MSstatsImport.RdImport files from signal processing tools.
MSstatsImport(input_files, type, tool, tool_version = NULL, ...)
| input_files | list of paths to input files or |
|---|---|
| type | chr, "MSstats" or "MSstatsTMT". |
| tool | chr, name of a signal processing tool that generated input files. |
| tool_version | not implemented yet. In the future, this parameter will allow handling different versions of each signal processing tools. |
| ... | optional additional parameters to |
an object of class MSstatsInputFiles.
evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", package = "MSstatsConvert") pg_path = system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", package = "MSstatsConvert") evidence = read.csv(evidence_path) pg = read.csv(pg_path) imported = MSstatsImport(list(evidence = evidence, protein_groups = pg), "MSstats", "MaxQuant")#> INFO [2021-05-10 23:03:41] ** Raw data from MaxQuant imported successfully.class(imported)#> [1] "MSstatsMaxQuantFiles" #> attr(,"package") #> [1] "MSstatsConvert"#> Sequence Length Modifications Modifiedsequence OxidationMProbabilities #> 1: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> 2: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> 3: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> 4: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> 5: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> 6: AEAPAAAPAAK 11 Unmodified _AEAPAAAPAAK_ #> OxidationMScoreDiffs AcetylProteinNterm OxidationM Missedcleavages Proteins #> 1: 0 0 0 P06959 #> 2: 0 0 0 P06959 #> 3: 0 0 0 P06959 #> 4: 0 0 0 P06959 #> 5: 0 0 0 P06959 #> 6: 0 0 0 P06959 #> LeadingProteins LeadingRazorProtein GeneNames #> 1: P06959 P06959 aceF #> 2: P06959 P06959 aceF #> 3: P06959 P06959 aceF #> 4: P06959 P06959 aceF #> 5: P06959 P06959 aceF #> 6: P06959 P06959 aceF #> ProteinNames #> 1: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> 2: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> 3: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> 4: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> 5: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> 6: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex #> Type Rawfile #> 1: MULTI-MSMS 121219_S_CCES_01_01_LysC_Try_1to10_Mixt_1_1 #> 2: MULTI-MSMS 121219_S_CCES_01_02_LysC_Try_1to10_Mixt_1_2 #> 3: MULTI-MSMS 121219_S_CCES_01_03_LysC_Try_1to10_Mixt_1_3 #> 4: MULTI-MSMS 121219_S_CCES_01_05_LysC_Try_1to10_Mixt_2_2 #> 5: MULTI-MSMS 121219_S_CCES_01_06_LysC_Try_1to10_Mixt_2_3 #> 6: MULTI-MSMS 121219_S_CCES_01_08_LysC_Try_1to10_Mixt_3_2 #> Experiment MSMSmz Charge mz Mass Resolution #> 1: 01_LysC_Try_1to10_Mixt_1_1 484.26 2 484.264 966.5134 60409.30 #> 2: 02_LysC_Try_1to10_Mixt_1_2 484.26 2 484.264 966.5134 61157.75 #> 3: 03_LysC_Try_1to10_Mixt_1_3 484.26 2 484.264 966.5134 61423.33 #> 4: 05_LysC_Try_1to10_Mixt_2_2 484.26 2 484.264 966.5134 60286.66 #> 5: 06_LysC_Try_1to10_Mixt_2_3 484.27 2 484.264 966.5134 60426.07 #> 6: 08_LysC_Try_1to10_Mixt_3_2 484.26 2 484.264 966.5134 61518.70 #> UncalibratedCalibratedmzppm UncalibratedCalibratedmzDa MassErrorppm #> 1: 0.112640 5.4549e-05 -0.0032325 #> 2: 0.070686 3.4231e-05 0.0570860 #> 3: 0.222730 1.0786e-04 -0.3117600 #> 4: 0.027139 1.3143e-05 -0.0047083 #> 5: 0.207260 1.0037e-04 -0.2215600 #> 6: -0.061896 -2.9974e-05 0.0102090 #> MassErrorDa UncalibratedMassErrorppm UncalibratedMassErrorDa Maxintensitymz0 #> 1: -1.5654e-06 0.109410 5.2984e-05 484.2639 #> 2: 2.7645e-05 0.127770 6.1876e-05 484.2639 #> 3: -1.5098e-04 -0.089031 -4.3115e-05 484.2637 #> 4: -2.2801e-06 0.022431 1.0863e-05 484.2639 #> 5: -1.0729e-04 -0.014302 -6.9259e-06 484.2637 #> 6: 4.9436e-06 -0.051687 -2.5030e-05 484.2639 #> Retentiontime Retentionlength Calibratedretentiontime #> 1: 17.858 0.49251 17.858 #> 2: 18.200 0.41806 17.844 #> 3: 17.872 0.53369 18.072 #> 4: 18.619 0.49627 17.717 #> 5: 18.043 0.51981 18.193 #> 6: 18.902 0.45821 17.700 #> Calibratedretentiontimestart Calibratedretentiontimefinish #> 1: 17.562 18.054 #> 2: 17.613 18.031 #> 3: 17.794 18.327 #> 4: 17.443 17.940 #> 5: 17.922 18.442 #> 6: 17.415 17.873 #> Retentiontimecalibration Matchtimedifference Matchmzdifference Matchqvalue #> 1: 0.00000 NA NA NA #> 2: -0.35622 NA NA NA #> 3: 0.19934 NA NA NA #> 4: -0.90250 NA NA NA #> 5: 0.15029 NA NA NA #> 6: -1.20210 NA NA NA #> Matchscore Numberofdatapoints Numberofscans Numberofisotopicpeaks PIF #> 1: NA 52 18 4 0 #> 2: NA 44 13 4 0 #> 3: NA 41 15 4 0 #> 4: NA 32 9 5 0 #> 5: NA 34 12 4 0 #> 6: NA 39 13 4 0 #> Fractionoftotalspectrum Basepeakfraction PEP MSMSCount MSMSScanNumber #> 1: 0 0 0.00203910 1 2786 #> 2: 0 0 0.00064103 1 2994 #> 3: 0 0 0.00013657 2 3072 #> 4: 0 0 0.00031023 1 2560 #> 5: 0 0 0.00043291 1 2504 #> 6: 0 0 0.00040251 1 2597 #> Score Deltascore Combinatorics Intensity Reverse Potentialcontaminant id #> 1: 76.332 72.245 1 4023100 NA NA 6955 #> 2: 83.081 78.741 1 5132500 NA NA 6956 #> 3: 104.430 101.250 1 2761600 NA NA 6957 #> 4: 94.465 85.666 1 4091800 NA NA 6958 #> 5: 88.596 84.180 1 4727000 NA NA 6959 #> 6: 90.050 79.395 1 2258400 NA NA 6960 #> ProteingroupIDs PeptideID ModpeptideID MSMSIDs BestMSMS AIFMSMSIDs #> 1: 92 289 316 6071 6071 NA #> 2: 92 289 316 6072 6072 NA #> 3: 92 289 316 6073;6074 6073 NA #> 4: 92 289 316 6075 6075 NA #> 5: 92 289 316 6076 6076 NA #> 6: 92 289 316 6077 6077 NA #> OxidationMsiteIDs #> 1: #> 2: #> 3: #> 4: #> 5: #> 6: