MaxQtoMSstatsTMTFormat.RdConvert MaxQuant output into the required input format for MSstatsTMT.
MaxQtoMSstatsTMTFormat( evidence, proteinGroups, annotation, which.proteinid = "Proteins", rmProt_Only.identified.by.site = FALSE, useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE, rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE, summaryforMultipleRows = sum )
| evidence | name of 'evidence.txt' data, which includes feature-level data. |
|---|---|
| proteinGroups | name of 'proteinGroups.txt' data. |
| annotation | data frame which contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.mq' for the meaning of each column. |
| which.proteinid | Use 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.protein' or 'Gene.names' can be used instead to get the protein ID with single protein. However, those can potentially have the shared peptides. |
| rmProt_Only.identified.by.site | TRUE will remove proteins with '+' in 'Only.identified.by.site' column from proteinGroups.txt, which was identified only by a modification site. FALSE is the default. |
| useUniquePeptide | TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
| rmPSM_withMissing_withinRun | TRUE will remove PSM with any missing value within each Run. Defaut is FALSE. |
| rmPSM_withfewMea_withinRun | only for rmPSM_withMissing_withinRun = FALSE. TRUE(default) will remove the features that have 1 or 2 measurements within each Run. |
| rmProtein_with1Feature | TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE. |
| summaryforMultipleRows | sum(default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value. |
input for proteinSummarization function
#> 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#> Protein.IDs Majority.protein.IDs Peptide.counts..all. #> 1: O15042 O15042 9 #> 2: O76031 O76031 6 #> 3: P36578 P36578 19 #> 4: P37108 P37108 9 #> 5: Q6P2E9 Q6P2E9 8 #> 6: Q96P70 Q96P70 25 #> Peptide.counts..razor.unique. Peptide.counts..unique. #> 1: 9 9 #> 2: 6 6 #> 3: 19 19 #> 4: 9 9 #> 5: 8 8 #> 6: 25 25 #> Protein.names #> 1: U2 snRNP-associated SURP motif-containing protein #> 2: ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial #> 3: 60S ribosomal protein L4 #> 4: Signal recognition particle 14 kDa protein #> 5: Enhancer of mRNA-decapping protein 4 #> 6: Importin-9 #> Gene.names Fasta.headers Number.of.proteins Peptides Razor...unique.peptides #> 1: U2SURP NA 1 9 9 #> 2: CLPX NA 1 6 6 #> 3: RPL4 NA 1 19 19 #> 4: SRP14 NA 1 9 9 #> 5: EDC4 NA 1 8 8 #> 6: IPO9 NA 1 25 25 #> Unique.peptides Peptides.M1R1 Peptides.M1R2 Peptides.M1R3 Peptides.M2R1 #> 1: 9 4 4 5 4 #> 2: 6 2 2 1 1 #> 3: 19 17 14 15 17 #> 4: 9 7 8 7 9 #> 5: 8 2 3 1 2 #> 6: 25 13 15 6 17 #> Peptides.M2R2 Peptides.M2R3 Peptides.M3R1 Peptides.M3R2 Peptides.M3R3 #> 1: 5 6 4 5 6 #> 2: 2 2 2 2 1 #> 3: 15 14 14 14 14 #> 4: 7 9 7 7 7 #> 5: 1 2 2 2 1 #> 6: 12 17 15 14 11 #> Peptides.M4R1 Peptides.M4R2 Peptides.M4R3 Peptides.M5R1 Peptides.M5R2 #> 1: 3 5 5 5 5 #> 2: 6 2 2 3 0 #> 3: 16 14 13 15 15 #> 4: 6 8 6 8 9 #> 5: 1 1 1 3 2 #> 6: 14 11 13 11 11 #> Peptides.M5R3 Razor...unique.peptides.M1R1 Razor...unique.peptides.M1R2 #> 1: 8 4 4 #> 2: 2 2 2 #> 3: 16 17 14 #> 4: 8 7 8 #> 5: 1 2 3 #> 6: 15 13 15 #> Razor...unique.peptides.M1R3 Razor...unique.peptides.M2R1 #> 1: 5 4 #> 2: 1 1 #> 3: 15 17 #> 4: 7 9 #> 5: 1 2 #> 6: 6 17 #> Razor...unique.peptides.M2R2 Razor...unique.peptides.M2R3 #> 1: 5 6 #> 2: 2 2 #> 3: 15 14 #> 4: 7 9 #> 5: 1 2 #> 6: 12 17 #> Razor...unique.peptides.M3R1 Razor...unique.peptides.M3R2 #> 1: 4 5 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 15 14 #> Razor...unique.peptides.M3R3 Razor...unique.peptides.M4R1 #> 1: 6 3 #> 2: 1 6 #> 3: 14 16 #> 4: 7 6 #> 5: 1 1 #> 6: 11 14 #> Razor...unique.peptides.M4R2 Razor...unique.peptides.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 14 13 #> 4: 8 6 #> 5: 1 1 #> 6: 11 13 #> Razor...unique.peptides.M5R1 Razor...unique.peptides.M5R2 #> 1: 5 5 #> 2: 3 0 #> 3: 15 15 #> 4: 8 9 #> 5: 3 2 #> 6: 11 11 #> Razor...unique.peptides.M5R3 Unique.peptides.M1R1 Unique.peptides.M1R2 #> 1: 8 4 4 #> 2: 2 2 2 #> 3: 16 17 14 #> 4: 8 7 8 #> 5: 1 2 3 #> 6: 15 13 15 #> Unique.peptides.M1R3 Unique.peptides.M2R1 Unique.peptides.M2R2 #> 1: 5 4 5 #> 2: 1 1 2 #> 3: 15 17 15 #> 4: 7 9 7 #> 5: 1 2 1 #> 6: 6 17 12 #> Unique.peptides.M2R3 Unique.peptides.M3R1 Unique.peptides.M3R2 #> 1: 6 4 5 #> 2: 2 2 2 #> 3: 14 14 14 #> 4: 9 7 7 #> 5: 2 2 2 #> 6: 17 15 14 #> Unique.peptides.M3R3 Unique.peptides.M4R1 Unique.peptides.M4R2 #> 1: 6 3 5 #> 2: 1 6 2 #> 3: 14 16 14 #> 4: 7 6 8 #> 5: 1 1 1 #> 6: 11 14 11 #> Unique.peptides.M4R3 Unique.peptides.M5R1 Unique.peptides.M5R2 #> 1: 5 5 5 #> 2: 2 3 0 #> 3: 13 15 15 #> 4: 6 8 9 #> 5: 1 3 2 #> 6: 13 11 11 #> Unique.peptides.M5R3 Sequence.coverage.... #> 1: 8 11.3 #> 2: 2 12.5 #> 3: 16 40.3 #> 4: 8 67.6 #> 5: 1 7.9 #> 6: 15 31.3 #> Unique...razor.sequence.coverage.... Unique.sequence.coverage.... #> 1: 11.3 11.3 #> 2: 12.5 12.5 #> 3: 40.3 40.3 #> 4: 67.6 67.6 #> 5: 7.9 7.9 #> 6: 31.3 31.3 #> Mol..weight..kDa. Sequence.length Sequence.lengths Q.value Score #> 1: 118.290 1029 1029 0 74.881 #> 2: 69.223 633 633 0 27.411 #> 3: 47.697 427 427 0 136.630 #> 4: 14.570 136 136 0 189.270 #> 5: 151.660 1401 1401 0 24.338 #> 6: 115.960 1041 1041 0 184.990 #> Reporter.intensity.corrected.0 Reporter.intensity.corrected.1 #> 1: 130210 129130 #> 2: 34504 33832 #> 3: 607570 580720 #> 4: 233830 232450 #> 5: 14225 12424 #> 6: 244950 242660 #> Reporter.intensity.corrected.2 Reporter.intensity.corrected.3 #> 1: 127490 128990 #> 2: 35273 34385 #> 3: 594300 584000 #> 4: 230950 232750 #> 5: 13033 14061 #> 6: 244190 245920 #> Reporter.intensity.corrected.4 Reporter.intensity.corrected.5 #> 1: 133230 127520 #> 2: 36253 36050 #> 3: 587050 543670 #> 4: 230260 221060 #> 5: 14452 13125 #> 6: 251120 246080 #> Reporter.intensity.corrected.6 Reporter.intensity.corrected.7 #> 1: 132860 131420 #> 2: 35637 34646 #> 3: 607610 594260 #> 4: 241300 242750 #> 5: 13222 14258 #> 6: 248220 252790 #> Reporter.intensity.corrected.8 Reporter.intensity.corrected.9 #> 1: 129240 131400 #> 2: 33939 34038 #> 3: 547060 552980 #> 4: 224760 224890 #> 5: 14155 13451 #> 6: 241440 243370 #> Reporter.intensity.0 Reporter.intensity.1 Reporter.intensity.2 #> 1: 122520 122200 128320 #> 2: 32475 32018 35400 #> 3: 571680 549580 598000 #> 4: 220030 219980 232250 #> 5: 13380 11764 13181 #> 6: 230510 229660 245420 #> Reporter.intensity.3 Reporter.intensity.4 Reporter.intensity.5 #> 1: 132310 136410 129080 #> 2: 35251 37147 36380 #> 3: 598580 603290 551800 #> 4: 238650 236530 224230 #> 5: 14326 14735 13319 #> 6: 252070 257320 248920 #> Reporter.intensity.6 Reporter.intensity.7 Reporter.intensity.8 #> 1: 134850 130180 128810 #> 2: 36179 34382 33847 #> 3: 615120 586990 546500 #> 4: 244280 239740 224290 #> 5: 13487 14089 14071 #> 6: 252000 250280 240630 #> Reporter.intensity.9 Reporter.intensity.count.0 Reporter.intensity.count.1 #> 1: 130320 75 76 #> 2: 33772 30 29 #> 3: 549490 255 255 #> 4: 223500 120 119 #> 5: 13361 24 24 #> 6: 241590 194 191 #> Reporter.intensity.count.2 Reporter.intensity.count.3 #> 1: 76 76 #> 2: 30 30 #> 3: 255 255 #> 4: 120 120 #> 5: 24 24 #> 6: 191 193 #> Reporter.intensity.count.4 Reporter.intensity.count.5 #> 1: 76 76 #> 2: 30 30 #> 3: 255 254 #> 4: 119 120 #> 5: 24 24 #> 6: 194 192 #> Reporter.intensity.count.6 Reporter.intensity.count.7 #> 1: 76 76 #> 2: 30 30 #> 3: 254 254 #> 4: 120 120 #> 5: 24 24 #> 6: 192 193 #> Reporter.intensity.count.8 Reporter.intensity.count.9 #> 1: 76 76 #> 2: 30 30 #> 3: 254 255 #> 4: 119 120 #> 5: 24 24 #> 6: 191 193 #> Reporter.intensity.corrected.0.M1R1 Reporter.intensity.corrected.1.M1R1 #> 1: 5642.1 5023.40 #> 2: 2703.2 2240.60 #> 3: 39095.0 37730.00 #> 4: 14813.0 14988.00 #> 5: 1018.0 859.54 #> 6: 16670.0 15694.00 #> Reporter.intensity.corrected.2.M1R1 Reporter.intensity.corrected.3.M1R1 #> 1: 5422.80 5036.20 #> 2: 2330.00 2814.50 #> 3: 40256.00 39072.00 #> 4: 15250.00 14426.00 #> 5: 928.41 893.68 #> 6: 16693.00 16555.00 #> Reporter.intensity.corrected.4.M1R1 