 327 4105 2091 2091 1 QNKAVILLQGR Unmodified 1238.7459 0.74590457 26 A8MS28;Q8LCL3;P51419 At4g15000;RPL27B;RPL27C 60S ribosomal protein L27-2;60S ribosomal protein L27-3 yes no 0 0 1 By matching By matching By MS/MS By matching By MS/MS 1 1 1 1 1 21.26 21.17 3 0.0086348 13689 22-052-Murphy-SHP20-PEI-LL-1 47.603 40.222 14736000 508330 0 0 990750 0 0 6469000 3382200 3385800 0 0 0 0 0 0 339 26 328 4106;4107;4108;4109;4110 2092 2092 1 QTVAVGVIK Unmodified 913.55967 0.55966693 36 F4HUA0;Q8W4H7;Q8GTY0;Q0WL56;P0DH99 At1g07930;A2;A4;A3;A1 Elongation factor 1-alpha 2;Elongation factor 1-alpha 4;Elongation factor 1-alpha 3;Elongation factor 1-alpha 1 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 22.637 22.452 2 0.0087814 14284 22-052-Murphy-SHP20-PEI-LL-3 29.842 19.657 248530000 4692000 3931800 2100900 19015000 9124300 5474400 12376000 15661000 11939000 21690000 30600000 67486000 19998000 4409600 20030000 340 36 329 4111;4112;4113;4114;4115;4116;4117;4118;4119;4120;4121;4122;4123;4124;4125 2093;2094 2094 1 QVHPDIGISSK Unmodified 1179.6248 0.62478638 70 Q9LZT0;P40283;O23629;Q9FFC0;Q9LQQ4;Q9SI96 H2B Histone H2B.7;Histone H2B.11;Histone H2B.6;Histone H2B.10;Histone H2B.1;Histone H2B.3 yes no 0 0 0 By matching By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 2 1 2 2 2 2 1 2 9.5443 9.4279 2;3 4.8568E-10 4295 22-052-Murphy-SHP20-LL-3 67.113 44.427 320890000 0 0 0 10867000 28987000 15888000 0 61440000 65843000 22449000 28171000 0 38286000 0 48955000 341 70 330 4126;4127;4128;4129;4130;4131;4132;4133;4134;4135;4136;4137;4138;4139;4140 2095;2096;2097 2096 3 QVIEKYYSR Unmodified 1184.619 0.61897272 106 Q9SQZ1;Q9SJ36;Q9LZ17;P49205 RPS17C;RPS17B;RPS17D;RPS17A 40S ribosomal protein S17-3;40S ribosomal protein S17-2;40S ribosomal protein S17-4;40S ribosomal protein S17-1 yes no 0 0 1 By matching By MS/MS By MS/MS 1 1 1 8.8881 8.8119 2 0.012351 3869 22-052-Murphy-SHP20-PEI-LL-3 66.682 57.266 22787000 0 1959100 0 0 0 0 0 12941000 7886800 0 0 0 0 0 0 342 106 331 4141;4142;4143 2098;2099 2099 2 RANLNDFDRFK Unmodified 1394.7055 0.70549632 228 Q9T043 RPL14B 60S ribosomal protein L14-2 yes yes 0 0 2 By MS/MS 1 22.43 22.231 3 2.4282E-25 14741 22-052-Murphy-SHP20-PEI-LL-1 70.056 47.582 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 343 228 332 4144 2100 2100 1 RELQETVQYPVEHPEKFEK Unmodified 2385.1965 0.19647456 114 P54609;Q9LZF6;Q9SCN8 CDC48A;CDC48E;CDC48D Cell division control protein 48 homolog A;Cell division control protein 48 homolog E;Cell division control protein 48 homolog D yes no 0 0 2 By MS/MS By MS/MS 1 1 25.056 24.965 4 0.0012273 12839 22-052-Murphy-control-3 28.869 20.78 5939400 2525900 0 3413400 0 0 0 0 0 0 0 0 0 0 0 0 344 114 333 4145;4146 2101 2101 1 RGPQEPPKLGPR Unmodified 1330.747 0.7469672 223 Q9SUI7;Q9SUI6 PSAH1;PSAH2 Photosystem I reaction center subunit VI-1, chloroplastic;Photosystem I reaction center subunit VI-2, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 8.2464 8.1047 3 1.5392E-11 2804 22-052-Murphy-SHP20-LL-3 70.1 57.887 531470000 0 0 0 25080000 19810000 31257000 61432000 0 64378000 33824000 59744000 75323000 84194000 0 76429000 345 223 334 4147;4148;4149;4150;4151;4152;4153;4154;4155;4156 2102;2103;2104;2105;2106;2107 2104 6 RLATSGANFAR Unmodified 1162.6207 0.62070406 61 F4KC80;P49107 PSAN Photosystem I reaction center subunit N, chloroplastic yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 4 1 3 1 3 3 3 2 1 2 2 1 1 3 9.2135 9.0652 2;3 9.0943E-27 2940 22-052-Murphy-SHP20-PEI-infil-2 61.691 54.311 361780000 4336700 9612600 16608000 2701600 0 32756000 30060000 33591000 5797300 11281000 48769000 95328000 10874000 3222600 56841000 346 61 335 4157;4158;4159;4160;4161;4162;4163;4164;4165;4166;4167;4168;4169;4170;4171;4172;4173;4174;4175;4176;4177;4178;4179;4180;4181;4182;4183;4184;4185;4186;4187;4188 2108;2109;2110;2111;2112;2113;2114;2115;2116;2117;2118;2119;2120;2121;2122;2123 2118 16 RLVAAIDGQPDPGGPTVK Unmodified 1789.9686 0.96864688 237 Q9ZVL6 UPF0603 protein At1g54780, chloroplastic yes yes 0 0 1 By matching By matching By matching By MS/MS By MS/MS 1 1 1 1 1 27.6 27.414 3 5.4823E-05 19807 22-052-Murphy-SHP20-LL-3 52.823 42.902 23667000 0 0 0 0 1752800 0 6407700 5552400 0 0 6382800 0 0 0 3571100 347 237 336 4189;4190;4191;4192;4193 2124;2125 2125 2 RLVAAIDGQPDPGGPTVKDSK Unmodified 2120.1226 0.12258134 237 Q9ZVL6 UPF0603 protein At1g54780, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 1 23.457 23.179 3;4 1.2399E-05 12813 22-052-Murphy-SHP20-LL-2 44.816 40.106 54242000 0 0 0 0 0 0 0 0 0 10766000 8089400 0 13809000 13021000 8556500 348 237 337 4194;4195;4196;4197;4198;4199;4200;4201 2126;2127;2128 2128 3 RMEVVEETCKHMEEVVVK Unmodified 2174.0534 0.053380838 4 A0A1P8AQ97;A0A1P8AQ91;A0A1P8AQ79;A0A1P8AQ67 yes no 0 0 2 By MS/MS 1 22.51 22.203 3 0.0069125 18755 22-052-Murphy-SHP20infil-3 9.2834 0 400350000 0 0 0 0 0 0 0 0 0 0 0 400350000 0 0 0 349 4 338 4202 2129 2129 1 RSGLRPVTIDLK Unmodified 1353.8092 0.80923311 161 Q8RXC1 At1g78210 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 25.57 25.396 3 0.011896 16933 22-052-Murphy-SHP20-PEI-infil-1 26.118 9.864 159110000 6505100 5027000 9979900 8728800 6455600 6038700 5779500 9864300 7518400 15654000 16167000 31677000 17432000 6576600 5701700 350 161 339 4203;4204;4205;4206;4207;4208;4209;4210;4211;4212;4213;4214;4215;4216;4217 2130 2130 0 RTNPTTSNPEVSIR Acetyl (Protein N-term) 1612.8169 0.81689726 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 2 2 2 2 1 2 2 2 2 2 24.26 24.076 2;3 0 20868 22-052-Murphy-SHP20infil-3 166.55 113.76 1066000000 17867000 24399000 0 80346000 54224000 27621000 107930000 97256000 83768000 35704000 79753000 271260000 79237000 23862000 82730000 351 86 340 4218;4219;4220;4221;4222;4223;4224;4225;4226;4227;4228;4229;4230;4231;4232;4233;4234;4235;4236;4237;4238;4239;4240;4241;4242;4243 2131;2132;2133;2134;2135;2136;2137;2138;2139;2140;2141;2142;2143;2144;2145;2146;2147;2148;2149;2150;2151 2135 20 RTNPTTSNPEVSIREK Acetyl (Protein N-term) 1869.9545 0.95445338 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 1 2 2 2 1 1 2 2 2 1 1 1 18.625 18.432 2;3 1.3523E-56 8362 22-052-Murphy-SHP20-PEI-infil-3 103.76 93.839 1172100000 2741600 8757100 0 56183000 42234000 35775000 128760000 117680000 91417000 63126000 106120000 329950000 102840000 2259300 84272000 352 86 341 4244;4245;4246;4247;4248;4249;4250;4251;4252;4253;4254;4255;4256;4257;4258;4259;4260;4261;4262;4263;4264 2152;2153;2154;2155;2156;2157;2158;2159;2160;2161;2162;2163;2164;2165;2166 2162 15 RVEPYVTYGYPNLK Unmodified 1697.8777 0.8777066 46 F4IT48;P60039;Q9LHP1 At2g44120;RPL7C;RPL7D 60S ribosomal protein L7-3;60S ribosomal protein L7-4 yes no 0 0 1 By MS/MS 1 33.001 32.872 3 0.010338 25895 22-052-Murphy-SHP20-PEI-LL-1 26.711 22.243 3227400 0 0 0 0 0 0 3227400 0 0 0 0 0 0 0 0 353 46 342 4265 2167 2167 0 RVEVKAPGILER Unmodified 1365.8092 0.80923311 20 F4IMB5;A0A2P2CLF9;P92549 At2g07698;ATPA ATP synthase subunit alpha;ATP synthase subunit alpha, mitochondrial yes no 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 21.913 21.769 3 9.7765E-05 13207 22-052-Murphy-SHP20-PEI-infil-1 53.569 50.247 48699000 1833800 802650 3362600 0 3385200 0 10998000 6680800 8737000 0 0 12899000 0 0 0 354 20 343 4266;4267;4268;4269;4270;4271;4272;4273;4274 2168;2169;2170;2171;2172;2173;2174;2175 2171 7 RVGGSTHQVPIEIGSTQGKALAIR Unmodified 2474.3718 0.37175359 130 P61841 rps7-A 30S ribosomal protein S7, chloroplastic yes yes 0 0 2 By matching By matching By matching By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 27.174 27.08 4 5.3968E-10 19689 22-052-Murphy-SHP20-PEI-LL-1 48.656 48.656 27090000 1313800 1580200 2439800 3427900 0 0 7311400 6488900 4528400 0 0 0 0 0 0 355 130 344 4275;4276;4277;4278;4279;4280;4281 2176;2177 2176 2 SATLFRPKLIVAGASAYAR Unmodified 1991.1316 0.13162988 227 Q9SZJ5 SHM1 Serine hydroxymethyltransferase 1, mitochondrial yes yes 0 0 2 By matching By MS/MS By matching By MS/MS By matching 1 1 1 1 1 36.377 36.266 3 0.00037027 28987 22-052-Murphy-SHP20-PEI-LL-1 40.52 36.74 33301000 0 2461200 4477200 3023700 0 0 11987000 11352000 0 0 0 0 0 0 0 356 227 345 4282;4283;4284;4285;4286 2178 2178 1 SATLKLPSGEVR Unmodified 1256.7089 0.70885036 123 P56791 rpl2-A 50S ribosomal protein L2, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 23.275 23.149 3 0.0047341 9851 22-052-Murphy-control-2 47.844 41.175 45775000 2278700 2686200 3913800 4620100 2668600 0 8697800 10313000 0 2618900 0 7978000 0 0 0 357 123 346 4287;4288;4289;4290;4291;4292;4293;4294;4295 2179;2180 2179 2 SDDEHHFEASESGASKTYPQSAGNIRK Acetyl (Protein N-term) 2989.3438 0.34382009 167 Q93VP3 ELF5A-2 Eukaryotic translation initiation factor 5A-2 yes yes 1 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 20.306 20.187 4 2.9988E-124 17161 22-052-Murphy-SHP20infil-3 83.606 76.808 54170000 4952500 4157600 0 4714400 0 1476300 0 8859100 0 0 0 30010000 0 0 0 358 167 347 4296;4297;4298;4299;4300;4301 2181;2182 2181 2 SFESGDTTKLK Unmodified 1211.6034 0.60338224 142 Q38820 TIM23-2 Mitochondrial import inner membrane translocase subunit TIM23-2 yes yes 0 0 1 By MS/MS By MS/MS 1 1 43.504 43.489 2 0.00030735 34450 22-052-Murphy-SHP20-PEI-infil-1 53.166 25.642 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 359 142 348 4302;4303 2183;2184 2183 2 SFVALPVIAR Unmodified 