From 960557a1ce6c1deaaa13508fd04ccfdf5aa21f57 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Thu, 25 Jul 2024 15:28:18 -0400 Subject: [PATCH 1/7] feat(protein-prospector): Add TMT converter for protein prospector --- DESCRIPTION | 2 + NAMESPACE | 1 + R/MSstatsConvert_core_functions.R | 11 ++ R/clean_ProteinProspector.R | 45 +++++ ...ters_ProteinProspectortoMSstatsTMTFormat.R | 58 +++++++ .../raw_data/ProteinProspector/Annotation.csv | 73 ++++++++ .../ProteinProspector/Prospector_TotalTMT.txt | 164 ++++++++++++++++++ man/MSstatsClean.Rd | 7 + man/MSstatsInputFiles.Rd | 3 + man/ProteinProspectortoMSstatsTMTFormat.Rd | 67 +++++++ 10 files changed, 431 insertions(+) create mode 100644 R/clean_ProteinProspector.R create mode 100644 R/converters_ProteinProspectortoMSstatsTMTFormat.R create mode 100644 inst/tinytest/raw_data/ProteinProspector/Annotation.csv create mode 100644 inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt create mode 100644 man/ProteinProspectortoMSstatsTMTFormat.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 1ab2ad61..e5c495bc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,6 +31,7 @@ Suggests: knitr, rmarkdown Collate: + 'clean_ProteinProspector.R' 'clean_Metamorpheus.R' 'clean_DIANN.R' 'clean_Philosopher.R' @@ -53,6 +54,7 @@ Collate: 'converters_OpenSWATHtoMSstatsFormat.R' 'converters_PDtoMSstatsFormat.R' 'converters_ProgenesistoMSstatsFormat.R' + 'converters_ProteinProspectortoMSstatsTMTFormat.R' 'converters_SkylinetoMSstatsFormat.R' 'converters_SpectronauttoMSstatsFormat.R' 'utils_MSstatsConvert.R' diff --git a/NAMESPACE b/NAMESPACE index 102d450e..f81c30b3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -18,6 +18,7 @@ export(OpenMStoMSstatsFormat) export(OpenSWATHtoMSstatsFormat) export(PDtoMSstatsFormat) export(ProgenesistoMSstatsFormat) +export(ProteinProspectortoMSstatsTMTFormat) export(SkylinetoMSstatsFormat) export(SpectronauttoMSstatsFormat) export(getDataType) diff --git a/R/MSstatsConvert_core_functions.R b/R/MSstatsConvert_core_functions.R index 6a665976..dc3ab08e 100644 --- a/R/MSstatsConvert_core_functions.R +++ b/R/MSstatsConvert_core_functions.R @@ -67,6 +67,10 @@ setClass("MSstatsFragPipeFiles", contains = "MSstatsInputFiles") #' @rdname MSstatsInputFiles #' @keywords internal setClass("MSstatsMetamorpheusFiles", contains = "MSstatsInputFiles") +#' MSstatsProteinProspectorFiles: class for ProteinProspector files. +#' @rdname MSstatsInputFiles +#' @keywords internal +setClass("MSstatsProteinProspectorFiles", contains = "MSstatsInputFiles") #' Get one of files contained in an instance of `MSstatsInputFiles` class. @@ -282,6 +286,13 @@ setMethod("MSstatsClean", signature = "MSstatsDIANNFiles", #' @return data.table setMethod("MSstatsClean", signature = "MSstatsMetamorpheusFiles", .cleanRawMetamorpheus) +#' Clean Protein Prospector files +#' @include clean_ProteinProspector.R +#' @rdname MSstatsClean +#' @inheritParams .cleanRawProteinProspector +#' @return data.table +setMethod("MSstatsClean", signature = "MSstatsProteinProspectorFiles", + .cleanRawProteinProspector) #' Preprocess outputs from MS signal processing tools for analysis with MSstats diff --git a/R/clean_ProteinProspector.R b/R/clean_ProteinProspector.R new file mode 100644 index 00000000..7dbf8e4b --- /dev/null +++ b/R/clean_ProteinProspector.R @@ -0,0 +1,45 @@ +#' Clean raw Protein Prospector data +#' @param msstats_object object that inherits from MSstatsInputFiles class. +#' @return data.table +#' @keywords internal +#' @noRd +.cleanRawProteinProspector = function(msstats_object) { + protein_prospector_input = getInputFile(msstats_object, "input") + protein_prospector_input = + data.table::as.data.table(protein_prospector_input) + channels = .getChannelColumns( + colnames(protein_prospector_input), "Int") + req_cols = c('AccX', 'z', 'DBPeptide', 'Fraction', channels) + protein_prospector_input = protein_prospector_input[, req_cols, with = FALSE] + data.table::setnames( + protein_prospector_input, + c("AccX", "DBPeptide", "z", "Fraction"), + c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run"), + skip_absent = TRUE) + protein_prospector_input$PSM = paste( + protein_prospector_input$PeptideSequence, + protein_prospector_input$PrecursorCharge, + 1:nrow(protein_prospector_input), sep = "_" + ) + + protein_prospector_input = melt(protein_prospector_input, + measure.vars = channels, + id.vars = setdiff( + colnames(protein_prospector_input), + channels + ), + variable.name = "Channel", + value.name = "Intensity" + ) + protein_prospector_input$Channel = .standardizeColnames( + protein_prospector_input$Channel + ) + protein_prospector_input$Intensity = ifelse( + protein_prospector_input$Intensity == 0, + NA, + protein_prospector_input$Intensity + ) + + .logSuccess("ProteinProspector", "clean") + protein_prospector_input +} \ No newline at end of file diff --git a/R/converters_ProteinProspectortoMSstatsTMTFormat.R b/R/converters_ProteinProspectortoMSstatsTMTFormat.R new file mode 100644 index 00000000..12d6a438 --- /dev/null +++ b/R/converters_ProteinProspectortoMSstatsTMTFormat.R @@ -0,0 +1,58 @@ +#' Generate MSstatsTMT required input format from Protein Prospector output +#' +#' @inheritParams .sharedParametersAmongConverters +#' @param input txt report file from Protein Prospector with +#' `Keep Replicates` option selected. +#' @param annotation data frame which contains column Run, Fraction, +#' TechRepMixture, Mixture, Channel, BioReplicate, Condition. +#' +#' @return data.frame of class "MSstatsTMT" +#' +#' @export +#' +#' @examples +#' input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", +#' package = "MSstatsConvert") +#' input = data.table::fread(input) +#' annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", +#' package = "MSstatsConvert") +#' annot = data.table::fread(annot) +#' output <- ProteinProspectortoMSstatsTMTFormat(input, annot) +#' head(output) +#' +ProteinProspectortoMSstatsTMTFormat = function( + input, annotation, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, + removeProtein_with1Feature = FALSE, summaryforMultipleRows = sum, + use_log_file = TRUE, append = FALSE, verbose = TRUE, + log_file_path = NULL +) { + MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, + log_file_path, + base = "MSstatsTMT_converter_log_") + + input = MSstatsConvert::MSstatsImport(list(input = input), + "MSstatsTMT", "ProteinProspector") + input = MSstatsConvert::MSstatsClean(input) + annotation = MSstatsConvert::MSstatsMakeAnnotation(input, annotation) + + feature_columns = c("PeptideSequence", "PrecursorCharge") + input = MSstatsConvert::MSstatsPreprocess( + input, + annotation, + feature_columns, + remove_shared_peptides = useUniquePeptide, + remove_single_feature_proteins = removeProtein_with1Feature, + feature_cleaning = list( + remove_features_with_few_measurements = removeFewMeasurements, + summarize_multiple_psms = summaryforMultipleRows) + ) + input = MSstatsConvert::MSstatsBalancedDesign(input, feature_columns, + fix_missing = "zero_to_na") + + msg_final = paste("** Finished preprocessing. The dataset is ready", + "to be processed by the proteinSummarization function.") + getOption("MSstatsLog")("INFO", msg_final) + getOption("MSstatsMsg")("INFO", msg_final) + getOption("MSstatsLog")("INFO", "\n") + input +} \ No newline at end of file diff --git a/inst/tinytest/raw_data/ProteinProspector/Annotation.csv b/inst/tinytest/raw_data/ProteinProspector/Annotation.csv new file mode 100644 index 00000000..1f95da55 --- /dev/null +++ b/inst/tinytest/raw_data/ProteinProspector/Annotation.csv @@ -0,0 +1,73 @@ +Run,Fraction,TechRepMixture,Channel,Condition,Mixture,BioReplicate +Z20180606-01_FTMSms2hcd,1,1,Int 126,Control,Mixture1,S1 +Z20180606-02_FTMSms2hcd,2,1,Int 126,Control,Mixture1,S1 +Z20180606-03_FTMSms2hcd,3,1,Int 126,Control,Mixture1,S1 +Z20180606-04_FTMSms2hcd,4,1,Int 126,Control,Mixture1,S1 +Z20180606-05_FTMSms2hcd,5,1,Int 126,Control,Mixture1,S1 +Z20180606-06_FTMSms2hcd,6,1,Int 126,Control,Mixture1,S1 +Z20180606-07_FTMSms2hcd,7,1,Int 126,Control,Mixture1,S1 +Z20180606-08_FTMSms2hcd,8,1,Int 126,Control,Mixture1,S1 +Z20180606-09_FTMSms2hcd,9,1,Int 126,Control,Mixture1,S1 +Z20180606-10_FTMSms2hcd,10,1,Int 126,Control,Mixture1,S1 +Z20180606-11_FTMSms2hcd,11,1,Int 126,Control,Mixture1,S1 +Z20180606-12_FTMSms2hcd,12,1,Int 126,Control,Mixture1,S1 +Z20180606-01_FTMSms2hcd,1,1,Int 127,Control,Mixture1,S2 +Z20180606-02_FTMSms2hcd,2,1,Int 127,Control,Mixture1,S2 +Z20180606-03_FTMSms2hcd,3,1,Int 127,Control,Mixture1,S2 +Z20180606-04_FTMSms2hcd,4,1,Int 127,Control,Mixture1,S2 +Z20180606-05_FTMSms2hcd,5,1,Int 127,Control,Mixture1,S2 +Z20180606-06_FTMSms2hcd,6,1,Int 127,Control,Mixture1,S2 +Z20180606-07_FTMSms2hcd,7,1,Int 127,Control,Mixture1,S2 +Z20180606-08_FTMSms2hcd,8,1,Int 127,Control,Mixture1,S2 +Z20180606-09_FTMSms2hcd,9,1,Int 127,Control,Mixture1,S2 +Z20180606-10_FTMSms2hcd,10,1,Int 127,Control,Mixture1,S2 +Z20180606-11_FTMSms2hcd,11,1,Int 127,Control,Mixture1,S2 +Z20180606-12_FTMSms2hcd,12,1,Int 127,Control,Mixture1,S2 +Z20180606-01_FTMSms2hcd,1,1,Int 128,Control,Mixture1,S3 +Z20180606-02_FTMSms2hcd,2,1,Int 128,Control,Mixture1,S3 +Z20180606-03_FTMSms2hcd,3,1,Int 128,Control,Mixture1,S3 +Z20180606-04_FTMSms2hcd,4,1,Int 128,Control,Mixture1,S3 +Z20180606-05_FTMSms2hcd,5,1,Int 128,Control,Mixture1,S3 +Z20180606-06_FTMSms2hcd,6,1,Int 128,Control,Mixture1,S3 +Z20180606-07_FTMSms2hcd,7,1,Int 128,Control,Mixture1,S3 +Z20180606-08_FTMSms2hcd,8,1,Int 128,Control,Mixture1,S3 +Z20180606-09_FTMSms2hcd,9,1,Int 128,Control,Mixture1,S3 +Z20180606-10_FTMSms2hcd,10,1,Int 128,Control,Mixture1,S3 +Z20180606-11_FTMSms2hcd,11,1,Int 128,Control,Mixture1,S3 +Z20180606-12_FTMSms2hcd,12,1,Int 128,Control,Mixture1,S3 +Z20180606-01_FTMSms2hcd,1,1,Int 129,Disease,Mixture1,S4 +Z20180606-02_FTMSms2hcd,2,1,Int 129,Disease,Mixture1,S4 +Z20180606-03_FTMSms2hcd,3,1,Int 129,Disease,Mixture1,S4 +Z20180606-04_FTMSms2hcd,4,1,Int 129,Disease,Mixture1,S4 +Z20180606-05_FTMSms2hcd,5,1,Int 129,Disease,Mixture1,S4 +Z20180606-06_FTMSms2hcd,6,1,Int 129,Disease,Mixture1,S4 +Z20180606-07_FTMSms2hcd,7,1,Int 129,Disease,Mixture1,S4 +Z20180606-08_FTMSms2hcd,8,1,Int 129,Disease,Mixture1,S4 +Z20180606-09_FTMSms2hcd,9,1,Int 129,Disease,Mixture1,S4 +Z20180606-10_FTMSms2hcd,10,1,Int 129,Disease,Mixture1,S4 +Z20180606-11_FTMSms2hcd,11,1,Int 129,Disease,Mixture1,S4 +Z20180606-12_FTMSms2hcd,12,1,Int 129,Disease,Mixture1,S4 +Z20180606-01_FTMSms2hcd,1,1,Int 130,Disease,Mixture1,S5 +Z20180606-02_FTMSms2hcd,2,1,Int 130,Disease,Mixture1,S5 +Z20180606-03_FTMSms2hcd,3,1,Int 130,Disease,Mixture1,S5 +Z20180606-04_FTMSms2hcd,4,1,Int 130,Disease,Mixture1,S5 +Z20180606-05_FTMSms2hcd,5,1,Int 130,Disease,Mixture1,S5 +Z20180606-06_FTMSms2hcd,6,1,Int 130,Disease,Mixture1,S5 +Z20180606-07_FTMSms2hcd,7,1,Int 130,Disease,Mixture1,S5 +Z20180606-08_FTMSms2hcd,8,1,Int 130,Disease,Mixture1,S5 +Z20180606-09_FTMSms2hcd,9,1,Int 130,Disease,Mixture1,S5 +Z20180606-10_FTMSms2hcd,10,1,Int 130,Disease,Mixture1,S5 +Z20180606-11_FTMSms2hcd,11,1,Int 130,Disease,Mixture1,S5 +Z20180606-12_FTMSms2hcd,12,1,Int 130,Disease,Mixture1,S5 +Z20180606-01_FTMSms2hcd,1,1,Int 131,Disease,Mixture1,S6 +Z20180606-02_FTMSms2hcd,2,1,Int 131,Disease,Mixture1,S6 +Z20180606-03_FTMSms2hcd,3,1,Int 131,Disease,Mixture1,S6 +Z20180606-04_FTMSms2hcd,4,1,Int 131,Disease,Mixture1,S6 +Z20180606-05_FTMSms2hcd,5,1,Int 131,Disease,Mixture1,S6 +Z20180606-06_FTMSms2hcd,6,1,Int 131,Disease,Mixture1,S6 +Z20180606-07_FTMSms2hcd,7,1,Int 131,Disease,Mixture1,S6 +Z20180606-08_FTMSms2hcd,8,1,Int 131,Disease,Mixture1,S6 +Z20180606-09_FTMSms2hcd,9,1,Int 131,Disease,Mixture1,S6 +Z20180606-10_FTMSms2hcd,10,1,Int 131,Disease,Mixture1,S6 +Z20180606-11_FTMSms2hcd,11,1,Int 131,Disease,Mixture1,S6 +Z20180606-12_FTMSms2hcd,12,1,Int 131,Disease,Mixture1,S6 \ No newline at end of file diff --git a/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt b/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt new file mode 100644 index 00000000..c129bba1 --- /dev/null +++ b/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt @@ -0,0 +1,164 @@ +Search Name: Z20180606_YvA_TotalRPLC/SW201948rc2mc2mm + Z20180606_YvA_TotalRPLC/SW201948rc2mc2mm + Uniq Pep Acc # Gene Num Unique % Cov Best Disc Score Best Expect Val m/z z ppm DB Peptide Peptide Protein Mods Fraction RT Spectrum MSMS Info Int 126 Int 127 Int 128 Int 129 Int 130 Int 131 Score Expect # in DB Protein MW Species Protein Name +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1076.0138 2 0.11 QQYEQCMDLQLFYR TMT6plex-QQYEQC(Carbamidomethyl)MDLQLFYR Z20180606-03_FTMSms2hcd 158.517 8 66180 25394 28637 35828 35047 29376 35531 54.0 5.7e-19 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 773.5799 5 -0.53 GEIDAHEDSFKSADESGQALLAASHYASDEVR TMT6plex-GEIDAHEDSFK(TMT6plex)SADESGQALLAASHYASDEVR Z20180606-11_FTMSms2hcd 139.183 1 67708 39221 46197 41622 68307 68667 78506 77.2 9.8e-19 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1078.2767 4 0.14 VAEDLESEGLMAEEVQAVQQQEVYGAMPRDEADSK TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPRDEADSK(TMT6plex) Z20180606-09_FTMSms2hcd 179.733 3 76469 9194 8008 13329 11390 11518 12827 90.0 2.6e-18 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1025.4730 3 1.5 QDLEDSLQAQQYFADANEAESWMR TMT6plex-QDLEDSLQAQQYFADANEAESWMR Z20180606-12_FTMSms2hcd 187.600 1 77246 3648 1853 4731 3867 1463 4498 62.6 6.7e-18 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1092.5566 3 0.43 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex)R Z20180606-02_FTMSms2hcd 173.167 1 72534 15800 12250 13819 15844 15043 15657 79.8 3.1e-17 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1164.8916 3 1.1 SLGYDLPMVEEGEPDPEFEAILDTVDPNR TMT6plex-SLGYDLPM(Oxidation)VEEGEPDPEFEAILDTVDPNR Oxidation@2361 Z20180606-11_FTMSms2hcd 213.717 4 104394 890653 776233 1.127e+6 935587 887078 922503 65.2 4.8e-17 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2239 3 0.35 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=132 Z20180606-09_FTMSms2hcd 183.200 3 78049 3733 3029 4161 2766 4188 4907 74.1 1.1e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 980.7988 4 -0.035 QETFDAGLQAFQQEGIANITALKDQLLAAK TMT6plex-QETFDAGLQAFQQEGIANITALK(TMT6plex)DQLLAAK(TMT6plex) Z20180606-07_FTMSms2hcd 197.250 4 85851 6164 6510 9680 8892 8541 8108 79.9 1.3e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2241 3 0.56 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=131 Z20180606-08_FTMSms2hcd 183.367 2 78493 3058 2880 2968 3270 1845 1605 75.1 1.5e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2250 3 1.3 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=133 Z20180606-09_FTMSms2hcd 183.750 3 78300 1956 2281 2480 2248 1297 -34.49 73.7 1.7e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 853.1035 3 0.14 NQALNTDNYGHDLASVQALQR TMT6plex-NQALNTDNYGHDLASVQALQR Z20180606-01_FTMSms2hcd 125.783 4 47570 309173 329409 332731 350231 307258 305197 76.6 3.1e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2242 3 0.67 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=125 Z20180606-10_FTMSms2hcd 177.483 6 75624 1749 2566 4628 2239 1580 4127 79.1 4.0e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1159.5601 3 1.1 SLGYDLPMVEEGEPDPEFEAILDTVDPNR TMT6plex-SLGYDLPMVEEGEPDPEFEAILDTVDPNR Z20180606-11_FTMSms2hcd 213.867 1 104475 222278 157514 217045 209963 248903 417450 66.5 4.5e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 901.7899 3 0.10 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLMTSSAFDTSQVK(TMT6plex) Z20180606-03_FTMSms2hcd 157.617 3 65761 92746 80425 121848 91871 84235 99169 68.3 5.1e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 901.7903 3 0.64 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLMTSSAFDTSQVK(TMT6plex) Z20180606-02_FTMSms2hcd 158.817 5 65991 47749 40996 48919 45542 39275 44400 68.3 5.3e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 901.7909 3 1.2 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLMTSSAFDTSQVK(TMT6plex) Z20180606-04_FTMSms2hcd 173.083 4 73629 25655 20605 34273 25961 24976 30697 67.0 6.0e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 853.1039 3 0.63 NQALNTDNYGHDLASVQALQR TMT6plex-NQALNTDNYGHDLASVQALQR Z20180606-01_FTMSms2hcd 125.217 5 47303 14461 17129 21723 19823 16666 15841 73.3 6.1e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 869.9216 4 0.87 SLGYDLPMVEEGEPDPEFEAILDTVDPNR TMT6plex-SLGYDLPMVEEGEPDPEFEAILDTVDPNR Z20180606-11_FTMSms2hcd 213.867 2 104476 102478 72345 109400 76492 70064 100833 63.9 8.3e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 942.1824 3 -0.66 EAIVTSEELGQDLEHVEVLQK TMT6plex-EAIVTSEELGQDLEHVEVLQK(TMT6plex) Z20180606-12_FTMSms2hcd 170.133 4 69326 129452 98333 