Reporter.intensity.corrected.5.M1R1 #> 1: 5772.30 4996.20 #> 2: 2690.20 2559.00 #> 3: 37915.00 34949.00 #> 4: 14323.00 13747.00 #> 5: 947.68 868.68 #> 6: 17418.00 15860.00 #> Reporter.intensity.corrected.6.M1R1 Reporter.intensity.corrected.7.M1R1 #> 1: 5309.6 5206.7 #> 2: 2534.9 2490.7 #> 3: 39980.0 38323.0 #> 4: 15813.0 15907.0 #> 5: 1063.6 1046.5 #> 6: 16377.0 16483.0 #> Reporter.intensity.corrected.8.M1R1 Reporter.intensity.corrected.9.M1R1 #> 1: 5111.00 5794.2 #> 2: 2708.90 2523.6 #> 3: 34546.00 36881.0 #> 4: 14281.00 15147.0 #> 5: 904.74 1086.7 #> 6: 15895.00 16612.0 #> Reporter.intensity.corrected.0.M1R2 Reporter.intensity.corrected.1.M1R2 #> 1: 5935.90 5752.40 #> 2: 2089.10 2058.60 #> 3: 34361.00 33537.00 #> 4: 16357.00 16620.00 #> 5: 918.25 766.38 #> 6: 17987.00 18334.00 #> Reporter.intensity.corrected.2.M1R2 Reporter.intensity.corrected.3.M1R2 #> 1: 6281.2 6577.40 #> 2: 2512.8 2075.40 #> 3: 34856.0 34290.00 #> 4: 16309.0 16296.00 #> 5: 667.7 822.64 #> 6: 18347.0 18162.00 #> Reporter.intensity.corrected.4.M1R2 Reporter.intensity.corrected.5.M1R2 #> 1: 6790.30 6851.40 #> 2: 2369.90 2159.00 #> 3: 33962.00 31267.00 #> 4: 15929.00 14858.00 #> 5: 895.58 818.14 #> 6: 18542.00 16977.00 #> Reporter.intensity.corrected.6.M1R2 Reporter.intensity.corrected.7.M1R2 #> 1: 6393.70 6747.40 #> 2: 2641.80 2363.40 #> 3: 36226.00 34135.00 #> 4: 16161.00 17524.00 #> 5: 621.42 720.61 #> 6: 18039.00 18058.00 #> Reporter.intensity.corrected.8.M1R2 Reporter.intensity.corrected.9.M1R2 #> 1: 5726.50 5977.60 #> 2: 2129.10 2065.70 #> 3: 31274.00 31273.00 #> 4: 15829.00 16221.00 #> 5: 804.46 941.42 #> 6: 17537.00 17912.00 #> Reporter.intensity.corrected.0.M1R3 Reporter.intensity.corrected.1.M1R3 #> 1: 7919.30 7714.50 #> 2: 457.36 513.11 #> 3: 46233.00 44947.00 #> 4: 8712.60 8690.00 #> 5: 486.49 355.95 #> 6: 7367.00 6747.00 #> Reporter.intensity.corrected.2.M1R3 Reporter.intensity.corrected.3.M1R3 #> 1: 7565.30 7958.40 #> 2: 239.85 355.03 #> 3: 48765.00 46454.00 #> 4: 9380.30 9191.50 #> 5: 563.49 449.23 #> 6: 7631.40 7523.30 #> Reporter.intensity.corrected.4.M1R3 Reporter.intensity.corrected.5.M1R3 #> 1: 8038.30 7618.20 #> 2: 615.09 460.76 #> 3: 48862.00 42641.00 #> 4: 8953.20 8937.90 #> 5: 394.93 468.59 #> 6: 7565.50 7655.90 #> Reporter.intensity.corrected.6.M1R3 Reporter.intensity.corrected.7.M1R3 #> 1: 8172.10 7750.20 #> 2: 340.14 454.79 #> 3: 49722.00 47961.00 #> 4: 9700.60 9544.20 #> 5: 448.25 593.14 #> 6: 7283.40 7756.20 #> Reporter.intensity.corrected.8.M1R3 Reporter.intensity.corrected.9.M1R3 #> 1: 7707.60 7774.10 #> 2: 479.88 497.41 #> 3: 44549.00 46686.00 #> 4: 9066.40 9004.50 #> 5: 575.06 468.72 #> 6: 7614.90 7373.40 #> Reporter.intensity.corrected.0.M2R1 Reporter.intensity.corrected.1.M2R1 #> 1: 8045.00 8018.10 #> 2: 1622.90 1345.30 #> 3: 48078.00 46647.00 #> 4: 21315.00 21222.00 #> 5: 552.44 990.15 #> 6: 23155.00 21103.00 #> Reporter.intensity.corrected.2.M2R1 Reporter.intensity.corrected.3.M2R1 #> 1: 7191.20 7831.80 #> 2: 1122.80 1302.10 #> 3: 45454.00 44047.00 #> 4: 20114.00 20859.00 #> 5: 955.38 987.65 #> 6: 21967.00 21348.00 #> Reporter.intensity.corrected.4.M2R1 Reporter.intensity.corrected.5.M2R1 #> 1: 7729.10 7522.1 #> 2: 1669.30 1404.7 #> 3: 43887.00 40539.0 #> 4: 20362.00 20004.0 #> 5: 820.35 1018.9 #> 6: 22196.00 21039.0 #> Reporter.intensity.corrected.6.M2R1 Reporter.intensity.corrected.7.M2R1 #> 1: 8241.00 7539.2 #> 2: 1374.30 1628.3 #> 3: 45657.00 45292.0 #> 4: 22140.00 22014.0 #> 5: 920.33 1009.0 #> 6: 21904.00 23233.0 #> Reporter.intensity.corrected.8.M2R1 Reporter.intensity.corrected.9.M2R1 #> 1: 8021.90 8225.0 #> 2: 1541.20 1795.1 #> 3: 42142.00 42934.0 #> 4: 19444.00 18864.0 #> 5: 834.23 827.3 #> 6: 21199.00 20461.0 #> Reporter.intensity.corrected.0.M2R2 Reporter.intensity.corrected.1.M2R2 #> 1: 9148.80 9211.20 #> 2: 2376.60 2422.80 #> 3: 39970.00 39327.00 #> 4: 17741.00 18100.00 #> 5: 812.61 644.56 #> 6: 18012.00 17868.00 #> Reporter.intensity.corrected.2.M2R2 Reporter.intensity.corrected.3.M2R2 #> 1: 8967.60 8876.2 #> 2: 2288.10 2278.4 #> 3: 39554.00 38441.0 #> 4: 18138.00 17571.0 #> 5: 615.78 760.0 #> 6: 17636.00 17243.0 #> Reporter.intensity.corrected.4.M2R2 Reporter.intensity.corrected.5.M2R2 #> 1: 9747.3 9425.9 #> 2: 2099.4 2119.0 #> 3: 39091.0 36433.0 #> 4: 18347.0 17439.0 #> 5: 875.8 664.6 #> 6: 18690.0 19004.0 #> Reporter.intensity.corrected.6.M2R2 Reporter.intensity.corrected.7.M2R2 #> 1: 9409.10 9829.80 #> 2: 2111.20 1812.00 #> 3: 38288.00 41318.00 #> 4: 17412.00 19085.00 #> 5: 612.77 884.33 #> 6: 19173.00 18541.00 #> Reporter.intensity.corrected.8.M2R2 Reporter.intensity.corrected.9.M2R2 #> 1: 8770.00 9477.70 #> 2: 1892.50 2015.90 #> 3: 36631.00 36478.00 #> 4: 16930.00 16049.00 #> 5: 607.77 913.42 #> 6: 17358.00 18208.00 #> Reporter.intensity.corrected.0.M2R3 Reporter.intensity.corrected.1.M2R3 #> 1: 8205.00 7615.00 #> 2: 804.49 624.63 #> 3: 35862.00 34706.00 #> 4: 18304.00 16806.00 #> 5: 1343.90 1254.90 #> 6: 21080.00 21593.00 #> Reporter.intensity.corrected.2.M2R3 Reporter.intensity.corrected.3.M2R3 #> 1: 7889.90 8306.40 #> 2: 680.89 607.29 #> 3: 35656.00 36100.00 #> 4: 17260.00 17343.00 #> 5: 1356.40 1231.00 #> 6: 21586.00 21938.00 #> Reporter.intensity.corrected.4.M2R3 Reporter.intensity.corrected.5.M2R3 #> 1: 8907.0 8117.00 #> 2: 687.3 564.41 #> 3: 34193.0 34160.00 #> 4: 17095.0 16403.00 #> 5: 1315.0 1272.40 #> 6: 22028.0 22621.00 #> Reporter.intensity.corrected.6.M2R3 Reporter.intensity.corrected.7.M2R3 #> 1: 8661.50 9039.90 #> 2: 369.39 771.78 #> 3: 36641.00 36556.00 #> 4: 18554.00 19004.00 #> 5: 1494.90 978.58 #> 6: 21636.00 22298.00 #> Reporter.intensity.corrected.8.M2R3 Reporter.intensity.corrected.9.M2R3 #> 1: 8216.80 7920.30 #> 2: 568.05 720.73 #> 3: 33229.00 33628.00 #> 4: 16647.00 17519.00 #> 5: 1041.10 1127.10 #> 6: 22693.00 23153.00 #> Reporter.intensity.corrected.0.M3R1 Reporter.intensity.corrected.1.M3R1 #> 1: 8848.1 8384.8 #> 2: 3096.8 2529.7 #> 3: 33211.0 32845.0 #> 4: 10183.0 10123.0 #> 5: 1965.0 1815.5 #> 6: 20540.0 20637.0 #> Reporter.intensity.corrected.2.M3R1 Reporter.intensity.corrected.3.M3R1 #> 1: 8062.1 8022.7 #> 2: 2943.8 2889.4 #> 3: 33913.0 30798.0 #> 4: 10258.0 10378.0 #> 5: 1808.1 1771.0 #> 6: 20463.0 21094.0 #> Reporter.intensity.corrected.4.M3R1 Reporter.intensity.corrected.5.M3R1 #> 1: 8482.7 8085.2 #> 2: 2967.5 3042.7 #> 3: 33894.0 30795.0 #> 4: 10571.0 9948.3 #> 5: 1531.9 1836.3 #> 6: 20201.0 21061.0 #> Reporter.intensity.corrected.6.M3R1 Reporter.intensity.corrected.7.M3R1 #> 1: 7786.7 8490.1 #> 2: 3054.8 2874.6 #> 3: 34077.0 31986.0 #> 4: 10523.0 10587.0 #> 5: 1426.7 1883.0 #> 6: 20323.0 22655.0 #> Reporter.intensity.corrected.8.M3R1 Reporter.intensity.corrected.9.M3R1 #> 1: 8637.4 8245.1 #> 2: 2837.7 2661.3 #> 3: 30320.0 30734.0 #> 4: 10591.0 10189.0 #> 5: 1514.7 1659.5 #> 6: 21464.0 20427.0 #> Reporter.intensity.corrected.0.M3R2 Reporter.intensity.corrected.1.M3R2 #> 1: 7384.1 8138.60 #> 2: 2811.0 2971.30 #> 3: 39708.0 36843.00 #> 4: 14578.0 15205.00 #> 5: 1188.7 963.18 #> 6: 15692.0 15364.00 #> Reporter.intensity.corrected.2.M3R2 Reporter.intensity.corrected.3.M3R2 #> 1: 7835.5 7623.4 #> 2: 3338.4 2712.8 #> 3: 39597.0 38051.0 #> 4: 14344.0 14320.0 #> 5: 1136.4 1563.1 #> 6: 15903.0 16643.0 #> Reporter.intensity.corrected.4.M3R2 Reporter.intensity.corrected.5.M3R2 #> 1: 8357.8 7931.40 #> 2: 3035.4 2608.40 #> 3: 38211.0 37305.00 #> 4: 14942.0 13633.00 #> 5: 1124.9 714.63 #> 6: 16796.0 17153.00 #> Reporter.intensity.corrected.6.M3R2 Reporter.intensity.corrected.7.M3R2 #> 1: 7516.0 7385.9 #> 2: 2884.8 2232.1 #> 3: 40140.0 39911.0 #> 4: 15290.0 14531.0 #> 5: 1113.4 1383.9 #> 6: 16441.0 17068.0 #> Reporter.intensity.corrected.8.M3R2 Reporter.intensity.corrected.9.M3R2 #> 1: 8009.6 7945.8 #> 2: 2531.3 3062.5 #> 3: 38260.0 37468.0 #> 4: 14314.0 13789.0 #> 5: 1477.2 1247.5 #> 6: 16530.0 15613.0 #> Reporter.intensity.corrected.0.M3R3 Reporter.intensity.corrected.1.M3R3 #> 1: 12180.00 11842.00 #> 2: 1621.20 1653.80 #> 3: 38214.00 36594.00 #> 4: 15215.00 15333.00 #> 5: 599.54 348.47 #> 6: 9894.50 10407.00 #> Reporter.intensity.corrected.2.M3R3 