1071.6441 0.64406526 83 P16180 RPS17 30S ribosomal protein S17, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 45.449 45.323 2 0.003927 38079 22-052-Murphy-SHP20-PEI-LL-2 86.866 68.831 120750000 5592800 5098100 5313000 16078000 5147300 2704200 17887000 10072000 12425000 3438500 5490200 19978000 3953900 1996500 5579000 360 83 349 4304;4305;4306;4307;4308;4309;4310;4311;4312;4313;4314;4315;4316;4317;4318 2185;2186;2187;2188;2189;2190;2191;2192;2193;2194;2195;2196;2197;2198 2197 14 SGAGKKIADVAFK Acetyl (Protein N-term) 1332.7402 0.74015049 140 Q2V3P9;Q9FT52 ATPQ ATP synthase subunit d, mitochondrial yes no 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 25.727 25.591 3 0.0037608 17596 22-052-Murphy-SHP20-PEI-LL-2 50.207 26.832 123190000 4381400 3428800 10370000 0 0 0 43477000 28806000 25743000 0 0 0 0 0 6987000 361 140 350 4319;4320;4321;4322;4323;4324;4325 2199 2199 1 SGGEYGDKAGAPADYQPGFRGGAGGAR Unmodified 2568.1742 0.17417599 25 A8MRV0;Q9FFS8 At5g41520;RPS10B 40S ribosomal protein S10-2 yes no 0 0 2 By MS/MS By MS/MS By matching 1 1 1 21.89 21.744 4 1.5188E-21 14191 22-052-Murphy-SHP20-PEI-LL-1 56.247 41.921 32265000 0 0 0 0 0 0 14226000 10401000 7638000 0 0 0 0 0 0 362 25 351 4326;4327;4328 2200;2201 2200 2 SGKIELPTWTDIVK Unmodified 1585.8716 0.87155859 210 Q9SGA6 RPS19A 40S ribosomal protein S19-1 yes yes 0 0 1 By MS/MS By MS/MS 1 1 47.174 47.066 3 2.5903E-11 40312 22-052-Murphy-SHP20-PEI-LL-1 45.28 35.993 7496100 0 0 0 0 0 0 4880700 2615400 0 0 0 0 0 0 0 363 210 352 4329;4330 2202 2202 1 SGKYTLGYKSVLK Unmodified 1442.8133 0.81331543 165 Q9LSA3;Q9C8F7;Q8VZ19 RPL30C;RPL30A;RPL30B 60S ribosomal protein L30-3;Putative 60S ribosomal protein L30-1;60S ribosomal protein L30-2 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 20.931 20.8 3 3.2243E-14 13286 22-052-Murphy-SHP20-PEI-LL-1 77.124 74.086 94008000 5484800 5838100 11011000 3583500 0 0 28628000 20336000 17268000 0 0 0 0 0 1859500 364 165 353 4331;4332;4333;4334;4335;4336;4337;4338 2203;2204 2203 2 SIAKELSGTVR Unmodified 1159.6561 0.65608651 110 P50883;Q9LFH5 RPL12A;RPL12B 60S ribosomal protein L12-1;60S ribosomal protein L12-2 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 19.196 19.061 2;3 0.02073 10700 22-052-Murphy-SHP20-PEI-LL-3 51.346 30.826 26832000 0 0 0 1623100 0 0 9955900 8668500 6584200 0 0 0 0 0 0 365 110 354 4339;4340;4341;4342;4343;4344;4345 2205;2206 2206 2 SIGKNVSPIEVK Unmodified 1269.7293 0.72925145 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 2 1 2 2 4 2 2 2 2 2 2 20.129 19.931 2;3 3.2405E-224 12195 22-052-Murphy-SHP20-PEI-LL-1 152.47 112.11 5322200000 77488000 77681000 111000000 362380000 242160000 98663000 647230000 530160000 546660000 275040000 451970000 1109400000 375500000 119920000 296900000 366 202;207 355 4346;4347;4348;4349;4350;4351;4352;4353;4354;4355;4356;4357;4358;4359;4360;4361;4362;4363;4364;4365;4366;4367;4368;4369;4370;4371;4372;4373;4374;4375 2207;2208;2209;2210;2211;2212;2213;2214;2215;2216;2217;2218;2219;2220;2221;2222;2223;2224;2225;2226;2227;2228;2229;2230;2231;2232;2233;2234;2235;2236;2237;2238;2239;2240;2241;2242;2243;2244;2245 2233 39 SIGKNVSPIEVKFTGK Unmodified 1702.9618 0.96177059 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 2 1 1 1 1 1 1 26.885 26.74 3;4 6.2022E-56 13213 22-052-Murphy-control-2 84.566 84.219 603030000 20084000 22303000 18178000 42448000 33909000 2208700 162810000 129230000 114370000 5595900 11164000 23631000 5440800 3240800 8410000 367 202;207 356 4376;4377;4378;4379;4380;4381;4382;4383;4384;4385;4386;4387;4388;4389;4390;4391;4392;4393;4394;4395;4396;4397;4398 2246;2247;2248;2249;2250;2251;2252;2253;2254;2255;2256;2257;2258;2259;2260;2261;2262;2263;2264 2247 19 SKLQSEAVR Acetyl (Protein N-term) 1058.572 0.57202253 128 P59230;Q8VZB9;P59231 RPL10AB;RPL10AA;RPL10AC 60S ribosomal protein L10a-2;60S ribosomal protein L10a-1;60S ribosomal protein L10a-3 yes no 1 0 1 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 9.1572 9.0372 2 3.9555E-12 3936 22-052-Murphy-SHP20-PEI-LL-3 122.78 74.272 478780000 6623200 8813000 0 16134000 9187800 5673300 129460000 101730000 87397000 9463000 17708000 33797000 27163000 0 25636000 368 128 357 4399;4400;4401;4402;4403;4404;4405;4406;4407;4408;4409;4410;4411 2265;2266;2267;2268;2269;2270;2271;2272;2273 2273 9 SKYKITYQFYR Unmodified 1495.7823 0.78234966 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 24.631 24.514 3 0.018278 11141 22-052-Murphy-control-2 43.512 28.951 29328000 4837200 6719400 10672000 0 0 0 7098800 0 0 0 0 0 0 0 0 369 202;207 358 4412;4413;4414;4415 2274 2274 1 SLEGLQTNVQR Unmodified 1243.6521 0.65206377 21 P41127;A8MQA1 RPL13B;BBC1 60S ribosomal protein L13-1;60S ribosomal protein L13 yes no 0 0 0 By MS/MS By MS/MS By matching By matching 1 1 1 1 24.48 24.307 2 3.9096E-05 16289 22-052-Murphy-SHP20-PEI-LL-2 77.923 41.221 17748000 0 0 0 0 0 0 5925000 4810900 4139200 0 0 0 0 0 2872600 370 21 359 4416;4417;4418;4419 2275 2275 1 SLEGLQTNVQRLK Unmodified 1484.8311 0.83109076 21 P41127;A8MQA1 RPL13B;BBC1 60S ribosomal protein L13-1;60S ribosomal protein L13 yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 27.684 27.552 3 0.010054 20272 22-052-Murphy-SHP20-PEI-LL-1 45.077 24.615 19601000 0 0 1160400 0 0 0 8229400 5828800 4382800 0 0 0 0 0 0 371 21 360 4420;4421;4422;4423 2276 2276 0 SLGGAAAAEKKM Oxidation (M) 1148.586 0.58595803 77 O80929 RPL36A 60S ribosomal protein L36-1 yes yes 0 1 2 By MS/MS By matching 1 1 7.9566 7.4049 2 7.5748E-08 2483 22-052-Murphy-SHP20-PEI-LL-1 79.474 56.432 7734200 0 0 0 0 0 0 7422800 0 0 0 0 0 0 311350 0 372 77 361 4424;4425 2277 2277 10 1 SLNPKLPILIR Unmodified 1262.8074 0.8074422 181 Q9FIJ2 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 38.205 38.052 3 8.8863E-07 32539 22-052-Murphy-SHP20-LL-1 54.416 52.191 39013000 0 0 0 2145800 0 1287600 5016200 4236200 4389500 3677100 3314200 9503100 2489100 1021600 1933000 373 181 362 4426;4427;4428;4429;4430;4431;4432;4433;4434;4435;4436;4437 2278;2279;2280;2281;2282;2283;2284;2285;2286;2287;2288 2281 11 SLSTGNSKSFFVQQNK Unmodified 1770.8901 0.89006221 132 P61847 rpl32 50S ribosomal protein L32, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 23.88 23.7 3 1.8067E-56 9777 22-052-Murphy-control-1 91.858 71.751 364050000 13783000 14659000 18585000 27843000 12954000 0 78688000 51936000 57424000 11659000 11670000 17415000 21262000 7939800 18236000 374 132 363 4438;4439;4440;4441;4442;4443;4444;4445;4446;4447;4448;4449;4450;4451 2289;2290;2291;2292;2293;2294;2295;2296;2297;2298;2299;2300 2289 11 SLVANEEFQHILR Acetyl (Protein N-term) 1596.826 0.82600539 95 P34788 RPS18A 40S ribosomal protein S18 yes yes 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 51.18 51.088 2 4.5751E-33 43250 22-052-Murphy-SHP20-PEI-LL-3 121.96 106.38 67678000 1625100 2648600 5140900 2551900 1757000 0 26086000 15650000 9970200 0 0 0 2248600 0 0 375 95 364 4452;4453;4454;4455;4456;4457;4458;4459;4460 2301;2302;2303;2304;2305;2306;2307 2307 7 SMGLAY Oxidation (M) 656.28396 0.28396235 133 P62090 psaC Photosystem I iron-sulfur center yes yes 0 1 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 24.448 24.269 1 0.018123 16315 22-052-Murphy-SHP20-PEI-LL-2 86.627 86.627 390030000 4943900 6186800 11349000 34798000 24900000 8006200 56914000 35555000 31223000 13601000 25342000 74503000 23382000 5662200 33658000 376 133 365 4461;4462;4463;4464;4465;4466;4467;4468;4469;4470;4471;4472;4473;4474;4475 2308 2308 27 0 SMPIRKDDEVQIVR Unmodified 1684.893 0.89303909 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 1 2 2 2 2 2 2 2 2 2 21.254 21.055 3;4 3.9696E-20 12748 22-052-Murphy-SHP20-PEI-LL-2 77.593 77.058 350830000 6368900 15294000 14895000 7327500 1678900 0 74909000 88000000 58662000 7606600 13169000 22898000 16271000 5407800 18342000 377 111 366 4476;4477;4478;4479;4480;4481;4482;4483;4484;4485;4486;4487;4488;4489;4490;4491;4492;4493;4494;4495;4496;4497;4498;4499;4500;4501 2309;2310;2311;2312;2313 2311 3 SMPIRKDDEVQIVR Oxidation (M) 1700.888 0.88795372 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 1 2 By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 8.8772 8.7639 3 0.0018851 4137 22-052-Murphy-SHP20-PEI-LL-1 57.802 57.802 525130000 5282700 6193000 14635000 8521500 4602900 0 161050000 166960000 128790000 0 6352700 0 6900300 0 15837000 378 111 366 4502;4503;4504;4505;4506;4507;4508;4509;4510;4511;4512 2314;2315;2316 2315 21 3 SNAKEIGFIKYR Unmodified 1424.7776 0.77759863 153 Q680P8 RPS29A 40S ribosomal protein S29 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 20.688 20.565 3 1.6358E-11 12346 22-052-Murphy-SHP20-PEI-LL-2 70.977 62.873 146410000 11455000 14902000 18878000 0 0 0 40060000 27981000 33135000 0 0 0 0 0 0 379 153 367 4513;4514;4515;4516;4517;4518;4519 2317;2318;2319;2320;2321;2322;2323 2322 7 SNNTVYNATAGGIISK Unmodified 1608.8107 0.81074925 119 P56771 petA Cytochrome f yes yes 0 0 0 By matching By matching By matching By matching By matching By matching By MS/MS By matching 1 1 1 1 1 1 1 1 30.578 30.405 2 0.014939 24679 22-052-Murphy-SHP20-LL-1 72.006 56.115 32884000 0 0 0 2164100 1431900 0 0 2993600 0 4113400 4810100 7093300 5798100 0 4479500 380 119 368 4520;4521;4522;4523;4524;4525;4526;4527 2324 2324 1 SPEPEVKILVDRDPIK Unmodified 1834.02 0.020013746 118 P56766 psaA Photosystem I P700 chlorophyll