Raw file Experiment Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Fixed modifications Multi modifications Variable modifications first search Use variable modifications first search Requantify Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS MS3 MS/MS Submitted MS/MS Submitted (SIL) MS/MS Submitted (ISO) MS/MS Submitted (PEAK) MS/MS Identified MS/MS Identified (SIL) MS/MS Identified (ISO) MS/MS Identified (PEAK) MS/MS Identified [%] MS/MS Identified (SIL) [%] MS/MS Identified (ISO) [%] MS/MS Identified (PEAK) [%] Peptide Sequences Identified Peaks Peaks Sequenced Peaks Sequenced [%] Peaks Repeatedly Sequenced Peaks Repeatedly Sequenced [%] Isotope Patterns Isotope Patterns Sequenced Isotope Patterns Sequenced (z>1) Isotope Patterns Sequenced [%] Isotope Patterns Sequenced (z>1) [%] Isotope Patterns Repeatedly Sequenced Isotope Patterns Repeatedly Sequenced [%] Recalibrated Av. Absolute Mass Deviation [ppm] Mass Standard Deviation [ppm] Av. Absolute Mass Deviation [mDa] Mass Standard Deviation [mDa] Label free norm param Control_WT1_1 control_WT 1 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3609 6372 0 7331 5413 0 1918 1961 1905 0 56 26.75 35.19 NaN 2.92 1387 448587 5705 1.27 402 7.05 49166 4749 4693 9.66 13.44 442 9.31 + 0.39803 0.55174 0.2912 0.40145 Control_WT1_2 control_WT 2 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3215 7622 0 8568 6676 0 1892 2418 2387 0 31 28.22 35.75 NaN 1.64 1675 487279 6799 1.4 571 8.4 51536 5770 5704 11.2 14.55 659 11.42 + 0.37433 0.52132 0.2773 0.39374 Control_WT2_1 control_WT 3 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3496 6597 0 7443 5751 0 1692 2336 2284 0 52 31.39 39.71 NaN 3.07 1653 401504 6020 1.5 376 6.25 45512 5129 5091 11.27 15.61 466 9.09 + 0.33206 0.4588 0.24613 0.35003 Control_WT2_2 control_WT 4 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3362 6931 0 7628 6234 0 1394 2415 2372 0 43 31.66 38.05 NaN 3.08 1743 400861 6172 1.54 501 8.12 43683 5354 5330 12.26 17.02 626 11.69 + 0.32281 0.44242 0.23621 0.32878 Control_WT3_1 control_WT 5 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3426 6952 0 7782 6122 0 1660 2279 2247 0 32 29.29 36.7 NaN 1.93 1594 450808 6254 1.39 507 8.11 47598 5355 5301 11.25 15.28 579 10.81 + 0.32552 0.4511 0.24319 0.34287 Control_WT3_2 control_WT 6 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3160 7761 0 8768 6754 0 2014 2492 2448 0 44 28.42 36.25 NaN 2.18 1735 474808 6877 1.45 628 9.13 50317 5744 5672 11.42 14.82 715 12.45 + 0.35201 0.48655 0.25802 0.35846 Control_WT4_1 control_WT 7 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3290 7120 0 7768 6472 0 1296 2667 2631 0 36 34.33 40.65 NaN 2.78 1938 382905 6378 1.67 513 8.04 43683 5616 5591 12.86 17.67 630 11.22 + 0.31108 0.43915 0.22882 0.32789 Control_WT4_2 control_WT 8 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3036 7793 0 8526 7060 0 1466 2688 2643 0 45 31.53 37.44 NaN 3.07 1984 426606 6940 1.63 589 8.49 47631 6110 6080 12.83 16.57 702 11.49 + 0.37334 0.51446 0.26729 0.37504 Stress_WT1_1 stress_WT 1 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3760 6617 0 7641 5593 0 2048 2168 2126 0 42 28.37 38.01 NaN 2.05 1609 407431 5968 1.46 432 7.24 42297 4892 4844 11.57 16.76 509 10.4 + 0.29797 0.42548 0.2169 0.31448 Stress_WT1_2 stress_WT 2 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3271 7711 0 8899 6523 0 2376 2368 2315 0 53 26.61 35.49 NaN 2.23 1716 445015 6773 1.52 645 9.52 46819 5546 5474 11.85 15.96 723 13.04 + 0.31663 0.43707 0.23086 0.32363 Stress_WT2_1 stress_WT 3 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3650 6145 0 6843 5447 0 1396 2081 2040 0 41 30.41 37.45 NaN 2.94 1520 417747 5575 1.33 392 7.03 43704 4833 4805 11.06 15.74 474 9.81 + 0.30421 0.42053 0.22937 0.32456 Stress_WT2_2 stress_WT 4 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3510 6817 0 7732 5902 0 1830 2132 2090 0 42 27.57 35.41 NaN 2.3 1562 415809 6111 1.47 497 8.13 42921 5088 5036 11.85 16.69 604 11.87 + 0.32315 0.44117 0.2392 0.33952 Stress_WT3_1 stress_WT 5 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3644 6135 0 6757 5513 0 1244 2197 2161 0 36 32.51 39.2 NaN 2.89 1610 381664 5558 1.46 367 6.6 41398 4876 4854 11.78 17.28 453 9.29 + 0.31523 0.4552 0.23643 0.34745 Stress_WT3_2 stress_WT 6 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3362 7036 0 7742 6330 0 1412 2381 2334 0 47 30.75 36.87 NaN 3.33 1722 441286 6274 1.42 522 8.32 46472 5471 5437 11.77 16.03 615 11.24 + 0.33915 0.49018 0.25149 0.37788 Stress_WT4_1 stress_WT 7 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3691 5898 0 6874 4922 0 1952 1688 1655 0 33 24.56 33.62 NaN 1.69 1261 382300 5310 1.39 375 7.06 41145 4329 4268 10.52 15.32 397 9.17 + 0.31177 0.43313 0.23171 0.3311 Stress_WT4_2 stress_WT 8 Trypsin/P Specific False Oxidation (M);Acetyl (Protein N-term);Phospho (STY) Carbamidomethyl (C) False False 1 2 Standard 3349 7425 0 8666 6176 0 2490 1358 1336 0 22 15.67 21.63 NaN 0.88 1063 482276 6497 1.35 627 9.65 48087 5269 5165 10.96 14.63 640 12.15 + 0.37555 0.53002 0.27601 0.40648 Total 54831 110932 0 124968 96888 0 28080 35629 34974 0 655 28.51 36.1 NaN 2.33 3636 6846886 731969 84131 83345 11.49 15.77 9234 10.98 0.33522 0.46928 0.24695 0.35264