Raw file Experiment Enzyme Enzyme mode Enzyme first search Enzyme mode first search Use enzyme first search Variable modifications Variable modifications first search Use variable modifications first search Multiplicity Max. missed cleavages Labels0 LC-MS run type Time-dependent recalibration MS MS/MS 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 20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT1 HeLa(MBD3)_300_0.5_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9726 28857 31934 25780 0 6154 2951 2876 0 75 9.24 11.16 NaN 1.22 2091 1248468 25163 2.02 1952 7.76 140660 22129 21354 15.73 24.63 2060 9.31 + 0.93202 1.1631 0.57641 0.73528 20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT2 HeLa(MBD3)_300_0.5_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9867 27804 30925 24683 0 6242 3124 3063 0 61 10.1 12.41 NaN 0.98 2338 1129672 24649 2.18 1674 6.79 121355 21629 20787 17.82 24.54 1762 8.15 + 0.89205 1.1017 0.55961 0.72888 20140516_Q1_SA_PaJa_HNstudent_Helafrt_300mMsaltwash_WT3 HeLa(MBD3)_300_0.5_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 10005 27608 30701 24515 0 6186 3007 2944 0 63 9.79 12.01 NaN 1.02 2242 1142093 24508 2.15 1665 6.79 121906 21492 20649 17.63 24.26 1737 8.08 + 0.87527 1.0972 0.55443 0.73835 20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP1 MBD3_300_0.5_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8546 31730 34680 28780 0 5900 4354 4321 0 33 12.55 15.01 NaN 0.56 2925 1047859 28513 2.72 1920 6.73 126268 25451 24769 20.16 27.06 2202 8.65 + 0.77105 0.98385 0.49784 0.67199 20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP2 MBD3_300_0.5_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8151 33862 36417 31307 0 5110 6169 6080 0 89 16.94 19.42 NaN 1.74 4094 965207 30068 3.12 2273 7.56 125293 27256 26780 21.75 26.93 2635 9.67 + 0.72865 0.94982 0.46998 0.64018 20140516_Q1_SA_PaJa_HNstudent_Helafrt_MBD3gfp_300mMsaltwash_GFP3 MBD3_300_0.5_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8175 34566 37179 31953 0 5226 7030 6966 0 64 18.91 21.8 NaN 1.22 4346 976904 30475 3.12 2517 8.26 126225 27548 27068 21.82 26.85 2896 10.51 + 0.70461 0.93579 0.45893 0.64286 20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT1 HeLa(MBD3)_1000_0.5_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8093 33748 36851 30645 0 6206 6377 6306 0 71 17.3 20.58 NaN 1.14 4490 1058329 30018 2.84 2084 6.94 140981 27069 26433 19.2 24.41 2281 8.43 + 0.88173 1.1266 0.56444 0.75687 20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT2 HeLa(MBD3)_1000_0.5_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8834 31043 33866 28220 0 5646 4034 3957 0 77 11.91 14.02 NaN 1.36 2694 1057650 27441 2.59 2043 7.45 130051 24672 24005 18.97 24.72 2179 8.83 + 0.94889 1.1879 0.61211 0.81332 20140516_Q1_SA_PaJa_MBstudent_Helafrt_1Msaltwash_WT3 HeLa(MBD3)_1000_0.5_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8374 32137 34819 29455 0 5364 4407 4300 0 107 12.66 14.6 NaN 1.99 3103 1025576 28457 2.77 2038 7.16 133578 25759 25134 19.28 24.46 2221 8.62 + 0.96775 1.2005 0.61629 0.80056 20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP1 MBD3_1000_0.5_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 7815 35318 37772 32864 0 4908 7185 7063 0 122 19.02 21.49 NaN 2.49 4516 1025358 31072 3.03 2507 8.07 136625 28315 27850 20.72 26.36 2867 10.13 + 0.75545 0.98239 0.4947 0.68152 20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP2 MBD3_1000_0.5_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 7888 34979 37381 32577 0 4804 6452 6375 0 77 17.26 19.57 NaN 1.6 4062 982537 31165 3.17 2355 7.56 132374 28441 27998 21.49 26.06 2716 9.55 + 0.76053 1.0054 0.50072 0.69718 20140516_Q1_SA_PaJa_MBstudent_Helafrt_MBD3gfp_1Msaltwash_GFP3 MBD3_1000_0.5_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 7982 34814 37297 32331 0 4966 6371 6261 0 110 17.08 19.37 NaN 2.22 3961 997728 30916 3.1 2372 7.67 132784 28141 27663 21.19 26.11 2766 9.83 + 0.7806 1.015 0.51304 0.70558 20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP1 MBD3_300_0.15_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8163 32460 34934 29986 0 4948 5497 5435 0 62 15.74 18.13 NaN 1.25 3674 896731 26721 2.98 3274 