Raw file Experiment Fraction 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 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_102 PAP24_102 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3241 24853 6218 34640 15066 0 19574 2908 2490 0 418 8.4 17 0 2.1 1968 203537 13342 6.6 4728 35 32043 8993 8869 28 29 3667 41 + 0.84346 1.1232 0.50451 0.69704 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_103 PAP24_103 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3285 25362 5955 35093 15631 0 19462 3307 2919 0 388 9.4 19 0 2 2224 192844 13780 7.1 4649 34 30167 9400 9259 31 32 3642 39 + 0.73675 1.0022 0.4409 0.61923 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_104 PAP24_104 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3036 25635 6454 36071 15199 0 20872 2894 2522 0 372 8 17 0 1.8 1944 188575 13719 7.3 4839 35 30117 9072 8938 30 31 3742 41 + 0.76964 1.05 0.4647 0.65904 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_105 PAP24_105 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3645 24804 6298 34565 15043 0 19522 2940 2558 0 382 8.5 17 0 2 1923 179174 13426 7.5 4617 34 28808 9037 8924 31 32 3668 41 + 0.77455 1.0584 0.471 0.66307 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_102 PAP24_102 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3530 24481 6467 33427 15535 0 17892 2638 2339 0 299 7.9 15 0 1.7 1896 216759 13541 6.2 4901 36 33269 9239 9133 28 29 3858 42 + 0.79385 1.0893 0.45372 0.65083 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_103 PAP24_103 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3639 23988 6313 32539 15437 0 17102 2981 2610 0 371 9.2 17 0 2.2 2071 215089 13216 6.1 4846 37 32603 9037 8927 28 29 3807 42 + 0.75428 1.0175 0.42871 0.59916 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_104 PAP24_104 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3492 24593 6794 33518 15668 0 17850 2750 2393 0 357 8.2 15 0 2 1894 218735 13384 6.1 4978 37 33171 9061 8957 27 28 3913 43 + 0.73838 0.9977 0.41927 0.5844 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_105 PAP24_105 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4044 24265 6473 33312 15218 0 18094 2726 2378 0 348 8.2 16 0 1.9 1903 187869 13594 7.2 4832 36 31401 9173 9070 29 30 3860 42 + 0.77078 1.0303 0.43797 0.60041 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_102 PAP24_102 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3752 23562 6076 31482 15642 0 15840 2816 2443 0 373 8.9 16 0 2.4 1970 239364 13320 5.6 4784 36 35471 9314 9208 26 27 3805 41 + 0.79883 1.0745 0.43739 0.60899 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_103 PAP24_103 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3863 23455 5744 31481 15429 0 16052 3064 2629 0 435 9.7 17 0 2.7 2144 227079 13337 5.9 4611 35 33098 9250 9132 28 29 3715 40 + 0.73371 1.0066 0.40487 0.57097 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_104 PAP24_104 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3863 23554 6607 31492 15616 0 15876 2714 2375 0 339 8.6 15 0 2.1 1872 224598 13124 5.8 4884 37 34151 8985 8881 26 27 3905 43 + 0.8229 1.1 0.45271 0.6269 240711_C24_011_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_105 PAP24_105 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 1894 14147 4075 18727 9567 0 9160 1793 1542 0 251 9.6 16 0 2.7 1339 136775 8390 6.1 3071 37 23412 6177 6097 26 27 2528 41 + 0.82318 1.0927 0.43631 0.59814 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_106 PAP24_106 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3590 24842 6844 35956 13728 0 22228 2785 2285 0 500 7.7 17 0 2.2 1987 164139 12937 7.9 4870 38 29106 8390 8243 29 29 3638 43 + 0.98039 1.3004 0.58941 0.81197 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_107 PAP24_107 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3607 24892 6926 35726 14058 0 21668 2607 2121 0 486 7.3 15 0 2.2 1785 170485 13090 7.7 4773 36 30180 8463 8321 28 29 3646 43 + 0.95397 1.2521 0.5757 0.78659 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_108 PAP24_108 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3769 25209 6707 36085 14333 0 21752 2926 2432 0 494 8.1 17 0 2.3 2004 152110 13103 8.6 4637 35 26703 8655 8524 32 33 3599 42 + 0.79141 1.0906 0.47658 0.67751 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_109 PAP24_109 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3705 25169 6810 35858 14480 0 21378 2972 2512 0 460 8.3 17 0 2.2 2045 155946 13178 8.5 4770 36 27767 8832 8708 32 33 3640 41 + 0.90928 