a apoprotein A1 yes yes 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS 1 2 2 1 1 2 2 2 1 1 2 2 33.633 33.476 3;4 1.6382E-56 26439 22-052-Murphy-SHP20-PEI-LL-1 89.231 79.573 120770000 2985000 4468900 5809900 3592100 0 0 14406000 23074000 27071000 0 9611500 2975800 10269000 5668900 10840000 381 118 369 4528;4529;4530;4531;4532;4533;4534;4535;4536;4537;4538;4539;4540;4541;4542;4543;4544;4545;4546 2325;2326;2327;2328 2325 3 SPVAFSWNRF Unmodified 1209.5931 0.59309232 234 Q9ZUF6 At2g05920 yes yes 0 0 1 By matching By MS/MS By matching By MS/MS 1 1 1 1 46.636 46.503 2 0.013986 44777 22-052-Murphy-SHP20infil-3 50.878 50.878 10089000 0 1109800 0 0 0 0 2664500 1572200 0 0 0 4742500 0 0 0 382 234 370 4547;4548;4549;4550 2329 2329 1 SRLPGGFAAQK Unmodified 1130.6196 0.61964142 232 Q9XJ27 RPS9 30S ribosomal protein S9, chloroplastic yes yes 0 0 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 2 2 1 1 1 3 2 1 1 1 1 2 11.298 11.181 2;3 2.1832E-42 4183 22-052-Murphy-SHP20-LL-3 61.161 51.506 188810000 796750 7037200 439490 20909000 8186800 4513600 6313200 62696000 17789000 12154000 22630000 4002100 21163000 0 179810 383 232 371 4551;4552;4553;4554;4555;4556;4557;4558;4559;4560;4561;4562;4563;4564;4565;4566;4567;4568;4569;4570;4571 2330;2331;2332;2333;2334;2335;2336;2337;2338;2339 2334 10 SSISISEPGSQTAR Unmodified 1418.7001 0.70013617 168 Q93W28 Uncharacterized protein At4g15545 yes yes 0 0 0 By MS/MS 1 22.738 22.437 2 2.0205E-20 19182 22-052-Murphy-SHP20infil-3 59.908 44.278 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 384 168 372 4572 2340 2340 1 SSKAGLQFPVGR Unmodified 1245.683 0.68296996 66 Q9S9K7;O04848;Q9LD28;O81826;Q9LHQ5;Q9C681 RAT5 Probable histone H2AXb;Probable histone H2AXa;Histone H2A.6;Probable histone H2A.3;Probable histone H2A.2;Probable histone H2A.1 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 2 2 2 2 1 2 2 23.828 23.662 2;3 0.0046242 15548 22-052-Murphy-SHP20-PEI-LL-3 55.676 43.828 348300000 10422000 16252000 17438000 27156000 14522000 10949000 27121000 36388000 33462000 13581000 21222000 73797000 13634000 5608800 26746000 385 66 373 4573;4574;4575;4576;4577;4578;4579;4580;4581;4582;4583;4584;4585;4586;4587;4588;4589;4590;4591;4592;4593;4594;4595;4596;4597;4598;4599;4600 2341;2342;2343;2344;2345;2346;2347;2348;2349;2350;2351;2352 2352 9 SSKAGLQFPVGRIAR Unmodified 1585.9053 0.90525876 66 Q9S9K7;O04848;Q9LD28;O81826;Q9LHQ5;Q9C681 RAT5 Probable histone H2AXb;Probable histone H2AXa;Histone H2A.6;Probable histone H2A.3;Probable histone H2A.2;Probable histone H2A.1 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS 2 2 2 1 1 2 2 2 1 2 2 1 1 25.79 25.613 3;4 4.101E-10 18182 22-052-Murphy-SHP20-PEI-LL-1 65.179 62.211 143960000 9196400 9661400 7584100 0 2764500 1386400 24549000 19697000 18389000 0 5773700 25563000 10428000 1876500 7089500 386 66 374 4601;4602;4603;4604;4605;4606;4607;4608;4609;4610;4611;4612;4613;4614;4615;4616;4617;4618;4619;4620;4621 2353;2354 2353 2 SSTSWNIAPANWK Unmodified 1460.7048 0.70482762 144 Q38865 EXPA6 Expansin-A6 yes yes 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 40.715 40.539 2 0.029985 35316 22-052-Murphy-SHP20infil-2 39.148 32.489 29939000 0 1259800 0 0 0 724650 0 0 0 3146400 5171700 14870000 4766400 0 0 387 144 375 4622;4623;4624;4625;4626;4627 2355 2355 1 STMGPPQRIF Oxidation (M) 1148.5648 0.56482866 128 P59230;Q8VZB9 RPL10AB;RPL10AA 60S ribosomal protein L10a-2;60S ribosomal protein L10a-1 yes no 0 1 1 By MS/MS By MS/MS By MS/MS 1 1 1 27.244 27.13 2 0.0065091 19757 22-052-Murphy-SHP20-PEI-LL-1 65.672 61.535 110150000 0 0 0 0 0 0 46655000 34741000 28755000 0 0 0 0 0 0 388 128 376 4628;4629;4630 2356;2357 2356 25 2 STTVGKLLKPLNSEYGK Unmodified 1834.02 0.020013746 122 P56780 psbH Photosystem II reaction center protein H yes yes 0 0 2 By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 28.521 28.348 3 0.020876 25609 22-052-Murphy-SHP20infil-3 30.956 30.956 40729000 0 0 0 5465800 4275700 0 0 4989600 4831100 0 6236300 9315300 3105000 0 2510500 389 122 377 4631;4632;4633;4634;4635;4636;4637;4638 2358 2358 1 SVETYKIYIFK Unmodified 1389.7544 0.75440357 70 Q9LZT0;P40283;O23629 H2B Histone H2B.7;Histone H2B.11;Histone H2B.6 no no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 37.251 37.097 3 0.010514 30293 22-052-Murphy-SHP20-PEI-LL-1 45.137 37.032 90584000 0 0 14010000 0 0 0 27353000 13887000 16144000 2598900 3891500 8564500 0 0 4135300 390 70 378 4639;4640;4641;4642;4643;4644;4645;4646 2359;2360;2361 2359 3 SVLGDVGITEVFSDRADLSGITK Unmodified 2378.2329 0.23291965 33 CON__P34955 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 55.961 55.866 3 0.013015 47293 22-052-Murphy-SHP20infil-1 28.505 20.884 + 33238000 0 0 0 2440300 3004200 2933100 3530100 2852700 3647100 9165600 4250300 0 0 1415100 0 391 33 379 4647;4648;4649;4650;4651;4652;4653;4654;4655 2362 2362 1 TAATISPSFNANVKQNK Unmodified 1789.9323 0.93226137 16 A0A1P8BC48;F4K4M0 QWRF9 QWRF motif-containing protein 9 yes no 0 0 1 By MS/MS By MS/MS 1 1 34.032 33.914 3 0.013289 26253 22-052-Murphy-SHP20-PEI-LL-2 33.301 21.532 121070000 0 0 0 0 0 0 83230000 37843000 0 0 0 0 0 0 0 392 16 380 4656;4657 2363;2364 2364 2 TDKPFGINGSMDLR Unmodified 1549.7559 0.75587691 91 P27202 PSBR Photosystem II 10 kDa polypeptide, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 33.572 33.472 3 0.015426 20936 22-052-Murphy-control-3 40.066 37.098 33749000 4266100 4823700 8055900 0 0 0 8192000 5578400 2832400 0 0 0 0 0 0 393 91 381 4658;4659;4660;4661;4662;4663 2365;2366;2367 2365 3 TDKPFGINGSMDLR Oxidation (M) 1565.7508 0.75079153 91 P27202 PSBR Photosystem II 10 kDa polypeptide, chloroplastic yes yes 0 1 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 1 1 2 1 2 2 2 2 2 2 2 26.545 26.353 2;3 6.1678E-21 18966 22-052-Murphy-SHP20-PEI-LL-1 71.349 71.349 1058300000 10728000 14263000 33418000 2394800 0 9486100 354130000 23276000 204550000 50234000 63914000 77375000 83756000 42714000 88090000 394 91 381 4664;4665;4666;4667;4668;4669;4670;4671;4672;4673;4674;4675;4676;4677;4678;4679;4680;4681;4682;4683;4684;4685;4686 2368;2369;2370 2368 16 3 TDPNQNTGIVIQK Unmodified 1426.7416 0.74160705 71 O49006 PME3 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 22.29 22.135 2 1.8342E-07 18819 22-052-Murphy-SHP20infil-3 69.423 60.891 119220000 2171900 2171000 0 11061000 6023000 6878400 7119100 6342200 6372900 6581400 10106000 48313000 0 0 6082700 395 71 382 4687;4688;4689;4690;4691;4692;4693;4694;4695;4696;4697;4698 2371 2371 1 TEIPAATPSDPQLKE Unmodified 1595.8043 0.80426689 184 Q9FLX7 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 30.461 30.303 2 3.4983E-15 27541 22-052-Murphy-SHP20infil-3 103.26 103.26 1051800000 30801000 30238000 49464000 38855000 41520000 26715000 130670000 138300000 106020000 61860000 80190000 189980000 54140000 25898000 47188000 396 184 383 4699;4700;4701;4702;4703;4704;4705;4706;4707;4708;4709;4710;4711;4712;4713 2372;2373;2374;2375;2376;2377;2378;2379;2380;2381;2382;2383;2384 2377 11 TFKVGDYVDVK Unmodified 1269.6605 0.66050319 148 Q9FDZ9;Q43291 RPL21E;RPL21A 60S ribosomal protein L21-2;60S ribosomal protein L21-1 yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS 1 2 2 1 31.813 31.689 2;3 0.0023192 24595 22-052-Murphy-SHP20-PEI-LL-1 63.283 32.719 47112000 0 0 1743400 0 0 0 19080000 13634000 12654000 0 0 0 0 0 0 397 148 384 4714;4715;4716;4717;4718;4719 2385;2386;2387;2388;2389 2385 5 TFQGPPHGIQVER Unmodified 1464.7474 0.74736113 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 2 2 1 2 2 2 2 2 2 2 2 2 23.61 23.411 2;3 9.1421E-21 20179 22-052-Murphy-SHP20infil-3 93.649 82.485 1375700000 0 29326000 27783000 67380000 55065000 28624000 130450000 145260000 119830000 73005000 119500000 238450000 135720000 58514000 146840000 398 64 385 4720;4721;4722;4723;4724;4725;4726;4727;4728;4729;4730;4731;4732;4733;4734;4735;4736;4737;4738;4739;4740;4741;4742;4743;4744 2390;2391;2392;2393;2394;2395;2396;2397;2398;2399;2400;2401;2402;2403;2404 2394 14 TGDIVEIK Unmodified 873.48075 0.48074791 163 Q8RXX5;Q8W463 50S ribosomal protein L19-2, chloroplastic;50S ribosomal protein L19-1, chloroplastic yes no 0 0 0 By MS/MS By matching By matching 1 1 1 22.086 21.837 2 0.011207 14854 22-052-Murphy-SHP20-PEI-LL-1 92.467 40.894 39860000 0 0 0 0 0 0 36253000 3163000 0 0 0 0 0 443440 0 399 163 386 4745;4746;4747 2405 2405 0 TGDSSLVAYVKAPNANK Unmodified 1733.8948 0.89481323 236 Q9ZVA4 F9K20.10 yes yes 0 0 1 By matching By matching By MS/MS By matching By MS/MS By matching By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 29.145 28.987 3 0.026517 26300 22-052-Murphy-SHP20infil-3 34.101 22.839 64633000 0 0 0 6023200 4490500 5095700 5094400 7477700 5885300 0 9705200 16904000 0 0 3957400 400 236 387 4748;4749;4750;4751;4752;4753;4754;4755;4756 2406 2406 0 TGDSSLVAYVKAPNANKK Unmodified 1861.9898 0.98977625 236 Q9ZVA4 F9K20.10 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching By MS/MS 2 2 1 2 1 2 1 1 1 1 2 2 1 1 23.582 23.422 3;4 7.554E-05 17716 22-052-Murphy-SHP20infil-2 52.966 49.186 165180000 5686000 4394700 3672300 17853000 8828900 7830300 10728000 13298000 9591700 4081200 19552000 48063000 5883400 0 5720000 401 236 388 4757;4758;4759;4760;4761;4762;4763;4764;4765;4766;4767;4768;4769;4770;4771;4772;4773;4774;4775;4776 2407;2408;2409;2410 2407 4 TGFREGTEAKPR Unmodified 1347.6895 0.6895119 149 Q8LEM8;Q43292 RPL37C;RPL37B 60S ribosomal protein L37-3;60S ribosomal protein L37-2 yes no 0 0 2 By matching By matching By matching By MS/MS By matching By MS/MS By matching By matching 1 1 1 1 1 1 1 1 7.9775 7.8501 3 2.3982E-24 2393 22-052-Murphy-SHP20-PEI-LL-1 97.456 81.203 41538000 0 202740 929960 0 0 4771500 15231000 5520600 2807300 3412500 0 8663000 0 0 0 402 149 389 4777;4778;4779;4780;4781;4782;4783;4784 2411 2411 1 TGKGFTLEELK Unmodified 1221.6605 0.66050319 21 P41127;A8MQA1;F4IWP7 RPL13B;BBC1 60S ribosomal protein L13-1;60S ribosomal protein L13 yes no 0 0 1 By matching By matching By MS/MS By matching By matching 1 1 1 1 1 27.201 27.089 3 2.1154E-05 14725 22-052-Murphy-control-3 60.518 41.203 23255000 1498400 2979800 12510000 0 0 0 4230700 2035800 0 0 0 0 0 0 0 403 21 390 4785;4786;4787;4788;4789 2412 2412 1 TGLFVGLNKGHVVTR Unmodified 1596.91 0.91000979 77;198 O80929;Q9M352 RPL36A;RPL36B 60S ribosomal protein L36-1;60S ribosomal protein L36-2 no no 0 0 1 By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 2 2 2 1 2 2 2 2 2 26.488 26.343 3;4 2.3705E-06 18476 22-052-Murphy-SHP20-PEI-LL-2 58.21 53.662 65469000 1320400 2855000 4329300 5742900 1604300 0 20147000 10083000 9508800 0 0 0 5119800 0 4757200 404 77;198 391 4790;4791;4792;4793;4794;4795;4796;4797;4798;4799;4800;4801;4802;4803;4804;4805;4806;4807 2413;2414;2415;2416 2414 4 TGLFVGLNKGHVVTRR Unmodified 1753.0111 0.011120814 77;198 O80929;Q9M352 RPL36A;RPL36B 60S ribosomal protein L36-1;60S ribosomal protein L36-2 no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 21.272 21.167 4 0.020747 7655 22-052-Murphy-control-1 38.511 34.195 64544000 3966300 3863700 6285800 3541100 0 0 23077000 12592000 11218000 0 0 0 0 0 0 405 77;198 392 4808;4809;4810;4811;4812;4813;4814 2417;2418 2417 2 TGYHNMYKEYR Oxidation (M) 1476.6456 0.64559818 112;192 P51418;A0A1P8AY36;A8MRF3;Q8L7K0;Q9LUD4 RPL18AB;RPL18AA;RPL18AC 60S ribosomal protein L18a-2;60S ribosomal protein L18a-1;60S ribosomal protein L18a-3 no no 0 1 1 By MS/MS 1 8.1228 7.8978 2 0.025419 2673 22-052-Murphy-SHP20-PEI-LL-1 51.346 44.321 20125000 0 0 0 0 0 0 20125000 0 0 0 0 0 0 0 0 406 112;192 393 4815 2419 2419 22 0 TIALGK Acetyl (Protein N-term) 643.39048 0.39047634 117 P56761 psbD Photosystem II D2 protein yes yes 1 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 31.05 30.89 1 0.00042509 22518 22-052-Murphy-SHP20-PEI-infil-1 93.595 43.455 702500000 2727900 4104600 3140100 45816000 21847000 19586000 0 30012000 29600000 64647000 81131000 151490000 133170000 34305000 80927000 407 117 394 4816;4817;4818;4819;4820;4821;4822;4823;4824;4825;4826;4827;4828;4829 2420;2421;2422 2422 0 TIALGKFTK Acetyl (Protein N-term) 1019.6015 0.60153174 117 P56761 psbD Photosystem II D2 protein yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 36.958 36.804 2 3.1686E-05 31356 22-052-Murphy-SHP20-LL-1 88.942 88.942 133990000 0 2775200 2936200 7963400 3597400 1880600 10210000 7756900 6877100 8639500 16581000 31590000 12929000 6837000 13413000 408 117 395 4830;4831;4832;4833;4834;4835;4836;4837;4838;4839;4840;4841;4842;4843 2423;2424;2425;2426;2427;2428;2429;2430;2431;2432;2433;2434 2428 11 TIALGKFTKDEK Acetyl (Protein N-term) 1391.766 0.76603089 117 P56761 psbD Photosystem II D2 protein yes yes 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 1 2 2 2 2 2 2 2 1 2 30.657 30.494 2;3 1.6611E-26 24689 22-052-Murphy-SHP20-LL-1 109.71 96.677 1320700000 3756900 4325000 0 5345200 23705000 2263500 55575000 86920000 75131000 126110000 179110000 298120000 249400000 36865000 174030000 409 117 396 4844;4845;4846;4847;4848;4849;4850;4851;4852;4853;4854;4855;4856;4857;4858;4859;4860;4861;4862;4863;4864;4865;4866 2435;2436;2437;2438;2439;2440;2441;2442;2443;2444;2445;2446;2447;2448;2449;2450;2451;2452;2453 2442 19 TIATSATHYNGVR Unmodified 1389.7001 0.70007659 204 Q9S7Y7 XYL1 Alpha-xylosidase 1 yes yes 0 0 0 By matching By matching By matching By MS/MS By matching By matching By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 9.3127 9.1969 3 0.015279 4793 22-052-Murphy-SHP20infil-3 53.237 52.188 107490000 1311300 2065600 2300700 0 14215000 4517200 0 19664000 0 11622000 22647000 11203000 0 0 17941000 410 204 397 4867;4868;4869;4870;4871;4872;4873;4874;4875;4876 2454 2454 1 TIDRTYPIFTVR Acetyl (Protein N-term) 1522.8144 0.81437807 134 P62095 psbF Cytochrome b559 subunit beta yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 6 11 5 10 10 13 9 11 6 9 6 9 6 8 6 54.727 54.61 2;3 0 32170 22-052-Murphy-SHP20-PEI-infil-3 152.47 115.12 9623200000 69461000 11802000 34720000 11280000 383970000 160300000 769400000 820070000 988730000 772550000 1615800000 2172900000 1189100000 595330000 27784000 411 134 398 4877;4878;4879;4880;4881;4882;4883;4884;4885;4886;4887;4888;4889;4890;4891;4892;4893;4894;4895;4896;4897;4898;4899;4900;4901;4902;4903;4904;4905;4906;4907;4908;4909;4910;4911;4912;4913;4914;4915;4916;4917;4918;4919;4920;4921;4922;4923;4924;4925;4926;4927;4928;4929;4930;4931;4932;4933;4934;4935;4936;4937;4938;4939;4940;4941;4942;4943;4944;4945;4946;4947;4948;4949;4950;4951;4952;4953;4954;4955;4956;4957;4958;4959;4960;4961;4962;4963;4964;4965;4966;4967;4968;4969;4970;4971;4972;4973;4974;4975;4976;4977;4978;4979;4980;4981;4982;4983;4984;4985;4986;4987;4988;4989;4990;4991;4992;4993;4994;4995;4996;4997;4998;4999;5000;5001 2455;2456;2457;2458;2459;2460;2461;2462;2463;2464;2465;2466;2467;2468;2469;2470;2471;2472;2473;2474;2475;2476;2477;2478;2479;2480;2481;2482;2483;2484;2485;2486;2487;2488;2489;2490;2491;2492;2493;2494;2495;2496;2497;2498;2499;2500;2501;2502;2503;2504;2505;2506;2507;2508;2509;2510;2511;2512;2513;2514;2515;2516;2517;2518;2519;2520;2521;2522;2523;2524;2525;2526;2527;2528;2529;2530;2531;2532;2533;2534;2535;2536;2537;2538;2539;2540;2541;2542;2543;2544;2545;2546;2547;2548;2549;2550;2551;2552;2553;2554;2555;2556;2557;2558;2559;2560;2561;2562;2563;2564;2565;2566;2567;2568;2569;2570;2571;2572;2573;2574;2575;2576;2577;2578;2579;2580;2581;2582;2583;2584;2585;2586;2587;2588;2589;2590;2591;2592;2593;2594;2595;2596;2597;2598 2557 141 TIFHLNPSGR Unmodified 1140.604 0.60399136 85 Q9LUT2;P23686;P17562 METK4;SAM1;SAM2 S-adenosylmethionine synthase 4;S-adenosylmethionine synthase 1;S-adenosylmethionine synthase 2 yes no 0 0 0 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 24.202 24.028 3 0.013027 16307 22-052-Murphy-SHP20-LL-3 46.462 37.93 60870000 804110 0 0 5378600 1385900 0 11947000 9526000 7839600 3854700 0 6923300 4821200 1903900 6485800 412 85 399 5002;5003;5004;5005;5006;5007;5008;5009;5010;5011;5012 2599 2599 0 TIFHLNPSGRFVIGGPHGDAGLTGRK Unmodified 2703.4358 0.43575083 85 Q9LUT2;P23686;P17562 METK4;SAM1;SAM2 S-adenosylmethionine synthase 4;S-adenosylmethionine synthase 1;S-adenosylmethionine synthase 2 yes no 0 0 2 By matching By matching By MS/MS By MS/MS 1 1 1 1 33.115 32.994 6 0.007252 25278 22-052-Murphy-SHP20-PEI-LL-3 18.095 12.375 25896000 0 0 2584500 0 0 0 10912000 5736400 6663600 0 0 0 0 0 0 413 85 400 5013;5014;5015;5016 2600 2600 1 TIITGSRNVVDGSTTFHSATVAAVGER Unmodified 2745.4046 0.40456986 71 O49006;Q42534 PME3;PME2 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3;Pectinesterase 2 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 34.251 34.101 3;4 9.2251E-127 31685 22-052-Murphy-SHP20infil-3 114.84 107.65 889610000 18093000 21020000 22183000 70160000 37528000 20107000 168790000 117640000 75166000 30911000 58667000 146890000 31147000 20304000 51004000 414 71 401 5017;5018;5019;5020;5021;5022;5023;5024;5025;5026;5027;5028;5029;5030;5031;5032;5033;5034;5035;5036;5037;5038;5039;5040;5041;5042;5043;5044;5045;5046 2601;2602;2603;2604;2605;2606;2607;2608;2609;2610;2611;2612;2613;2614;2615;2616;2617;2618;2619;2620;2621;2622;2623;2624;2625;2626;2627;2628;2629;2630 2612 30 TIVFGSSAGQINGKQR Unmodified 1661.8849 0.88491725 40 F4I7X1 SKS6 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 1 1 1 23.043 22.88 3 4.8048E-56 14360 22-052-Murphy-SHP20-PEI-infil-1 113.65 101.27 98929000 2340100 1848500 0 7722500 3364800 5571800 0 4429500 5462100 8482200 9747500 37781000 6415300 0 5764000 415 40 402 5047;5048;5049;5050;5051;5052;5053;5054;5055;5056;5057;5058 2631;2632;2633;2634;2635 2633 5 TLGGILLPSTAQSKPQGGEVVAVGEGR Unmodified 2620.4184 0.41842901 74 O65282 CPN21 20 kDa chaperonin, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By matching 1 1 1 41.591 41.527 3 0.0063643 27983 22-052-Murphy-control-3 11.311 8.51 7231800 1994400 0 3784100 1453300 0 0 0 0 0 0 0 0 0 0 0 416 74 403 5059;5060;5061 2636 2636 1 TNTDFLPYNGDGFK Unmodified 1587.7205 0.72053726 146 Q42029 PSBP1 Oxygen-evolving enhancer protein 2-1, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 42.75 42.654 2 0.024875 35044 22-052-Murphy-SHP20-PEI-LL-3 48.64 42.399 26931000 3648500 3861400 4330900 0 0 0 5358100 3328900 6403100 0 0 0 0 0 0 417 146 404 5062;5063;5064;5065;5066;5067 2637 2637 1 TPGPGAQSALR Unmodified 1053.5567 0.55670682 98;176;213 P42036;Q9CAX6;Q9SIH0 RPS14C;RPS14B;RPS14A 40S ribosomal protein S14-3;40S ribosomal protein S14-2;40S ribosomal protein S14-1 no no 0 0 0 By matching By matching By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 8.8861 8.7188 2 0.014937 3730 22-052-Murphy-SHP20-PEI-LL-2 60.436 50.022 26035000 0 0 1327400 0 0 0 5426800 7671900 0 0 7985500 