evidence.RdExample of evidence.txt from MaxQuant. It is the input for MaxQtoMSstatsTMTFormat function, with proteinGroups.txt and annotation file. Annotation file should be made by users. It includes peak intensities for 10 proteins among 15 MS runs with TMT10. The important variables are as follows:
evidence
A data frame with 1075 rows and 105 variables.
Proteins
Protein.group.IDs
Modified.sequence
Charge
Raw.file
Score
Potential.contaminant
Reverse
Channels : Reporter.intensity.corrected.0, ..., Reporter.intensity.corrected.9
#> Sequence Length Modifications #> 1: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> 2: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> 3: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> 4: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> 5: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> 6: AAAAAAAAAPAAAATAPTTAATTAATAAQ 29 Unmodified #> Modified.sequence Arg10.Probabilities Lys8.Probabilities #> 1: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> 2: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> 3: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> 4: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> 5: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> 6: _AAAAAAAAAPAAAATAPTTAATTAATAAQ_ NA #> Lys8.TMT6.Probabilities Oxidation..M..Probabilities Arg10.Score.Diffs #> 1: #> 2: #> 3: #> 4: #> 5: #> 6: #> Lys8.Score.Diffs Lys8.TMT6.Score.Diffs Oxidation..M..Score.Diffs Arg10 Lys8 #> 1: NA 0 0 #> 2: NA 0 0 #> 3: NA 0 0 #> 4: NA 0 0 #> 5: NA 0 0 #> 6: NA 0 0 #> Lys8.TMT6 Oxidation..M. Missed.cleavages Proteins Leading.proteins #> 1: 0 0 0 P37108 P37108 #> 2: 0 0 0 P37108 P37108 #> 3: 0 0 0 P37108 P37108 #> 4: 0 0 0 P37108 P37108 #> 5: 0 0 0 P37108 P37108 #> 6: 0 0 0 P37108 P37108 #> Leading.razor.protein Gene.names Protein.names #> 1: P37108 SRP14 Signal recognition particle 14 kDa protein #> 2: P37108 SRP14 Signal recognition particle 14 kDa protein #> 3: P37108 SRP14 Signal recognition particle 14 kDa protein #> 4: P37108 SRP14 Signal recognition particle 14 kDa protein #> 5: P37108 SRP14 Signal recognition particle 14 kDa protein #> 6: P37108 SRP14 Signal recognition particle 14 kDa protein #> Type Raw.file Experiment MS.MS.m.z #> 1: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 M1R1 866.7972 #> 2: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02 M1R2 866.7974 #> 3: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03 M1R3 866.7979 #> 4: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01 M2R1 867.1326 #> 5: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02 M2R2 866.7980 #> 6: MULTI-MSMS 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03 M2R3 866.7976 #> Charge m.z Mass Resolution Uncalibrated...Calibrated.m.z..ppm. #> 1: 3 790.0749 2367.203 64859.60 1.1067 #> 2: 3 790.0749 2367.203 64792.27 1.0697 #> 3: 3 790.0749 2367.203 64889.25 1.2583 #> 4: 3 790.0749 2367.203 65019.08 1.0610 #> 5: 3 790.0749 2367.203 65360.63 0.8172 #> 6: 3 790.0749 2367.203 64884.01 1.0684 #> Uncalibrated...Calibrated.m.z..Da. Mass.Error..ppm. Mass.Error..Da. #> 1: 0.00087435 96684 76.388 #> 2: 0.00084515 96684 76.387 #> 3: 0.00099415 96684 76.388 #> 4: 0.00083828 96684 76.388 #> 5: 0.00064565 96684 76.388 #> 6: 0.00084409 96684 76.388 #> Uncalibrated.Mass.Error..ppm. Uncalibrated.Mass.Error..Da. #> 1: 96685 76.388 #> 2: 96685 76.388 #> 3: 96685 76.389 #> 4: 96685 76.388 #> 5: 96685 76.388 #> 6: 96685 76.389 #> Max.intensity.m.z.0 Retention.time Retention.length #> 1: 866.7968 147.11 0.90532 #> 2: 866.7969 146.59 1.14230 #> 3: 866.7970 146.76 0.90652 #> 4: 866.7971 147.73 1.17820 #> 5: 866.7968 147.06 0.94220 #> 6: 866.7971 146.86 0.83369 #> Calibrated.retention.time Calibrated.retention.time.start #> 1: 147.11 146.79 #> 2: 146.59 145.99 #> 3: 146.76 146.27 #> 4: 147.73 147.20 #> 5: 147.06 146.46 #> 6: 146.86 146.53 #> Calibrated.retention.time.finish Retention.time.calibration #> 1: 147.69 0.0000e+00 #> 2: 147.13 0.0000e+00 #> 3: 147.17 0.0000e+00 #> 4: 148.38 -1.5259e-05 #> 5: 147.40 0.0000e+00 #> 6: 147.37 0.0000e+00 #> Match.time.difference Match.m.z.difference Match.q.value Match.score #> 1: NA NA NA NA #> 2: NA NA NA NA #> 3: NA NA NA NA #> 4: NA NA NA NA #> 5: NA NA NA NA #> 6: NA NA NA NA #> Number.of.data.points Number.of.scans Number.of.isotopic.peaks PIF #> 1: 100 19 8 0.9898786 #> 2: 126 24 7 0.9632148 #> 3: 89 19 8 0.9676424 #> 4: 92 24 9 0.9824644 #> 5: 78 19 7 0.9520919 #> 6: 74 17 9 0.9838271 #> Fraction.of.total.spectrum Base.peak.fraction PEP MS.MS.Count #> 1: 0.015312518 0.16888824 5.4830e-06 1 #> 2: 0.004524438 0.11082462 5.7964e-06 1 #> 3: 0.013643097 0.20289205 3.0267e-07 1 #> 4: 0.004739841 0.08380772 5.9510e-03 1 #> 5: 0.005593725 0.07322775 1.8707e-07 1 #> 6: 0.013364772 0.15386328 1.4950e-06 1 #> MS.MS.Scan.Number Score Delta.score Combinatorics Intensity #> 1: 72111 76.152 54.379 1 187210000 #> 2: 72611 74.627 47.790 1 89081000 #> 3: 75614 96.181 68.927 1 242940000 #> 4: 74185 47.577 26.217 1 175640000 #> 5: 75664 100.140 66.039 1 228260000 #> 6: 72665 91.733 63.093 1 217170000 #> Reporter.intensity.corrected.0 Reporter.intensity.corrected.1 #> 1: 883.78 715.37 #> 2: 1113.30 1195.80 #> 3: 353.29 700.06 #> 4: 1214.70 1406.00 #> 5: 542.84 600.04 #> 6: 758.48 685.43 #> Reporter.intensity.corrected.2 Reporter.intensity.corrected.3 #> 1: 1090.60 1080.10 #> 2: 1318.40 1275.30 #> 3: 692.62 618.40 #> 4: 1012.10 1487.50 #> 5: 468.63 522.40 #> 6: 705.30 703.73 #> Reporter.intensity.corrected.4 Reporter.intensity.corrected.5 #> 1: 1006.40 1137.90 #> 2: 1252.40 1018.60 #> 3: 638.44 697.32 #> 4: 1167.40 1308.70 #> 5: 744.03 796.85 #> 6: 706.67 616.80 #> Reporter.intensity.corrected.6 Reporter.intensity.corrected.7 #> 1: 911.15 1192.90 #> 2: 1316.40 1236.10 #> 3: 608.54 767.08 #> 4: 1236.90 1352.50 #> 5: 517.49 580.42 #> 6: 841.08 819.50 #> Reporter.intensity.corrected.8 Reporter.intensity.corrected.9 #> 1: 983.95 881.13 #> 2: 1007.20 1430.90 #> 3: 668.39 743.17 #> 4: 1490.20 1110.30 #> 5: 447.01 775.76 #> 6: 866.20 872.60 #> Reporter.intensity.0 Reporter.intensity.1 Reporter.intensity.2 #> 1: 832.85 678.40 1082.10 #> 2: 1048.90 1131.90 1311.20 #> 3: 334.37 662.20 673.77 #> 4: 1142.00 1330.90 1030.90 #> 5: 510.43 567.55 477.27 #> 6: 713.48 648.73 712.16 #> Reporter.intensity.3 Reporter.intensity.4 Reporter.intensity.5 #> 1: 1088.00 1036.90 1148.80 #> 2: 1302.00 1290.30 1042.40 #> 3: 639.40 658.22 703.62 #> 4: 1520.10 1189.90 1329.30 #> 5: 542.02 744.44 794.17 #> 6: 720.24 726.99 629.87 #> Reporter.intensity.6 Reporter.intensity.7 Reporter.intensity.8 #> 1: 930.00 1175.90 977.88 #> 2: 1329.10 1222.30 1011.60 #> 3: 619.95 758.05 663.98 #> 4: 1256.90 1335.70 1477.10 #> 5: 533.37 585.13 447.13 #> 6: 848.92 807.31 861.94 #> Reporter.intensity.9 Reporter.intensity.count.0 Reporter.intensity.count.1 #> 1: 882.08 1 1 #> 2: 1413.90 1 1 #> 3: 737.65 1 1 #> 4: 1107.50 1 1 #> 5: 764.16 1 1 #> 6: 863.97 1 1 #> Reporter.intensity.count.2 Reporter.intensity.count.3 #> 1: 1 1 #> 2: 1 1 #> 3: 1 1 #> 4: 1 1 #> 5: 1 1 #> 6: 1 1 #> Reporter.intensity.count.4 Reporter.intensity.count.5 #> 1: 1 1 #> 2: 1 1 #> 3: 1 1 #> 4: 1 1 #> 5: 1 1 #> 6: 1 1 #> Reporter.intensity.count.6 Reporter.intensity.count.7 #> 1: 1 1 #> 2: 1 1 #> 3: 1 1 #> 4: 1 1 #> 5: 1 1 #> 6: 1 1 #> Reporter.intensity.count.8 Reporter.intensity.count.9 Reporter.PIF #> 1: 1 1 NA #> 2: 1 1 NA #> 3: 1 1 NA #> 4: 1 1 NA #> 5: 1 1 NA #> 6: 1 1 NA #> Reporter.fraction Reverse Potential.contaminant id Protein.group.IDs #> 1: NA NA NA 0 1294 #> 2: NA NA NA 1 1294 #> 3: NA NA NA 2 1294 #> 4: NA NA NA 3 1294 #> 5: NA NA NA 4 1294 #> 6: NA NA NA 5 1294 #> Peptide.ID Mod..peptide.ID MS.MS.IDs Best.MS.MS AIF.MS.MS.IDs Arg10.site.IDs #> 1: 0 0 0 0 NA #> 2: 0 0 1 1 NA #> 3: 0 0 2 2 NA #> 4: 0 0 3 3 NA #> 5: 0 0 4 4 NA #> 6: 0 0 5 5 NA #> Lys8.site.IDs Lys8.TMT6.site.IDs Oxidation..M..site.IDs #> 1: NA NA #> 2: NA NA #> 3: NA NA #> 4: NA NA #> 5: NA NA #> 6: NA NA