145714 104492 105819 105938 88.2 8.7e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2228 3 -0.60 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=122 Z20180606-09_FTMSms2hcd 177.000 2 75217 2824 4082 3398 3447 3679 4460 77.8 8.8e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1159.5598 3 0.92 SLGYDLPMVEEGEPDPEFEAILDTVDPNR TMT6plex-SLGYDLPMVEEGEPDPEFEAILDTVDPNR Z20180606-10_FTMSms2hcd 206.883 6 89002 2079 2401 3078 4020 2501 2939 69.4 9.2e-16 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7301 3 0.95 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-10_FTMSms2hcd 116.250 6 46331 36384 39295 46402 44911 44417 43820 70.6 1.0e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1092.5557 3 -0.47 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex)R Z20180606-04_FTMSms2hcd 171.250 1 72791 20115 19378 24282 19019 21041 25199 78.3 1.3e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 613.3093 3 -0.46 HQAFEAELHANADR TMT6plex-HQAFEAELHANADR Z20180606-11_FTMSms2hcd 77.450 6 31051 209946 220134 283347 240173 256718 263683 71.4 1.4e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 650.9844 3 -0.46 FEEFQTDLAAHEER TMT6plex-FEEFQTDLAAHEER Z20180606-11_FTMSms2hcd 126.333 6 60417 77053 64489 94444 78504 91308 76634 68.7 1.6e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 853.1035 3 0.14 NQALNTDNYGHDLASVQALQR TMT6plex-NQALNTDNYGHDLASVQALQR Z20180606-01_FTMSms2hcd 122.283 3 45918 22940 24787 30249 26680 29190 26898 78.8 1.6e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 873.9198 4 0.23 SLGYDLPMVEEGEPDPEFEAILDTVDPNR TMT6plex-SLGYDLPM(Oxidation)VEEGEPDPEFEAILDTVDPNR Oxidation@2361 Z20180606-11_FTMSms2hcd 213.750 5 104414 154247 191712 285989 170749 226149 178835 59.5 1.6e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 460.2340 4 -0.035 HQAFEAELHANADR TMT6plex-HQAFEAELHANADR Z20180606-11_FTMSms2hcd 83.083 7 34258 51803 47016 46274 51613 44682 46237 53.1 1.8e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1092.5566 3 0.43 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex)R Z20180606-03_FTMSms2hcd 172.200 4 72437 11021 10150 17458 12171 11086 11312 76.1 2.0e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2238 3 0.24 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=119 Z20180606-10_FTMSms2hcd 178.417 5 76053 3315 1914 4819 2987 2944 4371 78.5 2.3e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1025.4708 3 -0.64 QDLEDSLQAQQYFADANEAESWMR TMT6plex-QDLEDSLQAQQYFADANEAESWMR Z20180606-12_FTMSms2hcd 187.650 2 77269 3104 3993 4179 2684 3245 5126 68.2 2.9e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 975.9732 2 -0.19 FEEFQTDLAAHEER TMT6plex-FEEFQTDLAAHEER Z20180606-11_FTMSms2hcd 125.917 8 60181 57905 59155 80130 67666 67548 65014 61.5 3.1e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 693.3619 3 0.26 QFQDAGHFDAENIK TMT6plex-QFQDAGHFDAENIK(TMT6plex) Z20180606-01_FTMSms2hcd 118.717 4 44311 405388 341579 467366 378380 380307 369580 62.7 3.2e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1157.6154 3 -0.48 QQVAPMDDETGKELVLALYDYQEK TMT6plex-QQVAPMDDETGK(TMT6plex)ELVLALYDYQEK(TMT6plex) Z20180606-03_FTMSms2hcd 184.733 7 78141 18222 19487 28596 24249 25909 24806 65.3 3.2e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 994.5489 3 1.2 EAFLNTEDKGDSLDSVEALIK TMT6plex-EAFLNTEDK(TMT6plex)GDSLDSVEALIK(TMT6plex) Z20180606-03_FTMSms2hcd 175.133 2 73771 58543 46293 62226 51159 55753 53177 71.5 3.2e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 460.2344 4 0.84 HQAFEAELHANADR TMT6plex-HQAFEAELHANADR Z20180606-11_FTMSms2hcd 89.867 4 38284 44586 35940 50451 44353 38672 40423 51.3 4.3e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2241 3 0.56 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=119 Z20180606-10_FTMSms2hcd 184.583 2 78879 5519 3705 6258 3760 4173 5294 71.2 4.3e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1081.5521 2 0.80 GNAMVEEGHFAAEDVK TMT6plex-GNAMVEEGHFAAEDVK(TMT6plex) Z20180606-11_FTMSms2hcd 111.050 1 51323 72686 72763 97587 83471 83319 87863 70.0 4.5e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 901.7915 3 1.9 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLMTSSAFDTSQVK(TMT6plex) Z20180606-02_FTMSms2hcd 152.133 4 62918 12046 9581 14590 12829 10388 11556 64.2 4.6e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1025.4728 3 1.3 QDLEDSLQAQQYFADANEAESWMR TMT6plex-QDLEDSLQAQQYFADANEAESWMR Z20180606-11_FTMSms2hcd 186.650 4 91991 10653 8954 14287 11624 7735 9432 74.8 5.2e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 817.0798 3 0.77 LDETGNLMISEGHFASETIR TMT6plex-LDETGNLMISEGHFASETIR Z20180606-01_FTMSms2hcd 146.383 6 56954 7383 7333 8976 8658 8274 8308 55.2 5.7e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2233 3 -0.18 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=111 Z20180606-08_FTMSms2hcd 177.617 3 75864 3445 3248 5941 4670 4127 2862 75.3 6.0e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1040.5237 3 1.2 TYLLDGSCMVEESGTLESQLEATK TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex) Z20180606-01_FTMSms2hcd 185.033 3 74454 16264 14004 19997 15074 15489 18055 71.9 6.2e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7273 3 -2.6 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-11_FTMSms2hcd 130.350 1 62694 28527 28896 36445 30654 30879 35308 75.2 6.7e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1040.5221 3 -0.36 TYLLDGSCMVEESGTLESQLEATK TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex) Z20180606-01_FTMSms2hcd 187.567 2 75600 11576 10319 14433 13519 12378 15224 71.9 