0 3623800 0 0 418 98;176;213 405 5068;5069;5070;5071;5072;5073 2638;2639 2638 2 TPTVFDNK Unmodified 920.46035 0.46034682 218 Q9SMU8;Q9LHB9 PER34;PER32 Peroxidase 34;Peroxidase 32 yes no 0 0 0 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 17.785 17.574 2 0.021082 9015 22-052-Murphy-SHP20-PEI-LL-2 86.086 62.114 116290000 1269100 0 1053200 4270300 0 0 16779000 22534000 14485000 6724800 9317600 21094000 9765600 2306500 6695800 419 218 406 5074;5075;5076;5077;5078;5079;5080;5081;5082;5083;5084;5085 2640 2640 1 TPTVFDNKYYVNLKER Unmodified 1986.0211 0.021076378 218 Q9SMU8 PER34 Peroxidase 34 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 2 2 32.467 32.368 3;4 7.7067E-39 25429 22-052-Murphy-SHP20-PEI-LL-1 88.075 78.911 81064000 9223300 6511100 15805000 0 0 0 22321000 13769000 13435000 0 0 0 0 0 0 420 218 407 5086;5087;5088;5089;5090;5091;5092;5093;5094;5095;5096 2641;2642;2643;2644;2645;2646;2647 2645 7 TRTIITGSRNVVDGSTTFHSATVAAVGER Unmodified 3002.5534 0.55335936 71 O49006 PME3 Pectinesterase/pectinesterase inhibitor 3;Pectinesterase inhibitor 3;Pectinesterase 3 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching By matching 1 2 2 1 2 2 2 1 2 30.916 30.789 4;5 2.9686E-54 23591 22-052-Murphy-SHP20-PEI-LL-1 61.801 55.225 103770000 1698400 5622200 7227300 5380100 7462700 0 31231000 24979000 6489900 0 0 13681000 0 0 0 421 71 408 5097;5098;5099;5100;5101;5102;5103;5104;5105;5106;5107;5108;5109;5110;5111 2648;2649;2650;2651;2652 2649 5 TRYPVVVR Unmodified 988.5818 0.58179936 205;201 Q9S714;Q9S831 PSAE2;PSAE1 Photosystem I reaction center subunit IV B, chloroplastic;Photosystem I reaction center subunit IV A, chloroplastic no no 0 0 1 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 9.1507 9.0296 2 6.4498E-22 3876 22-052-Murphy-SHP20-PEI-LL-3 119.7 98.547 976960000 19417000 18200000 0 56275000 0 0 266290000 144460000 138090000 22787000 49514000 215410000 46516000 0 0 422 201;205 409 5112;5113;5114;5115;5116;5117;5118;5119;5120;5121 2653;2654;2655;2656 2656 2 TRYPVVVRFAK Unmodified 1334.7823 0.78229008 205;201 Q9S714;Q9S831 PSAE2;PSAE1 Photosystem I reaction center subunit IV B, chloroplastic;Photosystem I reaction center subunit IV A, chloroplastic no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 22.701 22.512 3 5.477E-05 14533 22-052-Murphy-SHP20-PEI-LL-3 63.283 59.962 251560000 11309000 8483500 13367000 10409000 8223800 1640600 59084000 39004000 41586000 0 8999300 12732000 10303000 7270600 19148000 423 201;205 410 5122;5123;5124;5125;5126;5127;5128;5129;5130;5131;5132;5133;5134;5135 2657;2658;2659;2660;2661 2661 5 TSAAIKVLKQIGAYDDAEK Unmodified 2020.0841 0.084070565 141;63 F4KDU5;P49691;Q2V3X4;Q9SF40 At5g02870;RPL4D;At3g09630;RPL4A 60S ribosomal protein L4-2;60S ribosomal protein L4-1 no no 0 0 2 By MS/MS By MS/MS By MS/MS 1 1 1 35.632 35.538 3 0.00030127 28617 22-052-Murphy-SHP20-PEI-LL-1 48.623 48.395 30407000 0 0 0 0 0 0 14184000 8897400 7325600 0 0 0 0 0 0 424 63;141 411 5136;5137;5138 2662 2662 1 TTEEKEILAAK Acetyl (Protein N-term) 1273.6765 0.67654718 188 Q9LHG9 Nascent polypeptide-associated complex subunit alpha-like protein 1 yes yes 1 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 29.623 29.469 2 6.5361E-42 21479 22-052-Murphy-SHP20-PEI-LL-3 95.531 75.744 117240000 0 0 0 9720700 8975500 4540800 29335000 23002000 0 0 10922000 30747000 0 0 0 425 188 412 5139;5140;5141;5142;5143;5144;5145;5146;5147;5148 2663;2664;2665;2666;2667;2668;2669;2670;2671;2672 2672 10 TTPQVKTGLFVGLNKGHVVTR Acetyl (Protein N-term) 2293.2906 0.29064972 198 Q9M352 RPL36B 60S ribosomal protein L36-2 yes yes 1 0 2 By matching By MS/MS By matching By MS/MS By matching 1 1 1 1 1 34.391 34.33 4 2.2281E-15 27335 22-052-Murphy-SHP20-PEI-LL-1 61.102 57.554 29366000 2249300 0 0 3683600 1645200 0 15370000 0 6417600 0 0 0 0 0 0 426 198 413 5149;5150;5151;5152;5153 2673 2673 1 TVNRAYGGVLSGSAVR Unmodified 1605.8587 0.8587025 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 no no 0 0 1 By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 23.338 23.168 3 2.3489E-20 15623 22-052-Murphy-SHP20-PEI-LL-1 71.279 60.621 106440000 0 3425000 0 12743000 4960200 2655400 25609000 20684000 14193000 2240600 0 10073000 3892300 0 5961700 427 178 414 5154;5155;5156;5157;5158;5159;5160;5161;5162;5163;5164 2674;2675 2674 2 TVNRAYGGVLSGSAVRER Unmodified 1891.0024 0.0024066216 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 no no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 19.716 19.609 4 1.0162E-24 11389 22-052-Murphy-SHP20-PEI-LL-2 65.943 48.541 63576000 2047300 2550000 3384400 3525300 1373600 0 21671000 16062000 12963000 0 0 0 0 0 0 428 178 415 5165;5166;5167;5168;5169;5170;5171;5172 2676;2677;2678;2679 2678 4 TVTSVGGAGTYSVK Unmodified 1325.6827 0.68269519 75 O65351 SBT1.7 Subtilisin-like protease SBT1.7 yes yes 0 0 0 By MS/MS By matching By MS/MS 1 1 1 22.501 22.299 2 4.6582E-20 19047 22-052-Murphy-SHP20infil-3 78.098 57.768 15556000 0 0 0 0 0 3798700 0 0 0 1941900 0 9815000 0 0 0 429 75 416 5173;5174;5175 2680 2680 1 TVVAAVPVDKLPLESK Unmodified 1664.9713 0.97127264 187 Q9LER7 PSRP5 50S ribosomal protein 5, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 2 1 2 2 2 2 2 1 2 2 2 2 2 1 37.746 37.6 2;3 5.7487E-22 30718 22-052-Murphy-SHP20infil-1 78.814 68.757 362070000 5898700 9558400 10458000 33392000 15175000 9060100 34680000 24954000 16861000 31682000 42070000 83837000 20347000 11171000 12924000 430 187 417 5176;5177;5178;5179;5180;5181;5182;5183;5184;5185;5186;5187;5188;5189;5190;5191;5192;5193;5194;5195;5196;5197;5198;5199;5200;5201 2681;2682;2683;2684;2685;2686;2687;2688;2689;2690;2691 2681 7 TVVAAVPVDKLPLESKEAK Unmodified 1993.1459 0.14594254 187 Q9LER7 PSRP5 50S ribosomal protein 5, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 1 2 2 1 2 2 1 2 2 2 1 32.23 32.101 3;4 4.306E-29 24902 22-052-Murphy-SHP20-PEI-LL-1 75.018 65.096 180320000 5084800 5693100 3207900 20322000 12048000 2796200 34681000 17762000 12390000 12058000 17069000 32547000 0 0 4665600 431 187 418 5202;5203;5204;5205;5206;5207;5208;5209;5210;5211;5212;5213;5214;5215;5216;5217;5218;5219;5220;5221;5222;5223 2692;2693;2694;2695;2696;2697;2698;2699 2696 7 TYKAKLVVFPR Unmodified 1320.7918 0.79179213 179 Q9FF90 RPL13D 60S ribosomal protein L13-3 yes yes 0 0 2 By matching By MS/MS By matching By matching 1 1 1 1 23.12 22.922 3 3.0052E-06 10955 22-052-Murphy-control-3 59.35 55.1 8647300 0 1430800 3985700 0 0 0 2565900 0 0 0 0 0 0 0 664990 432 179 419 5224;5225;5226;5227 2700 2700 1 TYKTKLVIFPR Unmodified 1364.818 0.81800688 21 P41127;A8MQA1 RPL13B;BBC1 60S ribosomal protein L13-1;60S ribosomal protein L13 yes no 0 0 2 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 25.487 25.391 3 6.0229E-10 12090 22-052-Murphy-control-2 56.563 53.525 103240000 8634400 11631000 35840000 1707200 0 0 22257000 12893000 10278000 0 0 0 0 0 0 433 21 420 5228;5229;5230;5231;5232;5233;5234 2701;2702;2703;2704;2705;2706 2701 6 VAGLGKILGPR Unmodified 1079.6815 0.6815134 51 F4J296;Q9LY66 At3g63490;RPL1 Ribosomal protein;50S ribosomal protein L1, chloroplastic yes no 0 0 1 By MS/MS By matching By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 27.425 27.27 3 0.0086348 24344 22-052-Murphy-SHP20infil-3 47.603 38.281 22475000 0 0 0 2313200 0 1593200 3139700 0 2278300 3229200 3516600 6404500 0 0 0 434 51 421 5235;5236;5237;5238;5239;5240;5241 2707 2707 1 VAGPPVVMNPISR Oxidation (M) 1351.7282 0.7282056 143 Q38842 ATOZI1 yes yes 0 1 0 By MS/MS 1 31.005 30.764 2 1.0075E-13 28193 22-052-Murphy-SHP20infil-3 74.92 54.05 6889200 0 0 0 0 0 0 0 0 0 0 0 6889200 0 0 0 435 143 422 5242 2708 2708 29 0 VAINGFGR Unmodified 832.45554 0.45553621 90 P25857 GAPB Glyceraldehyde-3-phosphate dehydrogenase GAPB, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 24.382 24.267 2 0.016174 12144 22-052-Murphy-control-3 78.002 14.42 189050000 17097000 20570000 17745000 0 0 0 50837000 38966000 43834000 0 0 0 0 0 0 436 90 423 5243;5244;5245;5246;5247;5248 2709;2710;2711 2710 3 VAKVTGGAPNKLSK Unmodified 1368.8089 0.80889876 3 A0A1I9LSB4;F4KDR2;Q9SF53;Q9M3D2;Q9LZ41;O80626 At5g02610;RPL35A;RPL35C;RPL35D;RPL35B 60S ribosomal protein L35-1;60S ribosomal protein L35-3;60S ribosomal protein L35-4;60S ribosomal protein L35-2 yes no 0 0 2 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching By matching 1 1 1 2 1 2 1 1 2 1 1 1 1 1 8.0422 7.8772 2;3 1.0285E-30 2713 22-052-Murphy-SHP20-PEI-LL-2 98.407 85.399 254770000 2500800 436460 4179800 14230000 0 4309800 61679000 38343000 38240000 17962000 16486000 28989000 11334000 1411200 14671000 437 3 424 5249;5250;5251;5252;5253;5254;5255;5256;5257;5258;5259;5260;5261;5262;5263;5264;5265 2712;2713;2714;2715 2714 2 VALVYGQMNEPPGAR Oxidation (M) 1616.7981 0.79807608 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 1 0 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 28.471 28.295 2 2.2892E-36 25395 22-052-Murphy-SHP20infil-3 95.502 64.938 151480000 2329800 3921500 4330200 0 5655500 4534600 17934000 17206000 16929000 6901900 8261400 25336000 15192000 6267400 16682000 438 86 425 5266;5267;5268;5269;5270;5271;5272;5273;5274;5275;5276;5277;5278;5279 2716;2717;2718;2719;2720;2721;2722;2723;2724;2725;2726 2717 14 11 VALVYGQMNEPPGAR Unmodified 1600.8032 0.80316145 86 P19366 atpB ATP synthase subunit beta, chloroplastic