Reporter.intensity.corrected.3.M3R3 #> 1: 12584.00 12581.00 #> 2: 1806.60 1389.00 #> 3: 38155.00 36453.00 #> 4: 16741.00 15888.00 #> 5: 465.72 613.09 #> 6: 11862.00 10837.00 #> Reporter.intensity.corrected.4.M3R3 Reporter.intensity.corrected.5.M3R3 #> 1: 11431.00 12285.00 #> 2: 1342.40 1641.60 #> 3: 35772.00 34478.00 #> 4: 15922.00 15688.00 #> 5: 754.76 337.41 #> 6: 10828.00 10605.00 #> Reporter.intensity.corrected.6.M3R3 Reporter.intensity.corrected.7.M3R3 #> 1: 11592.00 11878.00 #> 2: 1615.30 1577.50 #> 3: 38113.00 36192.00 #> 4: 16264.00 15949.00 #> 5: 539.56 703.46 #> 6: 10381.00 10574.00 #> Reporter.intensity.corrected.8.M3R3 Reporter.intensity.corrected.9.M3R3 #> 1: 12738.0 12159.00 #> 2: 1589.1 1595.90 #> 3: 35559.0 35296.00 #> 4: 14586.0 15670.00 #> 5: 562.6 467.32 #> 6: 11140.0 10959.00 #> Reporter.intensity.corrected.0.M4R1 Reporter.intensity.corrected.1.M4R1 #> 1: 4850.10 4800.10 #> 2: 6035.00 6728.30 #> 3: 42570.00 40500.00 #> 4: 9234.20 8459.50 #> 5: 567.93 405.38 #> 6: 17977.00 18604.00 #> Reporter.intensity.corrected.2.M4R1 Reporter.intensity.corrected.3.M4R1 #> 1: 4529.80 5254.50 #> 2: 6774.10 6392.00 #> 3: 35550.00 39452.00 #> 4: 7593.70 9499.50 #> 5: 287.24 256.79 #> 6: 17409.00 18732.00 #> Reporter.intensity.corrected.4.M4R1 Reporter.intensity.corrected.5.M4R1 #> 1: 5169.70 4765.4 #> 2: 6715.80 7308.0 #> 3: 40919.00 37238.0 #> 4: 8656.90 8058.2 #> 5: 444.78 253.5 #> 6: 18733.00 17496.0 #> Reporter.intensity.corrected.6.M4R1 Reporter.intensity.corrected.7.M4R1 #> 1: 5302.60 5369.30 #> 2: 7007.00 7265.50 #> 3: 41349.00 40879.00 #> 4: 9099.50 9514.70 #> 5: 486.06 414.87 #> 6: 18360.00 18783.00 #> Reporter.intensity.corrected.8.M4R1 Reporter.intensity.corrected.9.M4R1 #> 1: 4734.10 5480.30 #> 2: 6203.00 6290.50 #> 3: 37258.00 36919.00 #> 4: 8565.90 8901.60 #> 5: 376.53 334.24 #> 6: 16537.00 17935.00 #> Reporter.intensity.corrected.0.M4R2 Reporter.intensity.corrected.1.M4R2 #> 1: 8706.40 9366.90 #> 2: 1864.10 2063.00 #> 3: 41551.00 40410.00 #> 4: 21712.00 20638.00 #> 5: 678.25 436.42 #> 6: 12306.00 12170.00 #> Reporter.intensity.corrected.2.M4R2 Reporter.intensity.corrected.3.M4R2 #> 1: 8115.8 8698.90 #> 2: 1906.9 1982.30 #> 3: 37266.0 40348.00 #> 4: 18959.0 19928.00 #> 5: 557.4 749.77 #> 6: 10286.0 11743.00 #> Reporter.intensity.corrected.4.M4R2 Reporter.intensity.corrected.5.M4R2 #> 1: 8989.8 8221.3 #> 2: 2106.8 2282.9 #> 3: 39971.0 37507.0 #> 4: 20642.0 20144.0 #> 5: 720.9 665.4 #> 6: 11805.0 11432.0 #> Reporter.intensity.corrected.6.M4R2 Reporter.intensity.corrected.7.M4R2 #> 1: 8959.30 9075.50 #> 2: 2148.00 1784.50 #> 3: 40413.00 40005.00 #> 4: 22323.00 21119.00 #> 5: 615.72 451.84 #> 6: 12799.00 11865.00 #> Reporter.intensity.corrected.8.M4R2 Reporter.intensity.corrected.9.M4R2 #> 1: 9266.10 8772.60 #> 2: 1783.20 1706.10 #> 3: 36452.00 36615.00 #> 4: 19844.00 20564.00 #> 5: 381.96 545.22 #> 6: 11584.00 11093.00 #> Reporter.intensity.corrected.0.M4R3 Reporter.intensity.corrected.1.M4R3 #> 1: 9621.20 8974.30 #> 2: 2141.80 1528.20 #> 3: 37508.00 34760.00 #> 4: 16118.00 15846.00 #> 5: 422.91 558.27 #> 6: 17385.00 17998.00 #> Reporter.intensity.corrected.2.M4R3 Reporter.intensity.corrected.3.M4R3 #> 1: 9135.30 9889.90 #> 2: 1775.40 2099.40 #> 3: 34111.00 35760.00 #> 4: 13412.00 14999.00 #> 5: 525.91 686.96 #> 6: 15378.00 18131.00 #> Reporter.intensity.corrected.4.M4R3 Reporter.intensity.corrected.5.M4R3 #> 1: 9579.30 9106.10 #> 2: 2058.90 2104.60 #> 3: 35646.00 32309.00 #> 4: 15435.00 14254.00 #> 5: 701.53 376.13 #> 6: 18182.00 17136.00 #> Reporter.intensity.corrected.6.M4R3 Reporter.intensity.corrected.7.M4R3 #> 1: 10318.00 9345.40 #> 2: 1943.00 1997.20 #> 3: 37696.00 36825.00 #> 4: 15826.00 16503.00 #> 5: 682.76 541.57 #> 6: 18238.00 17599.00 #> Reporter.intensity.corrected.8.M4R3 Reporter.intensity.corrected.9.M4R3 #> 1: 9052.80 9660.10 #> 2: 2093.50 1922.90 #> 3: 31199.00 32417.00 #> 4: 14953.00 14573.00 #> 5: 770.62 580.92 #> 6: 16177.00 17493.00 #> Reporter.intensity.corrected.0.M5R1 Reporter.intensity.corrected.1.M5R1 #> 1: 12800.0 12458.0 #> 2: 4376.0 4634.4 #> 3: 46843.0 43746.0 #> 4: 14842.0 15945.0 #> 5: 1396.8 1196.4 #> 6: 12312.0 12824.0 #> Reporter.intensity.corrected.2.M5R1 Reporter.intensity.corrected.3.M5R1 #> 1: 12397.00 11661.0 #> 2: 4760.80 4669.3 #> 3: 46816.00 44101.0 #> 4: 16507.00 15826.0 #> 5: 924.64 1162.1 #> 6: 12647.00 12626.0 #> Reporter.intensity.corrected.4.M5R1 Reporter.intensity.corrected.5.M5R1 #> 1: 12619.0 12244.0 #> 2: 4545.8 4823.8 #> 3: 43454.0 39914.0 #> 4: 15547.0 15014.0 #> 5: 1285.3 1524.0 #> 6: 12573.0 12299.0 #> Reporter.intensity.corrected.6.M5R1 Reporter.intensity.corrected.7.M5R1 #> 1: 13320.0 12267.0 #> 2: 4727.7 4594.5 #> 3: 46275.0 42863.0 #> 4: 16796.0 15837.0 #> 5: 1045.5 1252.3 #> 6: 12878.0 12856.0 #> Reporter.intensity.corrected.8.M5R1 Reporter.intensity.corrected.9.M5R1 #> 1: 12409.0 12801.0 #> 2: 5027.0 4805.9 #> 3: 41172.0 40592.0 #> 4: 15597.0 15460.0 #> 5: 1216.5 1235.4 #> 6: 12056.0 12379.0 #> Reporter.intensity.corrected.0.M5R2 Reporter.intensity.corrected.1.M5R2 #> 1: 8670.8 8565.2 #> 2: 0.0 0.0 #> 3: 37003.0 34654.0 #> 4: 20331.0 19671.0 #> 5: 2052.2 1501.5 #> 6: 12999.0 12135.0 #> Reporter.intensity.corrected.2.M5R2 Reporter.intensity.corrected.3.M5R2 #> 1: 8848.3 8430.9 #> 2: 0.0 0.0 #> 3: 36960.0 34891.0 #> 4: 21513.0 21660.0 #> 5: 1843.0 1815.7 #> 6: 13186.0 12805.0 #> Reporter.intensity.corrected.4.M5R2 Reporter.intensity.corrected.5.M5R2 #> 1: 8343.9 7836.1 #> 2: 0.0 0.0 #> 3: 35945.0 32740.0 #> 4: 19821.0 19323.0 #> 5: 2077.9 1866.8 #> 6: 12546.0 12873.0 #> Reporter.intensity.corrected.6.M5R2 Reporter.intensity.corrected.7.M5R2 #> 1: 8796.5 8504.4 #> 2: 0.0 0.0 #> 3: 38236.0 36945.0 #> 4: 20456.0 20659.0 #> 5: 1916.8 2123.3 #> 6: 12912.0 12667.0 #> Reporter.intensity.corrected.8.M5R2 Reporter.intensity.corrected.9.M5R2 #> 1: 8176.6 8021.7 #> 2: 0.0 0.0 #> 3: 33329.0 32401.0 #> 4: 20411.0 19380.0 #> 5: 2461.6 1708.5 #> 6: 11885.0 12146.0 #> Reporter.intensity.corrected.0.M5R3 Reporter.intensity.corrected.1.M5R3 #> 1: 12257.00 13262.00 #> 2: 2505.10 2518.10 #> 3: 47360.00 43475.00 #> 4: 14373.00 14805.00 #> 5: 221.95 327.24 #> 6: 21574.00 21182.00 #> Reporter.intensity.corrected.2.M5R3 Reporter.intensity.corrected.3.M5R3 #> 1: 12665.00 12242.00 #> 2: 2792.70 2818.10 #> 3: 47387.00 45741.00 #> 4: 15165.00 14566.00 #> 5: 397.19 298.69 #> 6: 23197.00 20544.00 #> Reporter.intensity.corrected.4.M5R3 Reporter.intensity.corrected.5.M5R3 #> 1: 13271.00 12520.00 #> 2: 3349.20 2970.70 #> 3: 45328.00 41396.00 #> 4: 13708.00 13614.00 #> 5: 561.18 439.15 #> 6: 23010.00 22875.00 #> Reporter.intensity.corrected.6.M5R3 Reporter.intensity.corrected.7.M5R3 #> 1: 13084.00 12988.00 #> 2: 2884.50 2799.40 #> 3: 44799.00 45068.00 #> 4: 14940.00 14974.00 #> 5: 234.16 271.69 #> 6: 21471.00 22355.00 #> Reporter.intensity.corrected.8.M5R3 Reporter.intensity.corrected.9.M5R3 #> 1: 12660.00 13150.00 #> 2: 2554.80 2374.30 #> 3: 41142.00 42660.00 #> 4: 13703.00 13560.00 #> 5: 626.21 308.05 #> 6: 21771.00 21601.00 #> Reporter.intensity.0.M1R1 Reporter.intensity.1.M1R1 #> 1: 5308.30 4754.00 #> 2: 2541.80 2121.70 #> 3: 36797.00 35712.00 #> 4: 13942.00 14181.00 #> 5: 957.51 813.57 #> 6: 15688.00 14861.00 #> Reporter.intensity.2.M1R1 Reporter.intensity.3.M1R1 #> 1: 5465.20 5164.80 #> 2: 2367.40 2853.30 #> 3: 40363.00 39975.00 #> 4: 15291.00 14824.00 #> 5: 938.81 914.62 #> 6: 16777.00 16923.00 #> Reporter.intensity.4.M1R1 Reporter.intensity.5.M1R1 #> 1: 5898.50 5059.00 #> 2: 2738.00 2595.40 #> 3: 39085.00 35527.00 #> 4: 14776.00 13955.00 #> 5: 973.07 882.15 #> 6: 17823.00 16072.00 #> Reporter.intensity.6.M1R1 Reporter.intensity.7.M1R1 #> 1: 5406.1 5165.6 #> 2: 2582.5 2472.0 #> 3: 40424.0 37871.0 #> 4: 15970.0 15694.0 #> 5: 1072.8 1032.9 #> 6: 16661.0 16326.0 #> Reporter.intensity.8.M1R1 Reporter.intensity.9.M1R1 #> 1: 5095.50 5730.6 #> 2: 2692.90 2501.9 #> 3: 34555.00 36614.0 #> 4: 14265.00 15042.0 #> 5: 905.44 1076.6 #> 6: 15843.00 16471.0 #> Reporter.intensity.0.M1R2 Reporter.intensity.1.M1R2 #> 1: 5587.90 5447.00 #> 2: 1968.30 1948.20 #> 3: 32339.00 31741.00 #> 4: 15393.00 15727.00 #> 5: 862.72 725.49 #> 6: 16928.00 17350.00 #> Reporter.intensity.2.M1R2 Reporter.intensity.3.M1R2 #> 1: 6292.30 6702.70 #> 2: 2496.80 2128.40 #> 3: 34988.00 35110.00 #> 4: 16389.00 16724.00 #> 5: 688.42 840.66 #> 6: 18414.00 18631.00 #> Reporter.intensity.4.M1R2 Reporter.intensity.5.M1R2 #> 1: 6934.80 6916.20 #> 2: 2444.60 2183.00 #> 3: 34943.00 31755.00 #> 4: 16377.00 15111.00 #> 5: 902.25 826.72 #> 6: 19016.00 17224.00 #> Reporter.intensity.6.M1R2 Reporter.intensity.7.M1R2 #> 1: 6496.80 6680.20 #> 2: 2663.30 2332.20 #> 3: 36611.00 33711.00 #> 4: 16393.00 17273.00 #> 5: 644.72 720.99 #> 6: 18327.00 17869.00 #> Reporter.intensity.8.M1R2 Reporter.intensity.9.M1R2 #> 1: 5721.50 5948.50 #> 2: 2134.60 2056.40 #> 3: 31283.00 31090.00 #> 4: 15774.00 16121.00 #> 5: 796.06 927.78 #> 6: 17478.00 17768.00 #> Reporter.intensity.0.M1R3 Reporter.intensity.1.M1R3 #> 1: 7450.60 7301.60 #> 2: 429.18 484.97 #> 3: 43522.00 42542.00 #> 4: 8202.80 8225.80 #> 5: 458.25 337.21 #> 6: 6934.30 6388.00 #> Reporter.intensity.2.M1R3 Reporter.intensity.3.M1R3 #> 1: 7627.50 8147.40 #> 2: 257.20 373.67 #> 3: 48839.00 47541.00 #> 4: 9380.30 9398.50 #> 5: 560.29 455.74 #> 6: 7650.00 7674.70 #> Reporter.intensity.4.M1R3 Reporter.intensity.5.M1R3 #> 1: 8224.50 7717.70 #> 2: 605.51 462.55 #> 3: 50161.00 43326.00 #> 4: 9225.20 9055.10 #> 5: 416.14 474.80 #> 6: 7766.30 7738.30 #> Reporter.intensity.6.M1R3 Reporter.intensity.7.M1R3 #> 1: 8284.20 7680.40 #> 2: 358.52 451.78 #> 3: 50367.00 47371.00 #> 4: 9808.80 9435.60 #> 5: 454.91 582.31 #> 6: 7411.00 7678.20 #> Reporter.intensity.8.M1R3 Reporter.intensity.9.M1R3 #> 1: 7688.80 7709.00 #> 2: 474.01 492.16 #> 3: 44510.00 46333.00 #> 4: 9046.70 8944.20 #> 5: 569.17 468.13 #> 6: 7571.10 7322.50 #> Reporter.intensity.0.M2R1 Reporter.intensity.1.M2R1 #> 1: 7566.10 7587.30 #> 2: 1524.40 1273.00 #> 3: 45230.00 44135.00 #> 4: 20052.00 20082.00 #> 5: 522.14 937.03 #> 6: 21784.00 19972.00 #> Reporter.intensity.2.M2R1 Reporter.intensity.3.M2R1 #> 1: 7284.30 8041.7 #> 2: 1163.60 1338.8 #> 3: 45835.00 45302.0 #> 4: 20291.00 21411.0 #> 5: 933.23 1013.4 #> 6: 22147.00 21882.0 #> Reporter.intensity.4.M2R1 Reporter.intensity.5.M2R1 #> 1: 7908.00 7619.7 #> 2: 1677.10 1421.1 #> 3: 45165.00 41179.0 #> 4: 20901.00 20280.0 #> 5: 851.41 1028.7 #> 6: 22766.00 21313.0 #> Reporter.intensity.6.M2R1 Reporter.intensity.7.M2R1 #> 1: 8342.80 7485.50 #> 2: 1409.70 1610.40 #> 3: 46229.00 44725.00 #> 4: 22365.00 21714.00 #> 5: 929.03 997.64 #> 6: 22238.00 22918.00 #> Reporter.intensity.8.M2R1 Reporter.intensity.9.M2R1 #> 1: 7995.0 8138.70 #> 2: 1530.2 1775.90 #> 3: 42066.0 42641.00 #> 4: 19432.0 18791.00 #> 5: 833.2 825.25 #> 6: 21131.0 20365.00 #> Reporter.intensity.0.M2R2 Reporter.intensity.1.M2R2 #> 1: 8608.60 8715.80 #> 2: 2236.00 2292.30 #> 3: 37612.00 37214.00 #> 4: 16697.00 17127.00 #> 5: 763.61 610.43 #> 6: 16948.00 16907.00 #> Reporter.intensity.2.M2R2 Reporter.intensity.3.M2R2 #> 1: 9027.30 9127.0 #> 2: 2303.90 2344.1 #> 3: 39770.00 39467.0 #> 4: 18202.00 18052.0 #> 5: 632.96 772.5 #> 6: 17739.00 17733.0 #> Reporter.intensity.4.M2R2 Reporter.intensity.5.M2R2 #> 1: 9954.60 9519.80 #> 2: 2166.50 2144.10 #> 3: 40144.00 36972.00 #> 4: 18809.00 17657.00 #> 5: 880.16 678.67 #> 6: 19128.00 19153.00 #> Reporter.intensity.6.M2R2 Reporter.intensity.7.M2R2 #> 1: 9556.30 9727.90 #> 2: 2139.60 1809.00 #> 3: 38879.00 40740.00 #> 4: 17708.00 18823.00 #> 5: 632.59 870.69 #> 6: 19414.00 18386.00 #> Reporter.intensity.8.M2R2 Reporter.intensity.9.M2R2 #> 1: 8751.70 9408.50 #> 2: 1890.80 1993.80 #> 3: 36527.00 36303.00 #> 4: 16874.00 15996.00 #> 5: 605.41 905.08 #> 6: 17337.00 18066.00 #> Reporter.intensity.0.M2R3 Reporter.intensity.1.M2R3 #> 1: 7719.60 7209.20 #> 2: 756.38 591.05 #> 3: 33747.00 32850.00 #> 4: 17219.00 15906.00 #> 5: 1264.70 1187.50 #> 6: 19841.00 20436.00 #> Reporter.intensity.2.M2R3 Reporter.intensity.3.M2R3 #> 1: 7954.40 8480.6 #> 2: 692.21 623.6 #> 3: 35834.00 36939.0 #> 4: 17410.00 17753.0 #> 5: 1362.00 1264.2 #> 6: 21661.00 22488.0 #> Reporter.intensity.4.M2R3 Reporter.intensity.5.M2R3 #> 1: 9079.00 8225.90 #> 2: 701.15 575.21 #> 3: 35217.00 34638.00 #> 4: 17576.00 16655.00 #> 5: 1354.60 1281.40 #> 6: 22580.00 22852.00 #> Reporter.intensity.6.M2R3 Reporter.intensity.7.M2R3 #> 1: 8796.60 8916.70 #> 2: 390.85 758.15 #> 3: 37049.00 36124.00 #> 4: 18749.00 18739.00 #> 5: 1503.50 981.43 #> 6: 21999.00 22131.00 #> Reporter.intensity.8.M2R3 Reporter.intensity.9.M2R3 #> 1: 8195.40 7884.30 #> 2: 560.19 716.11 #> 3: 33188.00 33427.00 #> 4: 16632.00 17413.00 #> 5: 1049.40 1113.80 #> 6: 22570.00 22939.00 #> Reporter.intensity.0.M3R1 Reporter.intensity.1.M3R1 #> 1: 8322.1 7933.6 #> 2: 2913.4 2395.4 #> 3: 31257.0 31075.0 #> 4: 9582.8 9581.3 #> 5: 1848.3 1717.9 #> 6: 19329.0 19532.0 #> Reporter.intensity.2.M3R1 Reporter.intensity.3.M3R1 #> 1: 8154.3 8249.8 #> 2: 2968.1 2944.8 #> 3: 34032.0 31704.0 #> 4: 10304.0 10628.0 #> 5: 1825.4 1819.5 #> 6: 20551.0 21612.0 #> Reporter.intensity.4.M3R1 Reporter.intensity.5.M3R1 #> 1: 8673.5 8180.2 #> 2: 3045.7 3069.0 #> 3: 34795.0 31159.0 #> 4: 10831.0 10084.0 #> 5: 1587.7 1855.0 #> 6: 20754.0 21316.0 #> Reporter.intensity.6.M3R1 Reporter.intensity.7.M3R1 #> 1: 7946.6 8401.5 #> 2: 3094.5 2851.6 #> 3: 34531.0 31656.0 #> 4: 10687.0 10471.0 #> 5: 1454.1 1861.9 #> 6: 20646.0 22377.0 #> Reporter.intensity.8.M3R1 Reporter.intensity.9.M3R1 #> 1: 8578.2 8183.3 #> 2: 2832.0 2644.9 #> 3: 30300.0 30512.0 #> 4: 10546.0 10115.0 #> 5: 1506.0 1651.7 #> 6: 21344.0 20317.0 #> Reporter.intensity.0.M3R2 Reporter.intensity.1.M3R2 #> 1: 6951.4 7700.10 #> 2: 2648.3 2810.90 #> 3: 37367.0 34872.00 #> 4: 13717.0 14386.00 #> 5: 1118.4 913.82 #> 6: 14768.0 14545.00 #> Reporter.intensity.2.M3R2 Reporter.intensity.3.M3R2 #> 1: 7847.4 7850.4 #> 2: 3318.8 2796.3 #> 3: 39788.0 38959.0 #> 4: 14433.0 14734.0 #> 5: 1145.2 1564.3 #> 6: 15972.0 17004.0 #> Reporter.intensity.4.M3R2 Reporter.intensity.5.M3R2 #> 1: 8537.4 8004.50 #> 2: 3132.0 2638.10 #> 3: 39330.0 37785.00 #> 4: 15307.0 13822.00 #> 5: 1155.2 760.29 #> 6: 17183.0 17321.00 #> Reporter.intensity.6.M3R2 Reporter.intensity.7.M3R2 #> 1: 7672.1 7348.2 #> 2: 2929.4 2237.9 #> 3: 40646.0 39452.0 #> 4: 15494.0 14368.0 #> 5: 1136.5 1349.9 #> 6: 16707.0 16917.0 #> Reporter.intensity.8.M3R2 Reporter.intensity.9.M3R2 #> 1: 7962.9 7865.1 #> 2: 2530.7 3015.1 #> 3: 38154.0 37222.0 #> 4: 14282.0 13695.0 #> 5: 1461.0 1240.7 #> 6: 16459.0 15514.0 #> Reporter.intensity.0.M3R3 Reporter.intensity.1.M3R3 #> 1: 11465.00 11209.0 #> 2: 1526.60 1564.1 #> 3: 35961.00 34630.0 #> 4: 14327.00 14512.0 #> 5: 563.46 330.8 #> 6: 9322.30 9850.7 #> Reporter.intensity.2.M3R3 Reporter.intensity.3.M3R3 #> 1: 12612.00 12862.0 #> 2: 1800.80 1441.2 #> 3: 38331.00 37386.0 #> 4: 16719.00 16265.0 #> 5: 478.27 612.3 #> 6: 11787.00 11090.0 #> Reporter.intensity.4.M3R3 Reporter.intensity.5.M3R3 #> 1: 11805.00 12428.00 #> 2: 1409.10 1651.00 #> 3: 36891.00 34957.00 #> 4: 16397.00 15875.00 #> 5: 754.78 355.13 #> 6: 11171.00 10733.00 #> Reporter.intensity.6.M3R3 Reporter.intensity.7.M3R3 #> 1: 11781.00 11793.00 #> 2: 1628.60 1566.20 #> 3: 38561.00 35817.00 #> 4: 16473.00 15800.00 #> 5: 556.77 682.64 #> 6: 10569.00 10491.00 #> Reporter.intensity.8.M3R3 Reporter.intensity.9.M3R3 #> 1: 12654.00 12051.00 #> 2: 1583.30 1582.20 #> 3: 35484.00 35028.00 #> 4: 14573.00 15548.00 #> 5: 559.64 469.69 #> 6: 11073.00 10858.00 #> Reporter.intensity.0.M4R1 Reporter.intensity.1.M4R1 #> 1: 4562.50 4544.40 #> 2: 5683.40 6366.10 #> 3: 40022.00 38323.00 #> 4: 8680.80 8009.80 #> 5: 532.89 383.07 #> 6: 16914.00 17606.00 #> Reporter.intensity.2.M4R1 Reporter.intensity.3.M4R1 #> 1: 4576.10 5361.20 #> 2: 6759.00 6581.40 #> 3: 36206.00 40511.00 #> 4: 7742.50 9676.50 #> 5: 307.65 271.64 #> 6: 17529.00 19198.00 #> Reporter.intensity.4.M4R1 Reporter.intensity.5.M4R1 #> 1: 5270.00 4844.90 #> 2: 6900.80 7357.40 #> 3: 41688.00 37776.00 #> 4: 8828.10 8217.00 #> 5: 447.65 258.69 #> 6: 19145.00 17742.00 #> Reporter.intensity.6.M4R1 Reporter.intensity.7.M4R1 #> 1: 5369.40 5307.20 #> 2: 7089.80 7188.70 #> 3: 41900.00 40356.00 #> 4: 9212.30 9379.80 #> 5: 490.13 405.18 #> 6: 18626.00 18570.00 #> Reporter.intensity.8.M4R1 Reporter.intensity.9.M4R1 #> 1: 4730.40 5431.9 #> 2: 6199.90 6264.2 #> 3: 37219.00 36718.0 #> 4: 8545.50 8844.1 #> 5: 378.03 333.6 #> 6: 16519.00 17808.0 #> Reporter.intensity.0.M4R2 Reporter.intensity.1.M4R2 #> 1: 8189.9 8861.90 #> 2: 1754.5 1952.00 #> 3: 39078.0 38242.00 #> 4: 20417.0 19528.00 #> 5: 637.6 414.21 #> 6: 11570.0 11515.00 #> Reporter.intensity.2.M4R2 Reporter.intensity.3.M4R2 #> 1: 8198.30 8956.80 #> 2: 1914.50 2039.80 #> 3: 37739.00 41371.00 #> 4: 19239.00 20482.00 #> 5: 568.84 751.07 #> 6: 10475.00 12067.00 #> Reporter.intensity.4.M4R2 Reporter.intensity.5.M4R2 #> 1: 9175.2 8342.20 #> 2: 2151.1 2291.10 #> 3: 40874.0 38053.00 #> 4: 21109.0 20378.00 #> 5: 728.9 672.73 #> 6: 12040.0 11576.00 #> Reporter.intensity.6.M4R2 Reporter.intensity.7.M4R2 #> 1: 9102.00 8967.40 #> 2: 2173.40 1782.80 #> 3: 40950.00 39533.00 #> 4: 22558.00 20901.00 #> 5: 625.71 455.89 #> 6: 12936.00 11738.00 #> Reporter.intensity.8.M4R2 Reporter.intensity.9.M4R2 #> 1: 9219.4 8708.00 #> 2: 1786.0 1694.00 #> 3: 36412.0 36402.00 #> 4: 19831.0 20409.00 #> 5: 386.9 538.23 #> 6: 11570.0 11021.00 #> Reporter.intensity.0.M4R3 Reporter.intensity.1.M4R3 #> 1: 9051.40 8496.50 #> 2: 2013.50 1448.40 #> 3: 35278.00 32900.00 #> 4: 15153.00 14993.00 #> 5: 398.56 528.82 #> 6: 16349.00 17033.00 #> Reporter.intensity.2.M4R3 Reporter.intensity.3.M4R3 #> 1: 9213.50 10088.00 #> 2: 1809.30 2121.70 #> 3: 34505.00 36602.00 #> 4: 13664.00 15427.00 #> 5: 522.82 695.39 #> 6: 15598.00 18584.00 #> Reporter.intensity.4.M4R3 Reporter.intensity.5.M4R3 #> 1: 9815.70 9239.5 #> 2: 2095.00 2126.4 #> 3: 36524.00 32838.0 #> 4: 15728.00 14468.0 #> 5: 709.37 393.2 #> 6: 18497.00 17369.0 #> Reporter.intensity.6.M4R3 Reporter.intensity.7.M4R3 #> 1: 10427.00 9263.50 #> 2: 1979.60 1982.10 #> 3: 38081.00 36298.00 #> 4: 16039.00 16263.00 #> 5: 695.29 532.65 #> 6: 18483.00 17433.00 #> Reporter.intensity.8.M4R3 Reporter.intensity.9.M4R3 #> 1: 9050.70 9571.80 #> 2: 2080.60 1909.00 #> 3: 31251.00 32265.00 #> 4: 14916.00 14503.00 #> 5: 765.01 575.07 #> 6: 16162.00 17351.00 #> Reporter.intensity.0.M5R1 Reporter.intensity.1.M5R1 #> 1: 12042.0 11787.0 #> 2: 4120.3 4385.9 #> 3: 44082.0 41400.0 #> 4: 13977.0 15089.0 #> 5: 1311.8 1132.1 #> 6: 11588.0 12134.0 #> Reporter.intensity.2.M5R1 Reporter.intensity.3.M5R1 #> 1: 12485.00 12009.0 #> 2: 4757.80 4788.6 #> 3: 47026.00 45188.0 #> 4: 16474.00 16235.0 #> 5: 961.67 1196.4 #> 6: 12686.00 12960.0 #> Reporter.intensity.4.M5R1 Reporter.intensity.5.M5R1 #> 1: 12949.0 12366.0 #> 2: 4681.4 4870.5 #> 3: 44841.0 40541.0 #> 4: 16032.0 15222.0 #> 5: 1294.7 1525.2 #> 6: 12915.0 12457.0 #> Reporter.intensity.6.M5R1 Reporter.intensity.7.M5R1 #> 1: 13481.0 12170.0 #> 2: 4797.2 4565.5 #> 3: 46789.0 42371.0 #> 4: 16984.0 15670.0 #> 5: 1073.7 1249.4 #> 6: 13049.0 12721.0 #> Reporter.intensity.8.M5R1 Reporter.intensity.9.M5R1 #> 1: 12383.0 12681.0 #> 2: 4998.0 4760.5 #> 3: 41145.0 40316.0 #> 4: 15566.0 15342.0 #> 5: 1206.8 1225.7 #> 6: 12030.0 12290.0 #> Reporter.intensity.0.M5R2 Reporter.intensity.1.M5R2 #> 1: 8160.7 8105.2 #> 2: 0.0 0.0 #> 3: 34822.0 32796.0 #> 4: 19140.0 18624.0 #> 5: 1930.0 1422.2 #> 6: 12234.0 11487.0 #> Reporter.intensity.2.M5R2 Reporter.intensity.3.M5R2 #> 1: 8876.9 8651.3 #> 2: 0.0 0.0 #> 3: 37136.0 35762.0 #> 4: 21532.0 22092.0 #> 5: 1866.8 1845.3 #> 6: 13234.0 13097.0 #> Reporter.intensity.4.M5R2 Reporter.intensity.5.M5R2 #> 1: 8600.7 7953.1 #> 2: 0.0 0.0 #> 3: 36986.0 33232.0 #> 4: 20456.0 19635.0 #> 5: 2116.9 1889.0 #> 6: 12921.0 13012.0 #> Reporter.intensity.6.M5R2 Reporter.intensity.7.M5R2 #> 1: 8903.0 8403.8 #> 2: 0.0 0.0 #> 3: 38652.0 36430.0 #> 4: 20742.0 20421.0 #> 5: 1960.9 2090.7 #> 6: 13068.0 12556.0 #> Reporter.intensity.8.M5R2 Reporter.intensity.9.M5R2 #> 1: 8160.2 7968.0 #> 2: 0.0 0.0 #> 3: 33328.0 32253.0 #> 4: 20329.0 19253.0 #> 5: 2436.3 1705.4 #> 6: 11865.0 12053.0 #> Reporter.intensity.0.M5R3 Reporter.intensity.1.M5R3 #> 1: 11537.00 12547.00 #> 2: 2359.10 2384.20 #> 3: 44569.00 41152.00 #> 4: 13530.00 14010.00 #> 5: 209.86 309.58 #> 6: 20310.00 20044.00 #> Reporter.intensity.2.M5R3 Reporter.intensity.3.M5R3 #> 1: 12703.00 12616.00 #> 2: 2790.90 2874.90 #> 3: 47604.00 46763.00 #> 4: 15179.00 14948.00 #> 5: 388.75 308.91 #> 6: 23204.00 21124.00 #> Reporter.intensity.4.M5R3 Reporter.intensity.5.M5R3 #> 1: 13584.00 12660.00 #> 2: 3398.80 2995.60 #> 3: 46645.00 42057.00 #> 4: 14174.00 13816.00 #> 5: 562.16 437.09 #> 6: 23612.00 23043.00 #> Reporter.intensity.6.M5R3 Reporter.intensity.7.M5R3 #> 1: 13285.00 12865.00 #> 2: 2942.10 2773.60 #> 3: 45447.00 44534.00 #> 4: 15100.00 14783.00 #> 5: 256.91 274.96 #> 6: 21865.00 22167.00 #> Reporter.intensity.8.M5R3 Reporter.intensity.9.M5R3 #> 1: 12620.00 13037.00 #> 2: 2553.40 2365.90 #> 3: 41074.00 42371.00 #> 4: 13681.00 13485.00 #> 5: 612.73 304.54 #> 6: 21673.00 21442.00 #> Reporter.intensity.count.0.M1R1 Reporter.intensity.count.1.M1R1 #> 1: 4 4 #> 2: 2 1 #> 3: 19 19 #> 4: 7 7 #> 5: 2 2 #> 6: 13 14 #> Reporter.intensity.count.2.M1R1 Reporter.intensity.count.3.M1R1 #> 1: 4 4 #> 2: 2 2 #> 3: 19 19 #> 4: 7 7 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.4.M1R1 Reporter.intensity.count.5.M1R1 #> 1: 4 4 #> 2: 2 2 #> 3: 19 19 #> 4: 7 7 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.6.M1R1 Reporter.intensity.count.7.M1R1 #> 1: 4 4 #> 2: 2 2 #> 3: 19 19 #> 4: 7 7 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.8.M1R1 Reporter.intensity.count.9.M1R1 #> 1: 4 4 #> 2: 2 2 #> 3: 19 19 #> 4: 7 7 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.0.M1R2 Reporter.intensity.count.1.M1R2 #> 1: 4 4 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.2.M1R2 Reporter.intensity.count.3.M1R2 #> 1: 4 4 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.4.M1R2 Reporter.intensity.count.5.M1R2 #> 1: 4 4 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.6.M1R2 Reporter.intensity.count.7.M1R2 #> 1: 4 4 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.8.M1R2 Reporter.intensity.count.9.M1R2 #> 1: 4 4 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.0.M1R3 Reporter.intensity.count.1.M1R3 #> 1: 5 5 #> 2: 1 1 #> 3: 20 20 #> 4: 7 7 #> 5: 1 1 #> 6: 5 5 #> Reporter.intensity.count.2.M1R3 Reporter.intensity.count.3.M1R3 #> 1: 5 5 #> 2: 1 1 #> 3: 20 20 #> 4: 7 7 #> 5: 1 1 #> 6: 5 5 #> Reporter.intensity.count.4.M1R3 Reporter.intensity.count.5.M1R3 #> 1: 5 5 #> 2: 1 1 #> 3: 20 20 #> 4: 7 7 #> 5: 1 1 #> 6: 6 5 #> Reporter.intensity.count.6.M1R3 Reporter.intensity.count.7.M1R3 #> 1: 5 5 #> 2: 1 1 #> 3: 20 20 #> 4: 7 7 #> 5: 1 1 #> 6: 6 5 #> Reporter.intensity.count.8.M1R3 Reporter.intensity.count.9.M1R3 #> 1: 5 5 #> 2: 1 1 #> 3: 20 20 #> 4: 7 7 #> 5: 1 1 #> 6: 5 6 #> Reporter.intensity.count.0.M2R1 Reporter.intensity.count.1.M2R1 #> 1: 4 4 #> 2: 1 1 #> 3: 17 17 #> 4: 10 9 #> 5: 2 2 #> 6: 17 16 #> Reporter.intensity.count.2.M2R1 Reporter.intensity.count.3.M2R1 #> 1: 4 4 #> 2: 1 1 #> 3: 17 17 #> 4: 10 10 #> 5: 2 2 #> 6: 16 17 #> Reporter.intensity.count.4.M2R1 Reporter.intensity.count.5.M2R1 #> 1: 4 4 #> 2: 1 1 #> 3: 17 17 #> 4: 9 10 #> 5: 2 2 #> 6: 16 17 #> Reporter.intensity.count.6.M2R1 Reporter.intensity.count.7.M2R1 #> 1: 4 4 #> 2: 1 1 #> 3: 17 17 #> 4: 10 10 #> 5: 2 2 #> 6: 16 16 #> Reporter.intensity.count.8.M2R1 Reporter.intensity.count.9.M2R1 #> 1: 4 4 #> 2: 1 1 #> 3: 17 17 #> 4: 9 10 #> 5: 2 2 #> 6: 16 16 #> Reporter.intensity.count.0.M2R2 Reporter.intensity.count.1.M2R2 #> 1: 5 5 #> 2: 2 2 #> 3: 18 18 #> 4: 8 8 #> 5: 1 1 #> 6: 12 11 #> Reporter.intensity.count.2.M2R2 Reporter.intensity.count.3.M2R2 #> 1: 5 5 #> 2: 2 2 #> 3: 18 18 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.4.M2R2 Reporter.intensity.count.5.M2R2 #> 1: 5 5 #> 2: 2 2 #> 3: 18 18 #> 4: 8 8 #> 5: 1 1 #> 6: 12 12 #> Reporter.intensity.count.6.M2R2 Reporter.intensity.count.7.M2R2 #> 1: 5 5 #> 2: 2 2 #> 3: 18 18 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.8.M2R2 