6.8e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 907.1215 3 0.13 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLM(Oxidation)TSSAFDTSQVK(TMT6plex) Oxidation@1725 Z20180606-01_FTMSms2hcd 139.783 1 53937 114763 94417 123461 112301 102351 106529 61.9 7.0e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 853.4752 4 2.2 EKEPIVGSTDYGKDEDSAEALLK TMT6plex-EK(TMT6plex)EPIVGSTDYGK(TMT6plex)DEDSAEALLK(TMT6plex) Z20180606-01_FTMSms2hcd 137.700 2 52986 97907 90016 117288 93059 109068 98845 83.8 7.5e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 942.1839 3 0.96 EAIVTSEELGQDLEHVEVLQK TMT6plex-EAIVTSEELGQDLEHVEVLQK(TMT6plex) Z20180606-12_FTMSms2hcd 161.800 7 65514 14140 11161 16793 14864 8693 11664 73.2 7.8e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1092.5547 3 -1.4 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex)R Z20180606-03_FTMSms2hcd 171.850 5 72283 45245 36379 52698 49084 49796 52988 92.1 8.0e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 650.9839 3 -1.2 FEEFQTDLAAHEER TMT6plex-FEEFQTDLAAHEER Z20180606-12_FTMSms2hcd 128.100 1 49653 69840 51176 55373 46289 38046 50382 62.9 8.6e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 859.6712 4 0.59 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-09_FTMSms2hcd 212.983 6 91554 -4.490 1060 1327 1038 2101 2010 53.5 8.9e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 629.8627 4 0.55 IAALQAFADQLIAVDHYAK TMT6plex-IAALQAFADQLIAVDHYAK(TMT6plex) Z20180606-12_FTMSms2hcd 206.200 3 85665 3546 4606 4275 4190 2733 4590 64.6 9.3e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 683.3515 4 0.27 EQADYCVSHMKPYVDGK TMT6plex-EQADYC(Carbamidomethyl)VSHM(Oxidation)K(TMT6plex)PYVDGK(TMT6plex) Oxidation@2445 Z20180606-02_FTMSms2hcd 102.650 7 39995 55489 46987 65542 65549 59849 58359 56.2 9.8e-15 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2242 3 0.67 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=115 Z20180606-09_FTMSms2hcd 176.100 3 74807 7612 4088 6987 5719 5293 6796 79.6 1.0e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 907.1212 3 -0.20 DLNSQADSLMTSSAFDTSQVK TMT6plex-DLNSQADSLM(Oxidation)TSSAFDTSQVK(TMT6plex) Oxidation@1725 Z20180606-02_FTMSms2hcd 141.233 6 57890 28842 21005 32092 26144 28330 30210 61.3 1.1e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 726.7018 3 0.38 GNAMVEEGHFAAEDVK TMT6plex-GNAM(Oxidation)VEEGHFAAEDVK(TMT6plex) Oxidation@850 Z20180606-11_FTMSms2hcd 99.983 1 44423 519086 477185 583524 431363 504550 449005 48.1 1.1e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 863.6703 4 1.1 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=110 Z20180606-09_FTMSms2hcd 177.000 5 75220 3402 2820 4184 4678 4385 3895 72.8 1.2e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 859.6717 4 1.2 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-10_FTMSms2hcd 193.917 5 83128 3401 2862 4007 5905 3350 3113 63.1 1.4e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2245 3 0.88 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=118 Z20180606-09_FTMSms2hcd 177.550 4 75472 1786 1896 3445 3085 1896 2213 72.1 1.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1091.0525 2 -0.37 SSLSSAQADFNQLAELDR TMT6plex-SSLSSAQADFNQLAELDR Z20180606-01_FTMSms2hcd 158.583 6 62499 12705 10385 16191 13560 11680 14529 67.6 1.8e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1038.5217 4 -0.63 DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-DINK(TMT6plex)VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=122 Z20180606-11_FTMSms2hcd 188.333 4 92786 7876 7542 8204 10578 9828 11855 65.4 2.6e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 839.4818 3 1.3 IAALQAFADQLIAVDHYAK TMT6plex-IAALQAFADQLIAVDHYAK(TMT6plex) Z20180606-12_FTMSms2hcd 206.150 3 85642 26874 26781 34611 25013 34561 31381 88.3 2.6e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7302 3 1.0 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-10_FTMSms2hcd 116.300 4 46352 48578 47944 52354 59709 60174 60190 71.0 2.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 984.5354 3 1.3 QETFDAGLQAFQQEGIANITALK TMT6plex-QETFDAGLQAFQQEGIANITALK(TMT6plex) Z20180606-06_FTMSms2hcd 196.750 3 86053 29667 21042 28738 25489 24756 20230 68.2 3.0e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 859.6716 4 1.1 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-10_FTMSms2hcd 193.567 6 82975 5360 2380 5371 3656 3170 4008 63.0 3.2e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7300 3 0.87 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-11_FTMSms2hcd 132.050 5 63651 17863 18284 22175 23695 20392 22087 66.0 3.2e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 679.3518 4 -1.2 EQADYCVSHMKPYVDGK TMT6plex-EQADYC(Carbamidomethyl)VSHMK(TMT6plex)PYVDGK(TMT6plex) Z20180606-03_FTMSms2hcd 115.833 2 46434 74487 65132 91415 73564 81503 68471 54.9 3.4e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7291 3 -0.26 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-12_FTMSms2hcd 131.333 2 51217 18316 16625 18341 16926 14829 19437 80.9 4.