yes yes 0 0 0 By matching By matching By MS/MS By matching 1 1 1 1 34.218 34.052 2 5.4234E-26 31770 22-052-Murphy-SHP20infil-3 96.331 59.219 23135000 0 1176400 0 0 0 0 0 0 3067200 0 0 13855000 5037200 0 0 439 86 425 5280;5281;5282;5283 2727 2727 1 VATGLFVGLNK Unmodified 1117.6495 0.64954457 195 Q9LZ57 RPL36C 60S ribosomal protein L36-3 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 38.771 38.622 2 5.3711E-15 28184 22-052-Murphy-SHP20-LL-2 107.66 81.764 114500000 0 0 0 3604400 3449200 4085000 2431200 7107100 6141600 11906000 11372000 17368000 20931000 13021000 13083000 440 195 426 5284;5285;5286;5287;5288;5289;5290;5291;5292;5293;5294;5295 2728;2729;2730;2731;2732;2733;2734;2735;2736 2732 4 VATGLFVGLNKGHVVTKR Unmodified 1895.1105 0.11050051 195 Q9LZ57 RPL36C 60S ribosomal protein L36-3 yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 3 3 3 3 1 1 3 3 5 3 3 3 3 3 3 24.535 24.359 3;4;5 1.5099E-72 20038 22-052-Murphy-SHP20-PEI-LL-3 110.77 98.752 596600000 22880000 30344000 48552000 28658000 5089100 3341300 130270000 84446000 117480000 16580000 25289000 29849000 21683000 12132000 20006000 441 195 427 5296;5297;5298;5299;5300;5301;5302;5303;5304;5305;5306;5307;5308;5309;5310;5311;5312;5313;5314;5315;5316;5317;5318;5319;5320;5321;5322;5323;5324;5325;5326;5327;5328;5329;5330;5331;5332;5333;5334;5335;5336;5337;5338 2737;2738;2739;2740;2741;2742;2743;2744;2745;2746;2747;2748;2749;2750;2751;2752;2753;2754;2755;2756;2757;2758;2759;2760;2761;2762;2763;2764;2765 2764 29 VATVSLPR Unmodified 841.50215 0.50215205 32 CON__P00761 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 23.459 23.277 2 6.2155E-06 9694 22-052-Murphy-control-1 94.669 59.563 + 1041900000 109200000 102840000 172490000 83488000 39588000 6508400 199320000 140310000 97140000 6890300 6111700 32743000 9325000 6170000 29810000 442 32 428 5339;5340;5341;5342;5343;5344;5345;5346;5347;5348;5349;5350;5351;5352;5353 2766;2767;2768;2769;2770;2771 2766 6 VDVVTLGPSVR Unmodified 1140.6503 0.65027285 213 Q9SIH0 RPS14A 40S ribosomal protein S14-1 yes yes 0 0 0 By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 34.016 33.914 2 0.00028593 26962 22-052-Murphy-SHP20-PEI-LL-1 60.436 48.08 26173000 0 0 0 2996300 2714400 0 0 7349900 8078500 0 0 5034100 0 0 0 443 213 429 5354;5355;5356;5357;5358;5359 2772;2773;2774 2772 3 VEKSGGEVNFPK Unmodified 1289.6616 0.66156582 196 Q9M1X3 F16M2_10 yes yes 0 0 1 By matching By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching 1 2 2 2 1 2 1 2 1 1 1 2 8.9482 8.8334 2;3 2.1609E-25 4031 22-052-Murphy-SHP20-PEI-LL-1 113.71 83.54 282010000 14043000 27166000 34370000 19326000 2482400 0 53386000 49549000 43967000 4225000 6208000 22813000 0 0 4472500 444 196 430 5360;5361;5362;5363;5364;5365;5366;5367;5368;5369;5370;5371;5372;5373;5374;5375;5376;5377 2775;2776;2777;2778 2777 4 VENVTLGPAVR Unmodified 1153.6455 0.64552182 98 P42036 RPS14C 40S ribosomal protein S14-3 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 27.064 26.976 2 2.4429E-08 19661 22-052-Murphy-SHP20-PEI-LL-1 65.252 44.97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 445 98 431 5378;5379;5380;5381 2779;2780;2781;2782 2780 4 VETVTLGPSVR Unmodified 1156.6452 0.64518747 176 Q9CAX6 RPS14B 40S ribosomal protein S14-2 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 28.184 28.02 2 5.1098E-54 20085 22-052-Murphy-SHP20-PEI-LL-3 133.55 76.267 275450000 5395200 7077400 7271300 21956000 16204000 11046000 56039000 49942000 40166000 6835600 10616000 19770000 7717800 3609300 11810000 446 176 432 5382;5383;5384;5385;5386;5387;5388;5389;5390;5391;5392;5393;5394;5395;5396 2783;2784;2785;2786;2787;2788;2789;2790;2791;2792;2793;2794;2795;2796;2797 2797 15 VEVKAPGILER Unmodified 1209.7081 0.70812208 20 F4IMB5;A0A2P2CLF9;P92549 At2g07698;ATPA ATP synthase subunit alpha;ATP synthase subunit alpha, mitochondrial yes no 0 0 1 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.946 26.783 3 9.5248E-10 23920 22-052-Murphy-SHP20infil-3 78.655 70.35 75792000 1656500 2564900 2639700 4470700 5417700 3273900 12205000 8140800 7219400 3063600 0 16193000 3398100 1204500 4344600 447 20 433 5397;5398;5399;5400;5401;5402;5403;5404;5405;5406;5407;5408;5409;5410 2798;2799;2800;2801;2802;2803;2804;2805 2801 8 VFPNGEVQYLHPK Unmodified 1526.7882 0.78816332 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 1 1 2 3 2 1 2 2 1 1 1 30.682 30.542 2;3 9.2528E-33 15349 22-052-Murphy-control-1 81.865 81.865 540950000 27315000 26741000 35113000 51668000 22861000 9498500 96630000 67116000 74454000 12738000 26988000 53310000 14060000 5539700 16914000 448 202;207 434 5411;5412;5413;5414;5415;5416;5417;5418;5419;5420;5421;5422;5423;5424;5425;5426;5427;5428;5429;5430;5431;5432;5433;5434;5435 2806;2807;2808;2809;2810;2811;2812;2813;2814;2815;2816;2817;2818;2819;2820;2821;2822;2823;2824;2825;2826;2827;2828;2829;2830;2831;2832;2833;2834;2835 2806 30 VFPNGEVQYLHPKDGVYPEK Unmodified 2315.1586 0.15863249 202;207 Q9S7H1;Q9SA56 psaD1;PSAD2 Photosystem I reaction center subunit II-1, chloroplastic;Photosystem I reaction center subunit II-2, chloroplastic no no 0 0 1 By matching By matching By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 33.251 33.125 4 0.012685 30616 22-052-Murphy-SHP20infil-3 31.801 28.877 60641000 2640800 1664200 2793100 2910400 6547500 2110100 10417000 5815700 9400800 0 5578600 10763000 0 0 0 449 202;207 435 5436;5437;5438;5439;5440;5441;5442;5443;5444;5445;5446 2836 2836 1 VFVVVQDDTFRK Unmodified 1451.7773 0.77726428 156 Q8GWL7 At2g41550 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 24.498 24.29 3 0.0090564 16516 22-052-Murphy-SHP20-LL-3 30.872 10.032 117600000 0 0 0 9323300 8716100 7035900 0 0 8663500 9952700 14319000 36300000 12039000 2358200 8890600 450 156 436 5447;5448;5449;5450;5451;5452;5453;5454;5455;5456 2837 2837 1 VGDYVDVK Unmodified 893.44945 0.44944778 148 Q9FDZ9;Q43291 RPL21E;RPL21A 60S ribosomal protein L21-2;60S ribosomal protein L21-1 yes no 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 19.43 19.23 2 8.1529E-06 10875 22-052-Murphy-SHP20-PEI-LL-2 97.071 40.561 79651000 915720 1272700 1705400 2623800 0 0 12179000 14637000 10781000 5142100 4279500 7199000 8565600 2129800 8219800 451 148 437 5457;5458;5459;5460;5461;5462;5463;5464;5465;5466;5467;5468;5469 2838 2838 0 VGETYLDLK Unmodified 1036.5441 0.54407645 73 Q2V4Q4;Q3EDH2;O50061 RPL4 50S ribosomal protein L4, chloroplastic yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 32.493 32.341 2 2.0372E-09 16780 22-052-Murphy-control-1 101.69 55.027 204980000 15300000 20854000 46621000 5290100 0 0 35709000 20384000 18072000 3310400 4144100 12630000 7840000 4664500 10164000 452 73 438 5470;5471;5472;5473;5474;5475;5476;5477;5478;5479;5480;5481;5482 2839;2840;2841;2842;2843;2844 2839 4 VGETYLDLKAAPEDTAR Unmodified 1847.9265 0.92650729 73 Q2V4Q4;Q3EDH2;O50061 RPL4 50S ribosomal protein L4, chloroplastic yes no 0 0 1 By MS/MS By matching 1 1 32.482 32.32 3 0.0048347 19940 22-052-Murphy-control-3 45.33 41.362 7701300 0 0 3281600 0 0 0 4419700 0 0 0 0 0 0 0 0 453 73 439 5483;5484 2845 2845 1 VGFFSSGPPAR Unmodified 1120.5665 0.56654322 19 A0A2H1ZEA9;O65396 GDCST Aminomethyltransferase, mitochondrial yes no 0 0 0 By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 32.262 32.102 2 1.1403E-08 29691 22-052-Murphy-SHP20infil-3 75.854 49.252 36203000 0 1789800 0 4020300 2578900 4730600 0 5674200 0 0 4133400 12546000 0 0 729740 454 19 440 5485;5486;5487;5488;5489;5490;5491;5492 2846;2847;2848;2849;2850 2847 5 VGFFSSGPPARSHSEVHDESGNK Unmodified 2427.1203 0.12034951 19 A0A2H1ZEA9;O65396 GDCST Aminomethyltransferase, mitochondrial yes no 0 0 1 By MS/MS By matching By matching By matching By matching By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 9.4459 9.3671 4 8.3272E-21 4359 22-052-Murphy-SHP20-PEI-LL-2 63.578 60.434 75104000 4475600 3111900 3874400 4603200 5278000 6920900 0 21048000 17623000 0 0 0 0 0 8168100 455 19 441 5493;5494;5495;5496;5497;5498;5499;5500;5501 2851;2852 2851 2 VGGQRLVIVPPELAYGKK Unmodified 1923.1306 0.13056725 219 Q9SR70 FKBP16-4 Peptidyl-prolyl cis-trans isomerase FKBP16-4, chloroplastic yes yes 0 0 2 By MS/MS By matching By matching By matching By MS/MS By MS/MS 1 1 1 1 1 1 34.742 34.546 4 0.0090659 27181 22-052-Murphy-SHP20-LL-3 28.956 18.472 20048000 0 0 0 2628100 0 0 0 0 0 0 4154600 4572600 3043600 1868400 3781000 456 219 442 5502;5503;5504;5505;5506;5507 2853 2853 1 VGGSTHQVPIEIGSTQGK Unmodified 1793.9272 0.92717599 130 P61841 rps7-A 30S ribosomal protein S7, chloroplastic yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 23.139 22.984 3 3.7094E-72 14361 22-052-Murphy-SHP20-PEI-infil-1 88.73 82.825 130310000 4112300 4727700 3805300 14924000 7193200 3645000 18198000 13760000 14366000 5072900 10142000 22274000 0 0 8087400 457 130 443 5508;5509;5510;5511;5512;5513;5514;5515;5516;5517;5518;5519;5520 2854;2855;2856;2857;2858;2859;2860 2858 7 VGGSTHQVPIEIGSTQGKALAIR Unmodified 2318.2706 0.27064256 130 P61841 rps7-A 30S ribosomal protein S7, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 1 1 2 2 2 1 2 2 2 1 1 1 1 1 30.93 30.794 3;4 2.1312E-77 23606 22-052-Murphy-SHP20-PEI-LL-1 97.095 93.758 219830000 8056800 11290000 19928000 20425000 15344000 4760000 33381000 34634000 28286000 4422200 5835400 20545000 5470900 0 7451700 458 130 444 