Reporter.intensity.count.9.M2R2 #> 1: 5 5 #> 2: 2 2 #> 3: 18 18 #> 4: 8 8 #> 5: 1 1 #> 6: 11 12 #> Reporter.intensity.count.0.M2R3 Reporter.intensity.count.1.M2R3 #> 1: 6 6 #> 2: 2 2 #> 3: 16 16 #> 4: 9 9 #> 5: 2 2 #> 6: 17 17 #> Reporter.intensity.count.2.M2R3 Reporter.intensity.count.3.M2R3 #> 1: 6 6 #> 2: 2 2 #> 3: 16 16 #> 4: 9 9 #> 5: 2 2 #> 6: 17 17 #> Reporter.intensity.count.4.M2R3 Reporter.intensity.count.5.M2R3 #> 1: 6 6 #> 2: 2 2 #> 3: 16 16 #> 4: 9 9 #> 5: 2 2 #> 6: 17 17 #> Reporter.intensity.count.6.M2R3 Reporter.intensity.count.7.M2R3 #> 1: 6 6 #> 2: 2 2 #> 3: 16 16 #> 4: 9 9 #> 5: 2 2 #> 6: 17 17 #> Reporter.intensity.count.8.M2R3 Reporter.intensity.count.9.M2R3 #> 1: 6 6 #> 2: 2 2 #> 3: 16 16 #> 4: 9 9 #> 5: 2 2 #> 6: 17 17 #> Reporter.intensity.count.0.M3R1 Reporter.intensity.count.1.M3R1 #> 1: 4 4 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 15 15 #> Reporter.intensity.count.2.M3R1 Reporter.intensity.count.3.M3R1 #> 1: 4 4 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 14 15 #> Reporter.intensity.count.4.M3R1 Reporter.intensity.count.5.M3R1 #> 1: 4 4 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 14 14 #> Reporter.intensity.count.6.M3R1 Reporter.intensity.count.7.M3R1 #> 1: 4 4 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 14 14 #> Reporter.intensity.count.8.M3R1 Reporter.intensity.count.9.M3R1 #> 1: 4 4 #> 2: 2 2 #> 3: 14 14 #> 4: 7 7 #> 5: 2 2 #> 6: 14 14 #> Reporter.intensity.count.0.M3R2 Reporter.intensity.count.1.M3R2 #> 1: 5 5 #> 2: 2 2 #> 3: 17 17 #> 4: 8 8 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.2.M3R2 Reporter.intensity.count.3.M3R2 #> 1: 5 5 #> 2: 2 2 #> 3: 17 17 #> 4: 8 8 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.4.M3R2 Reporter.intensity.count.5.M3R2 #> 1: 5 5 #> 2: 2 2 #> 3: 17 17 #> 4: 8 8 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.6.M3R2 Reporter.intensity.count.7.M3R2 #> 1: 5 5 #> 2: 2 2 #> 3: 17 17 #> 4: 8 8 #> 5: 2 2 #> 6: 13 14 #> Reporter.intensity.count.8.M3R2 Reporter.intensity.count.9.M3R2 #> 1: 5 5 #> 2: 2 2 #> 3: 17 17 #> 4: 8 8 #> 5: 2 2 #> 6: 13 13 #> Reporter.intensity.count.0.M3R3 Reporter.intensity.count.1.M3R3 #> 1: 6 6 #> 2: 1 1 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.2.M3R3 Reporter.intensity.count.3.M3R3 #> 1: 6 6 #> 2: 1 1 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.4.M3R3 Reporter.intensity.count.5.M3R3 #> 1: 6 6 #> 2: 1 1 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.6.M3R3 Reporter.intensity.count.7.M3R3 #> 1: 6 6 #> 2: 1 1 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.8.M3R3 Reporter.intensity.count.9.M3R3 #> 1: 6 6 #> 2: 1 1 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.0.M4R1 Reporter.intensity.count.1.M4R1 #> 1: 3 3 #> 2: 6 6 #> 3: 18 18 #> 4: 7 7 #> 5: 1 1 #> 6: 14 13 #> Reporter.intensity.count.2.M4R1 Reporter.intensity.count.3.M4R1 #> 1: 3 3 #> 2: 6 6 #> 3: 18 18 #> 4: 7 7 #> 5: 1 1 #> 6: 13 14 #> Reporter.intensity.count.4.M4R1 Reporter.intensity.count.5.M4R1 #> 1: 3 3 #> 2: 6 6 #> 3: 18 18 #> 4: 7 7 #> 5: 1 1 #> 6: 14 13 #> Reporter.intensity.count.6.M4R1 Reporter.intensity.count.7.M4R1 #> 1: 3 3 #> 2: 6 6 #> 3: 18 18 #> 4: 7 7 #> 5: 1 1 #> 6: 14 14 #> Reporter.intensity.count.8.M4R1 Reporter.intensity.count.9.M4R1 #> 1: 3 3 #> 2: 6 6 #> 3: 18 18 #> 4: 7 7 #> 5: 1 1 #> 6: 14 14 #> Reporter.intensity.count.0.M4R2 Reporter.intensity.count.1.M4R2 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.2.M4R2 Reporter.intensity.count.3.M4R2 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.4.M4R2 Reporter.intensity.count.5.M4R2 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.6.M4R2 Reporter.intensity.count.7.M4R2 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.8.M4R2 Reporter.intensity.count.9.M4R2 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 8 8 #> 5: 1 1 #> 6: 11 11 #> Reporter.intensity.count.0.M4R3 Reporter.intensity.count.1.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 7 7 #> 5: 1 1 #> 6: 12 12 #> Reporter.intensity.count.2.M4R3 Reporter.intensity.count.3.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 16 16 #> 4: 7 7 #> 5: 1 1 #> 6: 12 12 #> Reporter.intensity.count.4.M4R3 Reporter.intensity.count.5.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 16 15 #> 4: 7 7 #> 5: 1 1 #> 6: 12 12 #> Reporter.intensity.count.6.M4R3 Reporter.intensity.count.7.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 15 15 #> 4: 7 7 #> 5: 1 1 #> 6: 12 12 #> Reporter.intensity.count.8.M4R3 Reporter.intensity.count.9.M4R3 #> 1: 5 5 #> 2: 2 2 #> 3: 15 16 #> 4: 7 7 #> 5: 1 1 #> 6: 11 12 #> Reporter.intensity.count.0.M5R1 Reporter.intensity.count.1.M5R1 #> 1: 5 6 #> 2: 3 3 #> 3: 18 18 #> 4: 8 8 #> 5: 3 3 #> 6: 11 10 #> Reporter.intensity.count.2.M5R1 Reporter.intensity.count.3.M5R1 #> 1: 6 6 #> 2: 3 3 #> 3: 18 18 #> 4: 8 8 #> 5: 3 3 #> 6: 11 11 #> Reporter.intensity.count.4.M5R1 Reporter.intensity.count.5.M5R1 #> 1: 6 6 #> 2: 3 3 #> 3: 18 18 #> 4: 8 8 #> 5: 3 3 #> 6: 11 11 #> Reporter.intensity.count.6.M5R1 Reporter.intensity.count.7.M5R1 #> 1: 6 6 #> 2: 3 3 #> 3: 18 18 #> 4: 8 8 #> 5: 3 3 #> 6: 11 11 #> Reporter.intensity.count.8.M5R1 Reporter.intensity.count.9.M5R1 #> 1: 6 6 #> 2: 3 3 #> 3: 18 18 #> 4: 8 8 #> 5: 3 3 #> 6: 11 11 #> Reporter.intensity.count.0.M5R2 Reporter.intensity.count.1.M5R2 #> 1: 5 5 #> 2: 0 0 #> 3: 16 16 #> 4: 11 11 #> 5: 2 2 #> 6: 12 12 #> Reporter.intensity.count.2.M5R2 Reporter.intensity.count.3.M5R2 #> 1: 5 5 #> 2: 0 0 #> 3: 16 16 #> 4: 11 11 #> 5: 2 2 #> 6: 12 12 #> Reporter.intensity.count.4.M5R2 Reporter.intensity.count.5.M5R2 #> 1: 5 5 #> 2: 0 0 #> 3: 16 16 #> 4: 11 11 #> 5: 2 2 #> 6: 12 12 #> Reporter.intensity.count.6.M5R2 Reporter.intensity.count.7.M5R2 #> 1: 5 5 #> 2: 0 0 #> 3: 16 16 #> 4: 11 11 #> 5: 2 2 #> 6: 11 12 #> Reporter.intensity.count.8.M5R2 Reporter.intensity.count.9.M5R2 #> 1: 5 5 #> 2: 0 0 #> 3: 16 16 #> 4: 11 11 #> 5: 2 2 #> 6: 12 11 #> Reporter.intensity.count.0.M5R3 Reporter.intensity.count.1.M5R3 #> 1: 9 9 #> 2: 2 2 #> 3: 19 19 #> 4: 8 8 #> 5: 1 1 #> 6: 16 16 #> Reporter.intensity.count.2.M5R3 Reporter.intensity.count.3.M5R3 #> 1: 9 9 #> 2: 2 2 #> 3: 19 19 #> 4: 8 8 #> 5: 1 1 #> 6: 17 16 #> Reporter.intensity.count.4.M5R3 Reporter.intensity.count.5.M5R3 #> 1: 9 9 #> 2: 2 2 #> 3: 19 19 #> 4: 8 8 #> 5: 1 1 #> 6: 17 16 #> Reporter.intensity.count.6.M5R3 Reporter.intensity.count.7.M5R3 #> 1: 9 9 #> 2: 2 2 #> 3: 19 19 #> 4: 8 8 #> 5: 1 1 #> 6: 17 17 #> Reporter.intensity.count.8.M5R3 Reporter.intensity.count.9.M5R3 #> 1: 9 9 #> 2: 2 2 #> 3: 19 19 #> 4: 8 8 #> 5: 1 1 #> 6: 17 17 #> Sequence.coverage.M1R1.... Sequence.coverage.M1R2.... #> 1: 5.5 5.1 #> 2: 3.2 4.9 #> 3: 37.5 34.0 #> 4: 59.6 60.3 #> 5: 1.9 4.0 #> 6: 16.9 19.8 #> Sequence.coverage.M1R3.... Sequence.coverage.M2R1.... #> 1: 5.8 5.5 #> 2: 3.3 1.6 #> 3: 37.5 39.6 #> 4: 61.8 67.6 #> 5: 1.6 2.4 #> 6: 8.2 22.6 #> Sequence.coverage.M2R2.... Sequence.coverage.M2R3.... #> 1: 6.4 7.2 #> 2: 4.9 5.1 #> 3: 38.2 32.8 #> 4: 52.9 67.6 #> 5: 0.6 1.5 #> 6: 15.3 20.7 #> Sequence.coverage.M3R1.... Sequence.coverage.M3R2.... #> 1: 5.5 7.0 #> 2: 5.2 4.9 #> 3: 37.5 31.1 #> 4: 59.6 59.6 #> 5: 1.7 1.4 #> 6: 18.6 19.9 #> Sequence.coverage.M3R3.... Sequence.coverage.M4R1.... #> 1: 7.8 4.2 #> 2: 1.6 12.5 #> 3: 37.5 36.8 #> 4: 41.2 54.4 #> 5: 0.8 0.8 #> 6: 15.6 17.9 #> Sequence.coverage.M4R2.... Sequence.coverage.M4R3.... #> 1: 7.0 7.0 #> 2: 4.9 3.2 #> 3: 34.0 34.7 #> 4: 60.3 59.6 #> 5: 0.8 0.8 #> 6: 12.0 16.8 #> Sequence.coverage.M5R1.... Sequence.coverage.M5R2.... #> 1: 6.9 6.3 #> 2: 6.8 0.0 #> 3: 37.5 35.6 #> 4: 46.3 67.6 #> 5: 3.0 1.7 #> 6: 15.5 15.6 #> Sequence.coverage.M5R3.... Intensity Intensity.M1R1 Intensity.M1R2 #> 1: 9.9 8.2679e+08 8.143684e-317 1.696720e-316 #> 2: 4.9 2.6359e+08 4.665511e-317 5.418418e-317 #> 3: 39.6 5.4870e+10 1.448008e-314 1.108634e-314 #> 4: 62.5 1.3317e+10 2.725019e-315 2.194047e-315 #> 5: 1.6 1.5810e+08 1.349837e-316 6.221275e-317 #> 6: 19.7 3.8028e+09 7.366025e-316 1.185165e-315 #> Intensity.M1R3 Intensity.M2R1 Intensity.M2R2 Intensity.M2R3 Intensity.M3R1 #> 1: 3.351544e-316 