12.25 108588 23796 23431 21.91 27.57 3665 15.4 + 0.65553 0.8507 0.41704 0.5604 20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP2 MBD3_300_0.15_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8408 32742 35230 30254 0 4976 6927 6865 0 62 19.66 22.69 NaN 1.25 4427 902150 27620 3.06 3153 11.42 110203 24680 24251 22.4 27.22 3591 14.55 + 0.66666 0.87311 0.43044 0.58897 20140528_Q1_SA_PaJa_students_Helafrt_MBD3gfp_normalconditions_GFP3lessextract MBD3_300_0.15_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 8849 30598 33178 28018 0 5160 5096 5016 0 80 15.36 17.9 NaN 1.55 3241 886018 25845 2.92 2842 11 99776 22846 22464 22.9 28.17 3327 14.56 + 0.7138 0.92526 0.46207 0.63564 20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT1 HeLa(MBD3)_300_0.15_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9213 29193 31864 26522 0 5342 4286 4196 0 90 13.45 15.82 NaN 1.68 3211 1029922 24901 2.42 2466 9.9 113043 22076 21569 19.53 25.9 2731 12.37 + 0.81211 1.0256 0.52021 0.69253 20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT2 HeLa(MBD3)_300_0.15_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9523 28774 31353 26195 0 5158 3451 3418 0 33 11.01 13.05 NaN 0.64 2626 977930 23045 2.36 2908 12.62 101406 20392 19913 20.11 25.72 3101 15.21 + 0.80435 1.0109 0.50205 0.65451 20140528_Q1_SA_PaJa_students_Helafrt_normalconditions_WT3 HeLa(MBD3)_300_0.15_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9331 30041 32630 27452 0 5178 4780 4703 0 77 14.65 17.13 NaN 1.49 3494 857509 23944 2.79 3144 13.13 98969 21200 20737 21.42 26.29 3331 15.71 + 0.69962 0.90114 0.43689 0.5814 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP1 MTA2_300_0.15_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9955 28679 31134 26224 0 4910 3753 3707 0 46 12.05 14.14 NaN 0.94 3000 1115745 25758 2.31 1786 6.93 123406 23278 22807 18.86 25.79 2005 8.61 + 0.88573 1.1075 0.58034 0.75673 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP2 MTA2_300_0.15_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 10055 28299 30607 25991 0 4616 3816 3784 0 32 12.47 14.56 NaN 0.69 3041 1132457 25560 2.26 1658 6.49 120400 23204 22736 19.27 25.72 1898 8.18 + 0.80762 1.0125 0.52622 0.69061 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_MTA2gfp_GFP3 MTA2_300_0.15_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 9821 29181 31385 26977 0 4408 4609 4547 0 62 14.69 16.86 NaN 1.41 3554 1058131 26445 2.5 1690 6.39 120824 24194 23774 20.02 25.75 1973 8.15 + 0.80699 1.0176 0.52417 0.6913 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP1 HeLa(MTA2)_300_0.15_1 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 10421 27397 29726 25068 0 4658 3857 3800 0 57 12.98 15.16 NaN 1.22 3050 1201825 24699 2.06 1584 6.41 124423 22439 22028 18.03 24.75 1800 8.02 + 0.80414 1.0083 0.52426 0.68583 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP2 HeLa(MTA2)_300_0.15_2 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 10053 28341 30583 26099 0 4484 4090 4029 0 61 13.37 15.44 NaN 1.36 3197 1151062 25627 2.23 1580 6.17 124321 23344 22940 18.78 25.25 1852 7.93 + 0.81705 1.018 0.52142 0.67439 20150821_Q1_SA_PaJa_MB_HelaNE_500ug_Master_WT_GFP3 HeLa(MTA2)_300_0.15_3 Trypsin/P Specific False Acetyl (Protein N-term);Oxidation (M) False 1 2 Standard 10784 26389 28679 24099 0 4580 2979 2938 0 41 10.39 12.19 NaN 0.9 2337 1098032 23833 2.17 1537 6.45 112732 21545 21100 19.11 25.91 1763 8.18 + 0.8719 1.077 0.56353 0.72686 HeLa(MBD3)_1000_0.5_1 4490 HeLa(MBD3)_1000_0.5_2 2694 HeLa(MBD3)_1000_0.5_3 3103 HeLa(MBD3)_300_0.15_1 3211 HeLa(MBD3)_300_0.15_2 2626 HeLa(MBD3)_300_0.15_3 3494 HeLa(MBD3)_300_0.5_1 2091 HeLa(MBD3)_300_0.5_2 2338 HeLa(MBD3)_300_0.5_3 2242 HeLa(MTA2)_300_0.15_1 3050 HeLa(MTA2)_300_0.15_2 3197 HeLa(MTA2)_300_0.15_3 2337 MBD3_1000_0.5_1 4516 MBD3_1000_0.5_2 4062 MBD3_1000_0.5_3 3961 MBD3_300_0.15_1 3674 MBD3_300_0.15_2 4427 MBD3_300_0.15_3 3241 MBD3_300_0.5_1 2925 MBD3_300_0.5_2 4094 MBD3_300_0.5_3 4346 MTA2_300_0.15_1 3000 MTA2_300_0.15_2 3041 MTA2_300_0.15_3 3554 Total 218032 738560 801125 675995 0 125130 114602 112950 0 1652 14.31 16.71 NaN 1.32 12296 24964893 2926191 580896 568240 19.85 25.84 59359 10.22 0.79259 1.0161 0.51038 0.68645