5521;5522;5523;5524;5525;5526;5527;5528;5529;5530;5531;5532;5533;5534;5535;5536;5537;5538;5539;5540 2861;2862;2863;2864;2865;2866;2867;2868;2869;2870;2871;2872;2873;2874;2875;2876;2877 2872 17 VGHKVLEDGQKVR Unmodified 1463.8209 0.82086043 136 P92959;F4K1S8 RPL24;At5g54600 50S ribosomal protein L24, chloroplastic yes no 0 0 2 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 2 1 3 2 2 1 2 7.8017 7.5634 2;3;4 4.9082E-78 2348 22-052-Murphy-SHP20-PEI-LL-1 129.16 117.24 66448000 0 143030 4350400 3545900 0 0 31608000 12445000 7064700 0 0 5441900 0 1849300 0 459 136 445 5541;5542;5543;5544;5545;5546;5547;5548;5549;5550;5551;5552;5553;5554 2878;2879;2880;2881 2880 4 VGIVGK Unmodified 571.36935 0.36934696 162 Q8RXU5 RPL37AC 60S ribosomal protein L37a-2 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 8.4701 8.351 1 6.4968E-43 2289 22-052-Murphy-control-3 122.18 21.977 330370000 10113000 9885300 26845000 22410000 0 12162000 100910000 0 33291000 20248000 0 49000000 18389000 0 27113000 460 162 446 5555;5556;5557;5558;5559;5560;5561;5562;5563;5564;5565 2882;2883 2882 1 VGIVGKYGTR Unmodified 1048.6029 0.60292873 162 Q8RXU5 RPL37AC 60S ribosomal protein L37a-2 yes yes 0 0 1 By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 1 2 2 2 2 2 2 2 1 2 2 2 1 2 9.2893 9.1459 2;3 7.3532E-16 4199 22-052-Murphy-SHP20-LL-1 88.942 69.465 485190000 11252000 3201500 22297000 20302000 17271000 16998000 64522000 102340000 82493000 6465500 24755000 51060000 25762000 6252000 30221000 461 162 447 5566;5567;5568;5569;5570;5571;5572;5573;5574;5575;5576;5577;5578;5579;5580;5581;5582;5583;5584;5585;5586;5587;5588;5589;5590;5591;5592 2884;2885;2886;2887;2888;2889;2890;2891;2892 2885 7 VGLALALKP Unmodified 880.57459 0.57458871 220 Q9SRH5 VDAC1 Mitochondrial outer membrane protein porin 1 yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 38.728 38.608 2 2.8885E-28 31739 22-052-Murphy-SHP20-PEI-LL-1 115.01 0 42773000 1853100 1319800 2974500 3075500 0 0 9383000 6606700 6176400 2153600 2658500 5357300 0 1215100 0 462 220 448 5593;5594;5595;5596;5597;5598;5599;5600;5601;5602;5603 2893 2893 0 VGLIAARR Unmodified 854.54502 0.54501992 104;147 P46286;Q42064 RPL8A;RPL8C 60S ribosomal protein L8-1;60S ribosomal protein L8-3 no no 0 0 1 By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 8.4817 8.356 2 0.010345 3224 22-052-Murphy-SHP20-PEI-LL-1 78.002 57.017 190180000 5674000 0 14399000 5733100 5055400 0 46476000 37349000 32098000 5314200 9638500 19539000 8904400 0 0 463 104;147 449 5604;5605;5606;5607;5608;5609;5610;5611;5612;5613;5614 2894;2895 2894 2 VGVIIGKGGETIK Unmodified 1269.7656 0.76563696 79 O82762 At2g25970 yes yes 0 0 1 By MS/MS 1 22.216 22.041 3 0.012414 9781 22-052-Murphy-control-3 48.004 39.303 1823200 0 0 1823200 0 0 0 0 0 0 0 0 0 0 0 0 464 79 450 5615 2896 2896 1 VIAANKDRNLYELR Unmodified 1673.9213 0.92130275 177 Q9M9W1;Q9FE58 RPL22B;RPL22C 60S ribosomal protein L22-2;60S ribosomal protein L22-3 yes no 0 0 2 By MS/MS By MS/MS By MS/MS 1 1 1 20.772 20.621 4 3.1861E-41 13061 22-052-Murphy-SHP20-PEI-LL-1 74.46 64.672 75551000 0 0 0 0 0 0 32976000 20370000 22204000 0 0 0 0 0 0 465 177 451 5616;5617;5618 2897;2898;2899 2897 3 VKGPGLYTEIGKK Unmodified 1388.8028 0.80275075 220 Q9SRH5;Q9SMX3 VDAC1;VDAC3 Mitochondrial outer membrane protein porin 1;Mitochondrial outer membrane protein porin 3 yes no 0 0 2 By MS/MS By MS/MS 1 1 16.603 16.345 3 3.444E-13 4364 22-052-Murphy-SHP20-PEI-LL-3 45.661 32.257 6137200 0 0 0 0 0 0 6137200 0 0 0 0 0 0 0 0 466 220 452 5619;5620 2900;2901 2901 1 VKYSQEPDNQTK Unmodified 1435.6943 0.69432251 35 F4HRW5;P51413 At1g67430;RPL17B 60S ribosomal protein L17-2 yes no 0 0 1 By MS/MS 1 8.0149 7.7899 2 5.726E-09 2498 22-052-Murphy-SHP20-PEI-LL-1 84.498 74.544 10733000 0 0 0 0 0 0 10733000 0 0 0 0 0 0 0 0 467 35 453 5621 2902 2902 1 VLAKALR Unmodified 769.51741 0.51740818 64 O03042 rbcL Ribulose bisphosphate carboxylase large chain yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 8.2066 8.0868 2 0.0015074 3173 22-052-Murphy-SHP20-LL-1 104.48 49.349 373250000 8252100 9818600 29408000 16880000 10940000 9194100 53295000 52982000 58539000 14749000 19200000 39407000 24687000 0 25899000 468 64 454 5622;5623;5624;5625;5626;5627;5628;5629;5630;5631;5632;5633;5634;5635 2903;2904 2903 0 VLDPNTVFALVNYISFK Unmodified 1939.0455 0.045500215 33 CON__P34955 yes yes 0 0 0 By matching By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 1 1 1 71.52 71.435 3 0.0090621 53577 22-052-Murphy-SHP20-PEI-LL-2 48.177 43.373 + 33314000 7064200 0 2367200 3244800 873220 1455100 1520800 1617300 1432600 8723600 3485500 0 0 1529400 0 469 33 455 5636;5637;5638;5639;5640;5641;5642;5643;5644;5645;5646 2905 2905 1 VLELAGNAAR Unmodified 1012.5665 0.56654322 62 F4KCF4 HTA12 Histone H2A yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 2 1 1 1 2 1 1 1 1 1 1 2 22.57 22.392 2 1.8071E-16 8821 22-052-Murphy-control-1 113.25 75.014 547700000 24536000 27762000 32254000 24423000 24889000 18056000 61053000 51630000 57131000 22793000 29789000 88670000 31045000 9273100 44393000 470 62 456 5647;5648;5649;5650;5651;5652;5653;5654;5655;5656;5657;5658;5659;5660;5661;5662;5663;5664 2906;2907;2908;2909;2910;2911;2912;2913;2914;2915 2906 3 VLELAGNAARDNK Unmodified 1369.7314 0.73137672 62 F4KCF4 HTA12 Histone H2A yes yes 0 0 1 By MS/MS By MS/MS By MS/MS 2 1 1 14.808 14.456 2 2.354E-08 4818 22-052-Murphy-SHP20-LL-1 68.016 15.3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 471 62 457 5665;5666;5667;5668 2916;2917;2918;2919 2918 4 VLGGGSALNAGFYTR Unmodified 1481.7627 0.76267685 151 Q66GI5 At1g12570 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 37.976 37.808 2 7.9487E-19 35670 22-052-Murphy-SHP20infil-3 78.655 35.373 30285000 0 0 0 0 0 0 5977700 6199700 0 0 0 12182000 0 0 5925900 472 151 458 5669;5670;5671;5672 2920;2921 2920 2 VLKQVHPDIGISSK Unmodified 1519.8722 0.8722273 70 Q9LZT0;P40283;O23629;Q9FFC0;Q9LQQ4;Q9SI96 H2B Histone H2B.7;Histone H2B.11;Histone H2B.6;Histone H2B.10;Histone H2B.1;Histone H2B.3 yes no 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 18.651 18.476 3 4.5839E-06 9658 22-052-Murphy-SHP20-PEI-infil-1 52.495 45.125 136550000 1894200 3921300 9776700 7409700 9371900 4007400 24658000 0 0 7552200 15022000 33407000 10641000 0 8887300 473 70 459 5673;5674;5675;5676;5677;5678;5679;5680;5681;5682;5683;5684 2922;2923 2922 0 VMLRPASPGTGVIAGGAVR Oxidation (M) 1824.004 0.003986526 137 P93014 rps5 30S ribosomal protein S5, chloroplastic yes yes 0 1 1 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 1 28.592 28.449 3 2.4984E-45 20682 22-052-Murphy-SHP20-PEI-LL-2 89.624 79.703 68603000 1820000 0 0 0 4508500 0 12005000 14133000 11193000 6052200 0 17105000 0 1786500 0 474 137 460 5685;5686;5687;5688;5689;5690;5691;5692 2924;2925;2926;2927;2928 2927 28 5 VNGTTVNVGIQPSK Unmodified 1412.7623 0.7623425 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 24.586 24.408 2 1.4514E-24 21214 22-052-Murphy-SHP20infil-3 115.71 112.22 236290000 3578300 4223300 4750900 10369000 7707700 5381300 39184000 35892000 33099000 12397000 12730000 26679000 16848000 7540100 15913000 475 111 461 5693;5694;5695;5696;5697;5698;5699;5700;5701;5702;5703;5704;5705;5706;5707 2929;2930;2931;2932;2933;2934 2929 6 VQRLVYR Unmodified 932.55558 0.55558461 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 no no 0 0 1 By matching By matching By MS/MS By matching By matching By matching By matching By MS/MS 1 1 1 1 1 1 1 1 8.3524 8.218 2 5.9101E-134 2937 22-052-Murphy-SHP20-PEI-LL-1 132.53 77.398 161150000 0 5269600 0 11740000 0 0 48146000 34887000 0 7431300 11490000 19807000 0 0 22373000 476 178 462 5708;5709;5710;5711;5712;5713;5714;5715 2935 2935 1 VQRLVYRSR Unmodified 1175.6887 0.68872404 178 Q9FE65 RPL34B 60S ribosomal protein L34-2 no no 0 0 2 By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 8.2957 8.0307 2 0.011553 2611 22-052-Murphy-SHP20-PEI-LL-1 69.432 35.882 47899000 0 0 2817500 2929600 0 0 30710000 0 7251600 0 0 0 0 4190300 0 477 178 463 5716;5717;5718;5719;5720 2936 2936 1 VQVPAKWNPSK Unmodified 1252.6928 0.69280637 146 Q42029 PSBP1 Oxygen-evolving enhancer protein 2-1, chloroplastic yes yes 0 0 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 2 2 2 1 21.178 20.958 2;3 1.8868E-08 17564 22-052-Murphy-SHP20infil-3 73.248 54.466 327120000 8290300 10658000 2585100 0 0 0 0 0 16959000 13665000 61133000 178460000 31589000 0 3786700 478 146 464 5721;5722;5723;5724;5725;5726;5727;5728;5729;5730;5731;5732 2937;2938;2939;2940;2941;2942;2943 2940 6 VQVPAKWNPSKEIEYPGQVLR Unmodified 2437.3118 0.31177909 146 Q42029 PSBP1 Oxygen-evolving enhancer protein 2-1, chloroplastic yes yes 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 1 2 1 2 38.746 38.658 3;4 4.4294E-26 31004 22-052-Murphy-SHP20-PEI-LL-3 60.317 52.695 82752000 12605000 11742000 5123000 0 0 0 23373000 9780400 20129000 0 0 0 0 0 0 479 146 465 5733;5734;5735;5736;5737;5738;5739;5740;5741;5742 2944;2945;2946;2947;2948;2949;2950;2951 2951 8 VRVFMYPSNI Oxidation (M) 1240.6274 0.62742892 113 Q9FZH0;P51422;Q9LMK0;Q9C912 RPL35AB;RPL35AD;RPL35AA;RPL35AC 60S ribosomal protein L35a-2;60S ribosomal protein L35a-4;60S ribosomal protein L35a-1;60S ribosomal protein L35a-3 yes no 0 1 1 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 38.151 38.009 2 6.6765E-16 25086 22-052-Murphy-control-3 97.473 91.37 228960000 4278000 6193000 16240000 9984900 7181100 1918100 82902000 30364000 27534000 5463500 6547100 14361000 5757600 3814100 6424400 480 113 466 5743;5744;5745;5746;5747;5748;5749;5750;5751;5752;5753;5754;5755;5756;5757 2952;2953;2954 2952 23 2 VSDSVPAPSDDAEQLR Unmodified 1684.7904 0.79040774 226 Q9SYT0 ANN1 Annexin D1 yes yes 0 0 0 By MS/MS 1 28.915 28.725 2 5.741E-14 16398 22-052-Murphy-control-3 42.001 27.582 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 481 226 467 5758 2955 2955 1 VTANVVVAK Unmodified 899.54402 0.54401687 5 A0A1P8ARX5;Q1JPL7 PME18 Pectinesterase/pectinesterase inhibitor 18;Pectinesterase inhibitor 18;Bifunctional pectinesterase 18/rRNA N-glycosylase yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 10.151 10.004 2 6.5707E-12 4158 22-052-Murphy-SHP20-PEI-infil-1 107.74 71.559 401760000 8198900 8040100 19968000 35752000 25603000 36724000 0 52833000 35339000 0 76460000 55696000 0 4321000 42824000 482 5 468 5759;5760;5761;5762;5763;5764;5765;5766;5767;5768;5769;5770 2956;2957;2958;2959;2960;2961;2962;2963;2964;2965;2966;2967 2963 12 VTGGEVGAASSLAPK Unmodified 1342.7092 0.70924429 110 P50883;Q9LFH5;Q9FF52 RPL12A;RPL12B;RPL12C 60S ribosomal protein L12-1;60S ribosomal protein L12-2;60S ribosomal protein L12-3 yes no 0 0 0 By MS/MS By MS/MS By MS/MS 1 1 1 25.625 25.497 2 1.9638E-39 17484 22-052-Murphy-SHP20-PEI-LL-2 72.643 52.314 20462000 0 0 0 0 0 0 12413000 0 8048300 0 0 0 0 0 0 483 110 469 5771;5772;5773 2968;2969;2970 2969 3 VTGTYMPHREVK Oxidation (M) 1432.7133 0.71328381 31 C0SUW8 At1g21160 yes yes 0 1 1 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By matching 1 1 1 1 1 1 1 8.2238 8.0155 2 5.2906E-06 2622 22-052-Murphy-SHP20-PEI-LL-1 83.206 40.607 112000000 6056900 4897500 4007400 0 0 0 48219000 20015000 27958000 0 0 0 0 843090 0 484 31 470 5774;5775;5776;5777;5778;5779;5780 2971 2971 4 1 VTIRADEISNIIRER Acetyl (Protein N-term) 1826.001 0.0010096381 115 P56757 atpA ATP synthase subunit alpha, chloroplastic yes yes 1 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 48.983 48.86 3 2.4125E-07 42101 22-052-Murphy-SHP20-PEI-LL-1 66.708 49.828 80919000 2865800 2736900 5079300 0 4761200 2116600 23369000 9186700 14964000 1449700 3552100 0 3603100 2117800 5117700 485 115 471 5781;5782;5783;5784;5785;5786;5787;5788;5789;5790;5791;5792;5793 2972;2973;2974 2972 3 VTVNGAPSVGISVKPSK Unmodified 1638.9305 0.93047046 234 Q9ZUF6 At2g05920 yes yes 0 0 1 By matching By MS/MS By MS/MS By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 26.946 26.751 3 1.5708E-11 23763 22-052-Murphy-SHP20infil-3 43.297 34.01 134730000 0 0 0 4157200 4973400 10897000 3210200 0 4040200 20539000 23499000 37268000 14008000 5844100 6295200 486 234 472 5794;5795;5796;5797;5798;5799;5800;5801;5802;5803;5804 2975;2976;2977;2978;2979;2980;2981 2976 7 VTVVPSAAALVIK Unmodified 1266.7911 0.79112343 110 P50883;Q9LFH5;Q9FF52 RPL12A;RPL12B;RPL12C 60S ribosomal protein L12-1;60S ribosomal protein L12-2;60S ribosomal protein L12-3 yes no 0 0 0 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 44.058 43.945 2 7.4761E-21 36500 22-052-Murphy-SHP20-PEI-LL-2 92.439 87.656 198850000 0 0 0 17092000 10155000 0 57489000 46566000 28190000 9961800 7067500 15815000 0 0 6516200 487 110 473 5805;5806;5807;5808;5809;5810;5811;5812;5813;5814 2982;2983;2984;2985;2986;2987;2988 2987 6 VTVVPSAAALVIKALK Unmodified 1579.0073 0.0072642149 110 P50883;Q9LFH5;Q9FF52 RPL12A;RPL12B;RPL12C 60S ribosomal protein L12-1;60S ribosomal protein L12-2;60S ribosomal protein L12-3 yes no 0 0 1 By MS/MS By MS/MS 1 1 51.592 51.53 3 7.3182E-10 44768 22-052-Murphy-SHP20-PEI-LL-1 62.891 62.857 13643000 0 0 0 0 0 0 8776400 0 4866800 0 0 0 0 0 0 488 110 474 5815;5816 2989;2990 2989 2 VVITKLRLDK Unmodified 1183.7652 0.76524303 111 P51414 RPL26A 60S ribosomal protein L26-1 yes yes 0 0 2 By matching By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 19.892 19.692 3 0.016387 11351 22-052-Murphy-SHP20-PEI-LL-3 52.591 44.366 45486000 1263500 887720 851180 3933400 1231500 0 4193500 6523200 3872300 0 3313300 7474500 5384400 1852300 4705500 489 111 475 5817;5818;5819;5820;5821;5822;5823;5824;5825;5826;5827;5828;5829 2991;2992;2993 2993 3 WIPCVEFELEHGNTPGYYDGR Unmodified 2481.1059 0.10594499 60 F4KA76 At5g38410 Ribulose bisphosphate carboxylase small chain yes yes 0 0 0 By MS/MS By matching By MS/MS By matching By MS/MS 1 1 1 1 1 23.745 23.563 4 0.0065874 15597 22-052-Murphy-SHP20-PEI-LL-2 21.398 17.292 37090000 0 3840400 0 0 0 0 9419900 11103000 7809200 0 0 0 0 4917800 0 490 60 476 5830;5831;5832;5833;5834 2994;2995 2995 2 WVPVTKLGR Unmodified 1054.6287 0.62874955 109 P49688;Q9SCM3;Q93VB8;Q8L8Y0 RPS2C;RPS2D;RPS2B;RPS2A 40S ribosomal protein S2-3;40S ribosomal protein S2-4;40S ribosomal protein S2-2;40S ribosomal protein S2-1 yes no 0 0 1 By matching By MS/MS By MS/MS By MS/MS By matching By matching By matching By matching 1 1 1 1 1 1 1 1 24.717 24.523 3 0.0042703 16696 22-052-Murphy-SHP20-PEI-LL-3 65.252 57.032 39689000 0 0 0 0 0 726040 6898900 9863800 7006400 2657000 3182900 6090500 3262900 0 0 491 109 477 5835;5836;5837;5838;5839;5840;5841;5842 2996 2996 1 YDSMLGTFK Oxidation (M) 1076.4848 0.48484701 90 P25857 GAPB Glyceraldehyde-3-phosphate dehydrogenase GAPB, chloroplastic yes yes 0 1 0 By MS/MS By matching By matching By matching By MS/MS 1 1 1 1 1 26.175 26.079 2 0.023774 18142 22-052-Murphy-SHP20-PEI-LL-3 72.138 47.14 25648000 1277000 1175700 0 0 0 0 9945400 4402800 8847400 0 0 0 0 0 0 492 90 478 5843;5844;5845;5846;5847 2997 2997 15 1 YEDISVLGQRPVEE Unmodified 1632.7995 0.79951586 194 Q9LXJ2 F3C22_130 yes yes 0 0 1 By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By matching By matching 1 1 1 1 1 1 1 1 1 1 38.91 38.764 2 4.6874E-47 36646 22-052-Murphy-SHP20infil-3 108.67 96.954 122160000 0 0 0 7318600 5376000 1446800 35980000 19087000 16268000 0 8553600 19164000 4259500 0 4703500 493 194 479 5848;5849;5850;5851;5852;5853;5854;5855;5856;5857 2998;2999;3000;3001;3002;3003 2999 6 YEGVILNKSQNITG Unmodified 1534.7991 0.79912193 101 P42795;P42794 RPL11A;RPL11B 60S ribosomal protein L11-1;60S ribosomal protein L11-2 yes no 0 0 1 By matching By MS/MS 1 1 31.533 31.371 2 4.0718E-09 24037 22-052-Murphy-SHP20-PEI-LL-1 82.749 57.364 90011000 0 0 892990 0 0 0 89118000 0 0 0 0 0 0 0 0 494 101 480 5858;5859 3004 3004 1 YIATPGKGILAADESTGTIGK Unmodified 2062.0946 0.094635252 76 O65581 M3E9.40 Fructose-bisphosphate aldolase yes yes 0 0 1 By MS/MS By MS/MS By MS/MS 1 1 1 33.982 33.877 3 5.3736E-09 17974 22-052-Murphy-control-1 46.621 41.719 12553000 4403600 4980100 3169000 0 0 0 0 0 0 0 0 0 0 0 0 495 76 481 5860;5861;5862 3005 3005 1 YISRKGPLVVYGTEGSK Unmodified 1853.0047 0.0046980325 141 Q2V3X4;Q9SF40 At3g09630;RPL4A 60S ribosomal protein L4-1 yes no 0 0 2 By MS/MS By matching By matching 1 1 1 20.615 20.464 3 0.020026 12933 22-052-Murphy-SHP20-PEI-LL-1 32.341 25.209 18960000 0 0 0 0 0 0 7585700 5794300 5580200 0 0 0 0 0 0 496 141 482 5863;5864;5865 3006 3006 1 YSDQNGLQFVKKQ Unmodified 1553.7838 0.78380622 56 F4JM05;Q8W0Y8 PSB28 Photosystem II reaction center Psb28 protein;Photosystem II reaction center PSB28 protein, chloroplastic yes no 0 0 2 By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 22.987 22.804 2;3 5.2867E-22 15209 22-052-Murphy-SHP20-PEI-LL-1 97.798 90.773 1533000000 67690000 95345000 159440000 56480000 35035000 6358700 239170000 160060000 168590000 48155000 85220000 155700000 108050000 45361000 102340000 497 56 483 5866;5867;5868;5869;5870;5871;5872;5873;5874;5875;5876;5877;5878;5879;5880;5881;5882;5883;5884;5885;5886;5887;5888;5889;5890;5891;5892;5893;5894 3007;3008;3009;3010;3011;3012;3013;3014;3015;3016;3017;3018;3019 3016 11 YSEITFPILAPDPATNK Unmodified 1875.9618 0.96183016 119 P56771 petA Cytochrome f yes yes 0 0 0 By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 54.068 53.934 2 0.018351 52286 22-052-Murphy-SHP20infil-3 22.533 22.533 13415000 0 0 0 0 0 0 0 0 1753700 1497900 0 2148200 3292500 2700200 2022100 498 119 484 5895;5896;5897;5898;5899;5900 3020;3021 3020 2 YSQVVSNALDMK Oxidation (M) 1369.6548 0.65476588 95 P34788 RPS18A 40S ribosomal protein S18 yes yes 0 1 0 By MS/MS By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.913 26.745 2 3.3619E-05 19322 22-052-Murphy-SHP20-PEI-LL-1 66.621 58.972 74784000 2242500 1342200 3099600 2363900 1537900 0 14952000 11403000 10164000 2913400 3957500 7656100 6035500 2661800 4455200 499 95 485 5901;5902;5903;5904;5905;5906;5907;5908;5909;5910;5911;5912;5913;5914 3022;3023 3022 17 2 YSTFPHRSEGDYGAAK Unmodified 1784.8118 0.81181188 137 P93014 rps5 30S ribosomal protein S5, chloroplastic yes yes 0 0 1 By matching By matching By matching By MS/MS By matching By matching 1 1 1 1 1 1 8.5689 8.4312 3 0.02702 3278 22-052-Murphy-SHP20-PEI-LL-3 36.77 32.222 74647000 0 0 0 8119200 0 0 14518000 14323000 21333000 0 0 10013000 0 0 6341000 500 137 486 5915;5916;5917;5918;5919;5920 3024 3024 0 YTRTVTSVGGAGTYSVK Unmodified 1745.8948 0.89481323 75 O65351 SBT1.7 Subtilisin-like protease SBT1.7 yes yes 0 0 1 By MS/MS By matching By MS/MS By matching 1 1 1 1 21.415 21.144 3 4.352E-10 17845 22-052-Murphy-SHP20infil-3 48.405 44.371 22357000 0 0 0 0 0 3449200 0 0 0 0 3822000 11962000 3124400 0 0 501 75 487 5921;5922;5923;5924 3025;3026 3025 2