1.761986e-316 60948000 2.817706e-316 3.169629e-316 #> 2: 3.344330e-317 3.929798e-317 15602000 2.959157e-317 1.617176e-316 #> 3: 2.277297e-314 1.462088e-314 4041900000 1.755563e-314 1.748548e-314 #> 4: 4.384833e-315 5.646182e-315 851040000 4.149361e-315 3.727972e-315 #> 5: 3.379854e-317 1.819446e-317 4901300 5.078501e-317 8.293880e-317 #> 6: 4.026487e-316 1.426269e-315 297160000 1.199542e-315 1.851017e-315 #> Intensity.M3R2 Intensity.M3R3 Intensity.M4R1 Intensity.M4R2 Intensity.M4R3 #> 1: 2.324529e-316 3.666609e-316 1.243810e-316 3.119778e-316 3.730739e-316 #> 2: 9.967280e-317 5.843314e-317 1.710999e-316 7.810190e-317 8.014239e-317 #> 3: 1.592275e-314 2.430111e-314 1.592818e-314 1.622067e-314 2.282188e-314 #> 4: 3.128226e-315 5.184725e-315 2.367661e-315 5.307747e-315 6.276116e-315 #> 5: 4.335327e-317 2.786333e-317 2.861727e-317 2.801402e-317 2.664842e-317 #> 6: 1.044998e-315 1.244650e-315 9.214818e-316 1.232496e-315 1.743014e-315 #> Intensity.M5R1 Intensity.M5R2 Intensity.M5R3 iBAQ iBAQ.M1R1 iBAQ.M1R2 #> 1: 3.519724e-316 55626000 3.872091e-316 392.810 215.36 236.340 #> 2: 2.726402e-316 0 1.002311e-316 648.110 218.10 299.000 #> 3: 2.926795e-314 2506000000 1.628045e-314 42.328 187.59 83.156 #> 4: 7.999911e-315 884240000 4.129697e-315 54.792 191.22 97.919 #> 5: 1.343612e-316 9472700 3.831133e-317 986.250 215.07 318.660 #> 6: 1.929326e-315 214220000 1.344649e-315 207.970 205.18 160.790 #> iBAQ.M1R3 iBAQ.M2R1 iBAQ.M2R2 iBAQ.M2R3 iBAQ.M3R1 iBAQ.M3R2 iBAQ.M3R3 #> 1: 207.540 118.10 159.20 146.30 241.39 320.570 150.950 #> 2: 318.560 117.10 159.92 137.48 270.15 422.980 200.780 #> 3: 80.266 121.68 156.53 168.06 106.33 60.026 68.515 #> 4: 93.497 121.60 156.91 165.23 119.92 78.012 76.601 #> 5: 345.510 116.30 160.78 137.83 325.55 643.080 241.470 #> 6: 203.360 119.45 158.40 151.96 181.93 200.810 126.290 #> iBAQ.M4R1 iBAQ.M4R2 iBAQ.M4R3 iBAQ.M5R1 iBAQ.M5R2 iBAQ.M5R3 MS.MS.Count #> 1: 200.560 340.460 126.94 147.990 116.720 329.060 76 #> 2: 190.670 494.110 121.63 152.040 0.000 650.630 30 #> 3: 80.694 92.584 145.86 84.339 73.598 31.847 255 #> 4: 95.754 100.110 143.99 88.644 75.168 41.925 120 #> 5: 271.770 734.210 116.52 171.820 145.090 1324.400 25 #> 6: 147.730 240.030 132.22 124.570 103.000 182.300 200 #> Only.identified.by.site Reverse Potential.contaminant id #> 1: NA NA NA 205 #> 2: NA NA NA 505 #> 3: NA NA NA 1286 #> 4: NA NA NA 1294 #> 5: NA NA NA 2678 #> 6: NA NA NA 3478 #> Peptide.IDs #> 1: 9;3115;9737;10064;16980;19495;20587;22191;29796 #> 2: 2;7972;18493;18661;18767;21564 #> 3: 1;2162;6138;9150;9151;11503;12133;14117;16236;16813;17047;20971;22023;22939;23301;25327;26948;27722;33982 #> 4: 0;2072;10099;12693;15588;16199;21383;30218;32200 #> 5: 5;5921;8460;11103;11405;11963;13578;15295 #> 6: 8;1325;1426;3044;6021;7450;8832;10159;10973;13727;13926;14308;14475;15178;18189;18775;20388;24032;32104;32314;32347;32989;33490;33877;34954 #> Peptide.is.razor #> 1: True;True;True;True;True;True;True;True;True #> 2: True;True;True;True;True;True #> 3: True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True #> 4: True;True;True;True;True;True;True;True;True #> 5: True;True;True;True;True;True;True;True #> 6: True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True #> Mod..peptide.IDs #> 1: 9;3268;10182;10525;17775;20400;21532;23250;31163 #> 2: 2;8348;19349;19522;19629;22603 #> 3: 1;2255;6431;9576;9577;12031;12702;14785;17009;17599;17600;17848;21955;23078;23079;24034;24402;26498;28168;28169;28170;28986;35527;35528 #> 4: 0;2165;10564;13282;16336;16971;22405;31602;33678 #> 5: 5;6209;8856;11612;11932;12524;14225;16028 #> 6: 8;1385;1492;3192;6312;7806;9244;10628;11480;14381;14587;14982;15163;15908;19035;19638;21328;25156;33580;33795;33829;34494;35022;35416;36538 #> Evidence.IDs #> 1: 84;85;86;87;88;89;90;91;92;93;94;95;96;23160;23161;23162;23163;23164;23165;23166;23167;23168;23169;23170;23171;23172;23173;71872;74349;74350;74351;124133;142156;142157;142158;142159;142160;142161;142162;142163;149978;149979;149980;149981;149982;149983;149984;149985;149986;149987;149988;149989;149990;149991;161502;161503;161504;161505;161506;161507;161508;161509;161510;161511;161512;161513;161514;161515;161516;213284;213285;213286;213287;213288 #> 2: 28;29;30;31;32;33;34;35;36;37;38;58914;58915;58916;135213;135214;135215;136392;136393;136394;136395;136396;136397;136398;136399;136400;136401;137059;137060;156787 #> 3: 13;14;15;16;17;18;19;20;21;22;23;24;25;26;27;15988;15989;15990;15991;15992;15993;15994;15995;15996;15997;15998;15999;16000;16001;16002;45765;45766;45767;45768;45769;45770;45771;45772;45773;45774;45775;45776;45777;45778;45779;67196;67197;67198;67199;67200;67201;67202;67203;67204;67205;67206;67207;67208;67209;67210;67211;67212;67213;85382;90047;90048;90049;90050;90051;105006;105007;105008;105009;105010;105011;105012;105013;105014;105015;105016;105017;105018;105019;105020;105021;105022;105023;119762;119763;119764;119765;119766;119767;119768;119769;119770;119771;119772;119773;119774;122916;122917;122918;122919;122920;122921;122922;122923;122924;122925;122926;122927;122928;122929;122930;122931;122932;122933;122934;122935;122936;122937;122938;124853;124854;124855;124856;124857;124858;124859;124860;124861;124862;124863;124864;152874;152875;152876;152877;152878;152879;152880;152881;152882;152883;152884;152885;160260;160261;160262;160263;160264;160265;160266;160267;160268;160269;160270;166895;166896;166897;166898;166899;166900;166901;166902;166903;166904;166905;166906;166907;166908;166909;166910;169088;169089;169090;169091;169092;169093;169094;169095;169096;169097;169098;169099;169100;169101;169102;169103;169104;169105;169106;182204;182205;182206;182207;182208;182209;182210;182211;182212;182213;182214;182215;192673;192674;192675;192676;192677;192678;192679;192680;192681;192682;192683;192684;192685;192686;192687;192688;192689;192690;192691;192692;192693;192694;192695;192696;198084;198085;198086;198087;244254;244255;244256;244257;244258;244259;244260;244261;244262;244263;244264;244265;244266;244267;244268;244269;244270 #> 4: 0;1;2;3;4;5;6;7;8;9;10;11;12;15338;15339;15340;15341;15342;15343;15344;15345;15346;15347;15348;74645;74646;74647;74648;74649;74650;74651;94057;94058;94059;94060;94061;94062;94063;94064;94065;94066;94067;94068;94069;94070;94071;115579;115580;115581;115582;115583;115584;115585;115586;115587;115588;115589;115590;115591;115592;115593;119639;119640;119641;119642;119643;119644;119645;119646;119647;119648;119649;155427;155428;155429;155430;155431;155432;155433;155434;155435;155436;155437;155438;155439;216257;216258;216259;216260;216261;216262;216263;216264;216265;216266;216267;216268;216269;216270;231261;231262;231263;231264;231265;231266;231267;231268;231269;231270;231271;231272;231273;231274;231275;231276 #> 5: 66;44195;44196;62210;62211;62212;62213;62214;62215;62216;62217;62218;62219;62220;62221;82150;84728;88876;88877;88878;88879;88880;101174;101175;113636 #> 6: 81;82;83;9764;9765;9766;9767;9768;9769;9770;9771;9772;9773;9774;9775;9776;9777;10521;10522;10523;10524;10525;22697;22698;22699;22700;22701;44964;44965;44966;44967;44968;44969;44970;55234;55235;55236;55237;55238;55239;55240;55241;55242;55243;55244;64935;64936;64937;64938;64939;64940;64941;75184;75185;81251;81252;81253;81254;81255;81256;81257;81258;81259;81260;81261;81262;81263;102225;102226;102227;102228;102229;102230;102231;102232;102233;102234;102235;102236;102237;102238;103648;103649;103650;103651;103652;103653;103654;103655;103656;103657;103658;103659;103660;106309;106310;106311;106312;106313;107713;112895;112896;112897;112898;112899;112900;112901;112902;112903;112904;112905;112906;112907;133013;133014;133015;133016;133017;133018;133019;133020;133021;133022;133023;133024;133025;133026;137160;137161;137162;137163;137164;137165;137166;148611;148612;148613;148614;148615;148616;148617;148618;148619;148620;148621;173957;173958;173959;173960;173961;173962;173963;230514;230515;232125;232126;232127;232128;232129;232339;232340;236807;236808;236809;236810;236811;240450;240451;240452;240453;240454;240455;240456;243502;243503;243504;243505;243506;243507;243508;243509;243510;243511;243512;243513;251364;251365;251366;251367;251368;251369;251370;251371;251372;251373;251374 #> MS.MS.IDs #> 1: 85;86;87;88;89;90;91;92;93;94;95;96;97;23945;23946;23947;23948;23949;23950;23951;23952;23953;23954;23955;23956;23957;23958;23959;74371;76919;76920;76921;128376;146958;146959;146960;146961;146962;146963;146964;146965;155011;155012;155013;155014;155015;155016;155017;155018;155019;155020;155021;155022;155023;155024;166923;166924;166925;166926;166927;166928;166929;166930;166931;166932;166933;166934;166935;166936;166937;166938;220535;220536;220537;220538;220539 #> 2: 29;30;31;32;33;34;35;36;37;38;39;60968;60969;60970;139812;139813;139814;141030;141031;141032;141033;141034;141035;141036;141037;141038;141039;141713;141714;162054 #> 3: 14;15;16;17;18;19;20;21;22;23;24;25;26;27;28;16503;16504;16505;16506;16507;16508;16509;16510;16511;16512;16513;16514;16515;16516;16517;47271;47272;47273;47274;47275;47276;47277;47278;47279;47280;47281;47282;47283;47284;47285;47286;69535;69536;69537;69538;69539;69540;69541;69542;69543;69544;69545;69546;69547;69548;69549;69550;69551;69552;88316;93129;93130;93131;93132;93133;108716;108717;108718;108719;108720;108721;108722;108723;108724;108725;108726;108727;108728;108729;108730;108731;108732;108733;123874;123875;123876;123877;123878;123879;123880;123881;123882;123883;123884;123885;123886;127115;127116;127117;127118;127119;127120;127121;127122;127123;127124;127125;127126;127127;127128;127129;127130;127131;127132;127133;127134;127135;127136;127137;127138;127139;129138;129139;129140;129141;129142;129143;129144;129145;129146;129147;129148;129149;129150;129151;158025;158026;158027;158028;158029;158030;158031;158032;158033;158034;158035;158036;165656;165657;165658;165659;165660;165661;165662;165663;165664;165665;165666;172510;172511;172512;172513;172514;172515;172516;172517;172518;172519;172520;172521;172522;172523;172524;172525;174777;174778;174779;174780;174781;174782;174783;174784;174785;174786;174787;174788;174789;174790;174791;174792;174793;174794;174795;188319;188320;188321;188322;188323;188324;188325;188326;188327;188328;188329;188330;199165;199166;199167;199168;199169;199170;199171;199172;199173;199174;199175;199176;199177;199178;199179;199180;199181;199182;199183;199184;199185;199186;199187;199188;204771;204772;204773;204774;252515;252516;252517;252518;252519;252520;252521;252522;252523;252524;252525;252526;252527;252528;252529;252530;252531 #> 4: 0;1;2;3;4;5;6;7;8;9;10;11;12;13;15836;15837;15838;15839;15840;15841;15842;15843;15844;15845;15846;77223;77224;77225;77226;77227;77228;77229;97255;97256;97257;97258;97259;97260;97261;97262;97263;97264;97265;97266;97267;97268;97269;97270;119575;119576;119577;119578;119579;119580;119581;119582;119583;119584;119585;119586;119587;119588;119589;123749;123750;123751;123752;123753;123754;123755;123756;123757;123758;123759;123760;160651;160652;160653;160654;160655;160656;160657;160658;160659;160660;160661;160662;160663;223598;223599;223600;223601;223602;223603;223604;223605;223606;223607;223608;223609;223610;223611;239074;239075;239076;239077;239078;239079;239080;239081;239082;239083;239084;239085;239086;239087;239088;239089;239090;239091 #> 5: 67;45643;45644;64388;64389;64390;64391;64392;64393;64394;64395;64396;64397;64398;64399;84951;87636;91899;91900;91901;91902;91903;104741;104742;117580 #> 6: 82;83;84;10070;10071;10072;10073;10074;10075;10076;10077;10078;10079;10080;10081;10082;10083;10836;10837;10838;10839;10840;10841;23470;23471;23472;23473;23474;46436;46437;46438;46439;46440;46441;46442;57148;57149;57150;57151;57152;57153;57154;57155;57156;57157;57158;67206;67207;67208;67209;67210;67211;67212;77789;77790;84032;84033;84034;84035;84036;84037;84038;84039;84040;84041;84042;84043;84044;105849;105850;105851;105852;105853;105854;105855;105856;105857;105858;105859;105860;105861;105862;107302;107303;107304;107305;107306;107307;107308;107309;107310;107311;107312;107313;107314;110058;110059;110060;110061;110062;111508;116817;116818;116819;116820;116821;116822;116823;116824;116825;116826;116827;116828;116829;116830;116831;137540;137541;137542;137543;137544;137545;137546;137547;137548;137549;137550;137551;137552;137553;141822;141823;141824;141825;141826;141827;141828;153608;153609;153610;153611;153612;153613;153614;153615;153616;153617;153618;179821;179822;179823;179824;179825;179826;179827;179828;238309;238310;239962;239963;239964;239965;239966;240183;240184;244803;244804;244805;244806;244807;248548;248549;248550;248551;248552;248553;248554;251740;251741;251742;251743;251744;251745;251746;251747;251748;251749;251750;251751;259879;259880;259881;259882;259883;259884;259885;259886;259887;259888;259889 #> Best.MS.MS #> 1: 92;23952;74371;76920;128376;146964;155021;166929;220536 #> 2: 34;60969;139813;141030;141713;162054 #> 3: 14;16507;47271;69537;69551;88316;93129;108720;123882;127124;129147;158034;165661;172523;174777;188322;199187;204774;252526 #> 4: 4;15841;77225;97258;119578;123758;160657;223601;239075 #> 5: 67;45644;64390;84951;87636;91903;104742;117580 #> 6: 84;10075;10839;23471;46440;57153;67207;77789;84038;105850;107305;110062;111508;116818;137547;141826;153614;179826;238310;239963;240183;244803;248553;251741;259882 #> Arg10.site.IDs #> 1: 584;585;586 #> 2: 1632 #> 3: 5326;5327;5328;5329;5330;5331;5332;5333 #> 4: 5388;5389 #> 5: 11177;11178;11179;11180 #> 6: 13081;13082;13083;13084;13085;13086;13087;13088;13089;13090;13091;13092 #> Lys8.site.IDs #> 1: NA #> 2: NA #> 3: NA #> 4: NA #> 5: NA #> 6: NA #> Lys8.TMT6.site.IDs #> 1: 597;598;599;600;601;602 #> 2: 1806;1807;1808;1809 #> 3: 6179;6180;6181;6182;6183;6184;6185;6186;6187 #> 4: 6252;6253;6254;6255;6256 #> 5: 12669;12670 #> 6: 14455;14456;14457;14458;14459;14460;14461;14462;14463;14464;14465 #> Oxidation..M..site.IDs Arg10.site.positions #> 1: 433;474;635 #> 2: 462 #> 3: 422;423 33;45;97;205;248;258;268;291 #> 4: 15;88 #> 5: 222;846;974;1197 #> 6: 40;74;97;104;175;206;399;427;679;787;896;935 #> Lys8.site.positions Lys8.TMT6.site.positions #> 1: NA 131;418;608;670;685;862 #> 2: NA 158;349;398;591 #> 3: NA 14;29;140;157;172;219;234;259;364 #> 4: NA 31;43;55;74;95 #> 5: NA 1128;1232 #> 6: NA 195;277;466;549;615;631;773;857;865;876;916 #> Oxidation..M..site.positions #> 1: #> 2: #> 3: 95;138 #> 4: #> 5: #> 6:#> Run Fraction TechRepMixture Channel #> 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.0 #> 2 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.1 #> 3 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.2 #> 4 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.3 #> 5 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.4 #> 6 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 1 1 channel.5 #> Condition Mixture BioReplicate #> 1 Norm Mixture1 Mixture1_Norm #> 2 0.667 Mixture1 Mixture1_0.667 #> 3 0.125 Mixture1 Mixture1_0.125 #> 4 0.5 Mixture1 Mixture1_0.5 #> 5 1 Mixture1 Mixture1_1 #> 6 0.125 Mixture1 Mixture1_0.125input.mq <- MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation.mq)#>#>#>#>#> ProteinName PeptideSequence Charge PSM #> 1 O15042 AAAEIYEEFLAAFEGSDGNK(ly) 3 AAAEIYEEFLAAFEGSDGNK(ly)_3 #> 2 Q9P258 DGQILPVPNVVVR(ar) 3 DGQILPVPNVVVR(ar)_3 #> 3 Q96P70 ICPFTIAIFLK(ly) 3 ICPFTIAIFLK(ly)_3 #> 4 P36578 FCIWTESAFR(ar)K(ly) 3 FCIWTESAFR(ar)K(ly)_3 #> 5 Q9P258 AAAAAWEEPSSGNGTAR(ar) 2 AAAAAWEEPSSGNGTAR(ar)_2 #> 6 Q96P70 VWTANPQQFVEDEDDDTFSYTVR(ar) 3 VWTANPQQFVEDEDDDTFSYTVR(ar)_3 #> Mixture TechRepMixture Run Channel #> 1 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> 2 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> 3 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> 4 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> 5 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> 6 Mixture1 1 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01 channel.0 #> BioReplicate Condition Intensity #> 1 Mixture1_Norm Norm 1031.50 #> 2 Mixture1_Norm Norm 2219.20 #> 3 Mixture1_Norm Norm 478.17 #> 4 Mixture1_Norm Norm 534.43 #> 5 Mixture1_Norm Norm 866.26 #> 6 Mixture1_Norm Norm 388.78