1.232 0.55322 0.77971 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_110 PAP24_110 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3542 25193 6425 35594 14792 0 20802 3178 2725 0 453 8.9 18 0 2.2 2158 159409 13286 8.3 4792 36 28647 8919 8783 31 32 3648 41 + 0.86502 1.1906 0.52657 0.75618 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-45_#24_033_PAP24_111 PAP24_111 1 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3780 24864 6509 35315 14413 0 20902 2617 2170 0 447 7.4 15 0 2.1 1773 171241 13127 7.7 4565 35 28726 8721 8584 30 31 3521 40 + 0.86426 1.1845 0.52193 0.73198 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_106 PAP24_106 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3857 24039 7032 33631 14447 0 19184 2928 2601 0 327 8.7 18 0 1.7 2095 163450 13140 8 4817 37 28865 8782 8669 30 31 3724 42 + 0.84433 1.14 0.48 0.67159 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_107 PAP24_107 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3762 24682 7326 34372 14992 0 19380 2630 2224 0 406 7.7 15 0 2.1 1854 182687 13179 7.2 5039 38 31075 8790 8643 28 29 3918 45 + 0.88045 1.1729 0.50268 0.6906 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_108 PAP24_108 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3869 24750 7015 34427 15073 0 19354 2618 2218 0 400 7.6 15 0 2.1 1819 173155 13558 7.8 4939 36 30357 8969 8839 30 30 3810 42 + 0.78414 1.0617 0.45051 0.63076 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_109 PAP24_109 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3760 24558 7364 34610 14506 0 20104 2636 2259 0 377 7.6 16 0 1.9 1825 171151 13101 7.7 4993 38 29665 8664 8530 29 30 3739 43 + 0.90901 1.217 0.51895 0.7305 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_110 PAP24_110 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3879 24465 6935 34156 14774 0 19382 2920 2515 0 405 8.5 17 0 2.1 1985 177925 13272 7.5 4916 37 30147 8895 8760 30 30 3727 42 + 0.87854 1.1979 0.50713 0.72666 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-50_#24_033_PAP24_111 PAP24_111 2 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 3682 24771 7218 34761 14781 0 19980 2367 2002 0 365 6.8 14 0 1.8 1714 195552 13468 6.9 4837 36 31135 8852 8733 28 29 3675 42 + 0.90348 1.1878 0.51198 0.68635 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_105 PAP24_105 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4077 23743 7152 32636 14850 0 17786 2663 2226 0 437 8.2 15 0 2.5 1852 192812 12905 6.7 4901 38 30024 8548 8443 28 29 3701 43 + 0.77271 1.0774 0.41974 0.60148 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_106 PAP24_106 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4084 23838 6781 32172 15504 0 16668 3023 2615 0 408 9.4 17 0 2.4 2204 193640 13573 7 4872 36 32105 9404 9293 29 30 3852 41 + 0.80393 1.0808 0.44954 0.62415 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_107 PAP24_107 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4091 23494 7162 31895 15093 0 16802 2652 2246 0 406 8.3 15 0 2.4 1815 200215 13249 6.6 5020 38 32809 8930 8817 27 28 3909 44 + 0.87035 1.1631 0.48286 0.6758 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_108 PAP24_108 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4194 23668 6859 32179 15157 0 17022 2659 2274 0 385 8.3 15 0 2.3 1873 192072 13348 6.9 4967 37 31540 9143 9044 29 30 3864 42 + 0.79381 1.0763 0.43893 0.61334 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_109 PAP24_109 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4091 23752 7079 32307 15197 0 17110 2728 2309 0 419 8.4 15 0 2.4 1899 201861 13276 6.6 5015 38 32395 9108 8983 28 29 3891 43 + 0.81528 1.1138 0.44833 0.63163 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_110 PAP24_110 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4308 23089 6612 31517 14661 0 16856 2951 2509 0 442 9.4 17 0 2.6 1935 198125 13025 6.6 4693 36 32652 8866 8739 27 28 3674 41 + 0.89808 1.2023 0.49318 0.67721 240711_C24_013_Eclipse_Xlink_75min_FAIMS_CV-55_#24_033_PAP24_111 PAP24_111 3 Trypsin/P Specific Trypsin/P Specific True Oxidation (M);Acetyl (Protein N-term) Carbamidomethyl (C) Oxidation (M);Acetyl (Protein N-term) True False 1 4 Standard 4191 23660 6919 32000 15320 0 16680 2449 2168 0 281 7.7 14 0 1.7 1700 206767 13400 6.5 4863 36 31888 9150 9039 29 30 3805 42 + 0.74644 1.008 0.40948 0.5717 Total 115122 745377 205149 1031544 459210 0 572334 85840 73609 0 12231 8.3 16 0 2.1 8126 5853140 953497 274819 271090 29 30 115091 42 0.82514 1.1174 0.47458 0.66671