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1145.8897 3 -1.9 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-10_FTMSms2hcd 213.800 4 92127 0.1116 -26.34 2096 -118.2 -81.37 2421 55.6 4.8e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 613.3096 3 -0.064 HQAFEAELHANADR TMT6plex-HQAFEAELHANADR Z20180606-11_FTMSms2hcd 80.417 5 32755 40846 41771 43115 41922 35858 39455 60.8 5.5e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 984.5371 3 3.0 QETFDAGLQAFQQEGIANITALK TMT6plex-QETFDAGLQAFQQEGIANITALK(TMT6plex) Z20180606-07_FTMSms2hcd 196.283 1 85404 13361 13894 17213 15337 12147 14001 63.8 5.9e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1156.5576 3 2.2 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1163;Oxidation@1179 Z20180606-09_FTMSms2hcd 165.750 6 70062 3522 2514 3462 3657 2473 3195 59.9 6.1e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 706.8901 4 1.4 EAIVTSEELGQDLEHVEVLQK TMT6plex-EAIVTSEELGQDLEHVEVLQK(TMT6plex) Z20180606-12_FTMSms2hcd 161.817 7 65522 9310 10878 10768 9343 8329 8114 59.4 6.2e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7294 3 0.039 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-11_FTMSms2hcd 129.067 3 61950 129168 123658 167076 128464 139097 129680 79.5 7.0e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 650.9839 3 -1.2 FEEFQTDLAAHEER TMT6plex-FEEFQTDLAAHEER Z20180606-11_FTMSms2hcd 122.833 9 58411 65306 59406 66769 75289 53895 56106 60.3 8.1e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 726.7014 3 -0.20 GNAMVEEGHFAAEDVK TMT6plex-GNAM(Oxidation)VEEGHFAAEDVK(TMT6plex) Oxidation@850 Z20180606-10_FTMSms2hcd 103.033 5 39484 74538 66327 75109 75191 60940 69057 49.3 8.3e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1077.5056 3 0.40 RQDLEDSLQAQQYFADANEAESWMR TMT6plex-RQDLEDSLQAQQYFADANEAESWMR Z20180606-12_FTMSms2hcd 162.350 3 65765 9186 7492 9863 8548 10265 9995 69.3 8.4e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 817.0797 3 0.55 LDETGNLMISEGHFASETIR TMT6plex-LDETGNLMISEGHFASETIR Z20180606-04_FTMSms2hcd 149.317 2 62661 19753 17551 37157 63362 11638 102340 65.4 8.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1097.8874 3 -0.33 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)M(Oxidation)VEESGTLESQLEATK(TMT6plex)R Oxidation@2234 Z20180606-02_FTMSms2hcd 154.367 3 63939 18535 20117 26269 24782 19957 22457 67.9 9.3e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 640.0792 4 -0.23 NQALNTDNYGHDLASVQALQR TMT6plex-NQALNTDNYGHDLASVQALQR Z20180606-01_FTMSms2hcd 125.400 4 47389 12807 12774 14551 15281 12697 16294 58.9 9.9e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 863.6739 4 5.2 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=78 Z20180606-09_FTMSms2hcd 192.850 3 82445 -11.24 2652 2348 1289 1515 -40.29 54.1 9.9e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1145.8936 3 1.5 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-09_FTMSms2hcd 212.850 2 91491 1352 954.1 1930 1026 -97.57 1470 60.4 1.0e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1040.5240 3 1.5 TYLLDGSCMVEESGTLESQLEATK TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex) Z20180606-01_FTMSms2hcd 186.367 3 75058 13963 10762 14485 8991 13221 10914 69.2 1.0e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 853.1033 3 -0.081 NQALNTDNYGHDLASVQALQR TMT6plex-NQALNTDNYGHDLASVQALQR Z20180606-01_FTMSms2hcd 126.900 5 48081 9297 8152 10767 8223 8898 10206 65.5 1.1e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 723.8731 4 -1.2 SADESGQALLAASHYASDEVREK TMT6plex-SADESGQALLAASHYASDEVREK(TMT6plex) Z20180606-12_FTMSms2hcd 132.333 9 51705 41637 45788 41690 52230 49071 55075 75.9 1.2e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1092.5558 3 -0.35 TYLLDGSCMVEESGTLESQLEATKR TMT6plex-TYLLDGSC(Carbamidomethyl)MVEESGTLESQLEATK(TMT6plex)R Z20180606-03_FTMSms2hcd 171.617 3 72176 48096 44829 59058 51355 52614 55591 78.8 1.4e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1156.5561 3 0.90 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1163;Oxidation@1179 Z20180606-08_FTMSms2hcd 166.817 4 70934 1935 1922 3256 3692 3162 4431 62.5 1.4e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1156.5560 3 0.79 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1163;Oxidation@1179 Z20180606-09_FTMSms2hcd 166.633 5 70471 2853 1109 5593 2159 3263 2346 59.8 1.4e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 721.3697 3 -0.24 GNAMVEEGHFAAEDVK TMT6plex-GNAMVEEGHFAAEDVK(TMT6plex) Z20180606-11_FTMSms2hcd 111.933 2 51869 442644 344268 580856 476064 485703 467933 59.6 1.6e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1203.5902 2 -0.13 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-11_FTMSms2hcd 129.500 7 62206 16573 12783 21513 16301 19374 20353 60.3 1.6e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1045.8546 3 0.48 TYLLDGSCMVEESGTLESQLEATK TMT6plex-TYLLDGSC(Carbamidomethyl)M(Oxidation)VEESGTLESQLEATK(TMT6plex) Oxidation@2234 Z20180606-01_FTMSms2hcd 166.617 6 66117 6201 6941 9636 8051 8545 10155 61.2 1.6e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2234 3 -0.072 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=104 Z20180606-08_FTMSms2hcd 176.617 2 75409 2459 3466 3078 4580 3051 4470 76.4 1.7e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 935.7998 3 0.75 YTEHSTVGLAQQWDQLDQLGMR TMT6plex-YTEHSTVGLAQQWDQLDQLGMR Z20180606-03_FTMSms2hcd 157.433 5 65679 5972 3731 5337 4200 3611 5444 63.2 1.7e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1156.5598 3 4.1 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1163;Oxidation@1179 Z20180606-09_FTMSms2hcd 150.133 6 62824 2729 1846 2771 1940 2229 1449 56.7 1.7e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 618.3107 4 -0.11 QEFAQHANAFHQWIQETR TMT6plex-QEFAQHANAFHQWIQETR Z20180606-07_FTMSms2hcd 122.700 6 50401 261339 314666 287928 344389 284725 341280 75.3 1.7e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 863.6691 4 -0.41 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=100 Z20180606-09_FTMSms2hcd 176.100 1 74805 4256 9113 7752 7307 3149 5315 69.1 1.8e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1156.5546 3 -0.47 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1163;Oxidation@1179 Z20180606-08_FTMSms2hcd 166.017 1 70562 2282 2904 3264 2619 4177 3279 64.3 1.8e-13 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 897.4631 3 -0.29 SLPMQIDGEPWMQTPCTIK TMT6plex-SLPMQIDGEPWMQTPC(Carbamidomethyl)TIK(TMT6plex) Z20180606-06_FTMSms2hcd 177.250 6 77179 30556 25329 36435 25681 30169 32793 59.1 5.8e-14 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 700.0502 3 -0.27 SSPANTCSPEVIHLK TMT6plex-SSPANTC(Carbamidomethyl)SPEVIHLK(TMT6plex) Z20180606-03_FTMSms2hcd 110.750 5 44071 65328 53024 74512 59279 55524 66125 56.9 5.6e-13 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 1039.5507 3 1.7 DHILPPTTICPVVLTMPSAGASVPEER TMT6plex-DHILPPTTIC(Carbamidomethyl)PVVLTMPSAGASVPEER Z20180606-05_FTMSms2hcd 166.400 5 70790 4484 3381 4392 2651 3069 3295 54.1 9.8e-13 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 902.7957 3 0.76 SLPMQIDGEPWMQTPCTIK TMT6plex-SLPMQIDGEPWM(Oxidation)QTPC(Carbamidomethyl)TIK(TMT6plex) Oxidation@762=63 Z20180606-06_FTMSms2hcd 165.650 5 71847 14505 12364 15130 14534 15454 17056 55.8 1.6e-12 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 809.4026 2 1.8 QGLCCSFCK TMT6plex-QGLC(Carbamidomethyl)C(Carbamidomethyl)SFC(Carbamidomethyl)K(TMT6plex) Z20180606-08_FTMSms2hcd 111.783 1 44689 95483 89353 128521 98056 85049 104589 35.3 3.7e-11 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 1063.5811 2 0.67 QDILNQTIDFEGFK TMT6plex-QDILNQTIDFEGFK(TMT6plex) Z20180606-05_FTMSms2hcd 178.333 2 76259 35830 34670 49325 43464 45100 49575 58.9 3.2e-10 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 902.7955 3 0.55 SLPMQIDGEPWMQTPCTIK TMT6plex-SLPMQIDGEPWM(Oxidation)QTPC(Carbamidomethyl)TIK(TMT6plex) Oxidation@762=45 Z20180606-05_FTMSms2hcd 164.933 6 70118 8229 7822 13503 12157 11249 11080 52.8 3.3e-9 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 600.3116 3 0.20 WGGGYEGENLMK TMT6plex-WGGGYEGENLMK(TMT6plex) Z20180606-04_FTMSms2hcd 138.050 4 57335 123151 98105 154558 114114 105281 137472 39.8 5.4e-9 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 637.3135 4 0.10 NTDVMHHYWVEGNCPTK TMT6plex-NTDVMHHYWVEGNC(Carbamidomethyl)PTK(TMT6plex) Z20180606-03_FTMSms2hcd 111.483 1 44411 25715 25052 35943 24711 32446 31171 43.1 1.4e-8 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 819.4163 2 -0.0030 DIESSTEIMLDR TMT6plex-DIESSTEIMLDR Z20180606-10_FTMSms2hcd 139.750 7 57871 86175 72498 103458 77897 68510 78627 47.2 3.2e-8 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 709.3906 3 1.8 QDILNQTIDFEGFK TMT6plex-QDILNQTIDFEGFK(TMT6plex) Z20180606-05_FTMSms2hcd 178.233 6 76216 59681 60937 81080 53598 64320 68079 44.7 5.7e-8 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 657.3842 3 -0.18 HPPVAILPLGTGNDLAR TMT6plex-HPPVAILPLGTGNDLAR Z20180606-08_FTMSms2hcd 135.733 3 56367 12665 13581 16917 10973 7587 18806 50.4 3.0e-7 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 741.0906 3 2.7 ILKDIESSTEIMLDR TMT6plex-ILK(TMT6plex)DIESSTEIMLDR Z20180606-05_FTMSms2hcd 179.733 7 76897 11645 15196 19474 15814 19126 21208 30.3 6.2e-7 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 681.3919 2 -0.51 LAQCSSVVIR TMT6plex-LAQC(Carbamidomethyl)SSVVIR Z20180606-08_FTMSms2hcd 107.667 2 42677 169230 155667 195401 181479 163101 199154 34.7 7.5e-7 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 673.3498 4 0.63 SLPMQIDGEPWMQTPCTIK TMT6plex-SLPMQIDGEPWMQTPC(Carbamidomethyl)TIK(TMT6plex) Z20180606-06_FTMSms2hcd 177.417 5 77252 6807 6477 6491 10069 6389 7822 32.8 1.2e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 546.6133 3 0.060 DIESSTEIMLDR TMT6plex-DIESSTEIMLDR Z20180606-10_FTMSms2hcd 139.917 4 57947 7860 8355 9418 8931 6691 8421 32.1 1.6e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 805.4448 2 0.092 DIVCYLSLLER TMT6plex-DIVC(Carbamidomethyl)YLSLLER Z20180606-09_FTMSms2hcd 192.667 1 82360 37063 32420 50419 34120 39668 42109 40.2 1.7e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 660.3659 2 -0.15 YAEYSTK TMT6plex-YAEYSTK(TMT6plex) Z20180606-03_FTMSms2hcd 94.267 2 36236 201913 199496 259596 227527 227203 245297 24.7 2.6e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 496.5276 4 0.074 GRPEDKLEFMFR TMT6plex-GRPEDK(TMT6plex)LEFMFR Z20180606-08_FTMSms2hcd 130.683 1 53974 33401 27558 39045 28675 33019 31281 30.4 2.9e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 539.9366 3 0.016 QGLCCSFCK TMT6plex-QGLC(Carbamidomethyl)C(Carbamidomethyl)SFC(Carbamidomethyl)K(TMT6plex) Z20180606-08_FTMSms2hcd 111.750 3 44675 36685 28080 41395 31342 25779 29508 29.0 5.4e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 537.2993 3 0.81 DIVCYLSLLER TMT6plex-DIVC(Carbamidomethyl)YLSLLER Z20180606-09_FTMSms2hcd 192.750 4 82401 1431 -112.4 1797 2305 -179.3 2232 30.8 8.1e-6 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 494.7992 4 0.29 GSDKRPTLTDAK TMT6plex-GSDK(TMT6plex)RPTLTDAK(TMT6plex) Z20180606-06_FTMSms2hcd 83.217 3 32287 102499 96299 127058 105268 110667 119409 24.5 3.9e-5 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 536.2966 2 0.12 LEFMFR TMT6plex-LEFMFR Z20180606-11_FTMSms2hcd 152.850 7 75213 90595 57583 100001 62687 57489 65730 24.0 5.0e-5 2 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 489.2660 2 -0.67 DVPDFR TMT6plex-DVPDFR Z20180606-12_FTMSms2hcd 103.667 3 37662 75058 69123 91346 75810 66094 80694 16.4 5.2e-5 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 414.5456 3 -0.19 DDGQHVWR TMT6plex-DDGQHVWR Z20180606-10_FTMSms2hcd 72.650 5 24138 127316 87173 140839 93095 93943 108463 28.2 5.6e-5 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 660.3656 2 -0.62 YAEYSTK TMT6plex-YAEYSTK(TMT6plex) Z20180606-04_FTMSms2hcd 93.033 4 35567 171782 160086 206216 171521 168409 191802 21.8 2.0e-4 1 90272.8 MOUSE Diacylglycerol kinase beta +[1010] Q6NS52 Dgkb 19 26.3 7.87 5.8e-14 899.9650 2 1.6 WGGGYEGENLMK TMT6plex-WGGGYEGENLMK(TMT6plex) Z20180606-04_FTMSms2hcd 138.317 4 57458 15931 18498 20685 18930 12392 17782 18.1 3.1e-4 1 90272.8 MOUSE Diacylglycerol kinase beta +[4818] Q9WV30 Nfat5 4 2.9 3.82 1.0e-7 479.2788 3 -0.064 IVVQPETQHR TMT6plex-IVVQPETQHR Z20180606-04_FTMSms2hcd 80.417 8 29382 43518 49149 63325 59733 62849 66898 22.0 7.8e-5 1 165801.8 MOUSE Nuclear factor of activated T-cells 5 +[4819] Q60778 Nfkbib 2 12.5 9.13 2.7e-16 1076.2278 4 0.99 DASDTYLTQSQDCTPDTSHAPAAVDSQPNPENEEEPR TMT6plex-DASDTYLTQSQDC(Carbamidomethyl)TPDTSHAPAAVDSQPNPENEEEPR Z20180606-06_FTMSms2hcd 118.250 3 49417 1195 -92.62 1751 -149.9 1792 1841 69.6 2.7e-16 1 37965.3 MOUSE NF-kappa-B inhibitor beta +[791-2] 7 P45591 Cfl2 12 56.6 9.35 1.0e-16 694.4319 2 0.29 QIIVEEAK TMT6plex-QIIVEEAK(TMT6plex) Z20180606-02_FTMSms2hcd 114.650 1 45589 397149 391438 457870 394444 392321 391704 32.2 6.5e-4 1 18709.7 MOUSE Cofilin-2 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 786.3745 3 0.78 APDAWDYSQGFVNEEMIR TMT6plex-APDAWDYSQGFVNEEMIR Z20180606-01_FTMSms2hcd 170.167 7 67726 4556 4058 5983 4357 15606 4101 58.6 1.0e-15 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 854.7985 3 -0.28 IDGNLVIRPYTPVSSDDDK TMT6plex-IDGNLVIRPYTPVSSDDDK(TMT6plex) Z20180606-04_FTMSms2hcd 141.650 4 59038 156331 114585 144215 136545 125707 114838 71.1 1.7e-13 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 796.1301 3 0.44 STPAITLENPDIKYPLR TMT6plex-STPAITLENPDIK(TMT6plex)YPLR Z20180606-06_FTMSms2hcd 144.950 3 62231 110116 61744 103338 92655 84067 88576 75.8 1.3e-12 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 947.7292 4 1.8 DHLPTPGEEPLILMCGPPPMIQFACLPNLER TMT6plex-DHLPTPGEEPLILM(Oxidation)C(Carbamidomethyl)GPPPMIQFAC(Carbamidomethyl)LPNLER Oxidation@273=32 Z20180606-04_FTMSms2hcd 196.000 3 84073 4678 5114 5142 4154 2985 3170 47.5 1.7e-11 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 716.0692 3 0.16 SVGMIAGGTGITPMLQVIR TMT6plex-SVGM(Oxidation)IAGGTGITPMLQVIR Oxidation@177=99 Z20180606-11_FTMSms2hcd 165.950 6 81958 19730 15178 25324 20341 15477 18470 67.9 2.6e-11 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 716.0691 3 0.079 SVGMIAGGTGITPMLQVIR TMT6plex-SVGM(Oxidation)IAGGTGITPMLQVIR Oxidation@177=91 Z20180606-11_FTMSms2hcd 166.533 4 82247 11855 15751 19125 19833 16982 18978 68.8 2.6e-11 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 854.7982 3 -0.63 IDGNLVIRPYTPVSSDDDK TMT6plex-IDGNLVIRPYTPVSSDDDK(TMT6plex) Z20180606-04_FTMSms2hcd 144.317 7 60300 61286 47561 65299 57778 48782 51872 50.5 4.4e-11 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 877.6890 4 1.3 LWYTVDKAPDAWDYSQGFVNEEMIR TMT6plex-LWYTVDK(TMT6plex)APDAWDYSQGFVNEEM(Oxidation)IR Oxidation@257 Z20180606-06_FTMSms2hcd 181.850 7 79274 3951 4348 5596 4875 4991 5230 44.8 1.1e-10 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 1179.0588 2 1.5 APDAWDYSQGFVNEEMIR TMT6plex-APDAWDYSQGFVNEEMIR Z20180606-01_FTMSms2hcd 170.250 8 67764 7861 4463 6274 7005 4565 5753 43.4 2.8e-10 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 597.3488 4 -0.49 STPAITLENPDIKYPLR TMT6plex-STPAITLENPDIK(TMT6plex)YPLR Z20180606-06_FTMSms2hcd 145.000 5 62257 30588 19488 25335 21228 20312 21478 49.5 3.1e-10 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 801.4274 2 2.7 MSQYLENMK TMT6plex-MSQYLENMK(TMT6plex) Z20180606-07_FTMSms2hcd 136.283 8 57229 274369 260641 333608 292828 283466 292923 37.3 9.1e-10 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 809.4226 2 -0.079 MSQYLENMK TMT6plex-M(Oxidation)SQYLENMK(TMT6plex) Oxidation@127=93 Z20180606-04_FTMSms2hcd 111.783 4 44801 78794 64385 85546 91294 122657 98309 35.3 1.1e-9 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 913.0150 4 -2.0 IDGNLVIRPYTPVSSDDDKGFVDLVVK TMT6plex-IDGNLVIRPYTPVSSDDDK(TMT6plex)GFVDLVVK(TMT6plex) Z20180606-06_FTMSms2hcd 176.000 8 76608 17042 15018 19853 18954 19135 20350 42.8 1.4e-9 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 716.0692 3 0.16 SVGMIAGGTGITPMLQVIR TMT6plex-SVGMIAGGTGITPM(Oxidation)LQVIR Oxidation@187=78 Z20180606-11_FTMSms2hcd 158.833 8 78363 21599 20871 29493 26153 21770 23449 53.6 5.2e-9 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 575.6753 3 0.30 DILLRPELEELR TMT6plex-DILLRPELEELR Z20180606-03_FTMSms2hcd 144.617 7 59799 11292 7091 12628 11838 12432 10203 37.9 1.1e-8 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 716.0701 3 1.5 SVGMIAGGTGITPMLQVIR TMT6plex-SVGM(Oxidation)IAGGTGITPMLQVIR Oxidation@177=87 Z20180606-12_FTMSms2hcd 167.450 7 68104 10030 8339 12222 13637 7451 10594 47.2 1.3e-8 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 619.6960 3 0.12 STPAITLENPDIK TMT6plex-STPAITLENPDIK(TMT6plex) Z20180606-02_FTMSms2hcd 137.800 2 56299 45615 21317 31804 26127 22500 24651 33.9 3.8e-8 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 721.4000 3 -0.90 SVGMIAGGTGITPMLQVIR TMT6plex-SVGM(Oxidation)IAGGTGITPM(Oxidation)LQVIR Oxidation@177;Oxidation@187 Z20180606-09_FTMSms2hcd 149.800 6 62670 13666 13986 15069 15707 14391 17117 47.0 1.3e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 929.0393 2 -1.1 STPAITLENPDIK TMT6plex-STPAITLENPDIK(TMT6plex) Z20180606-02_FTMSms2hcd 137.917 4 56354 27268 16975 26186 16114 14777 17144 32.8 2.0e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 615.3682 3 0.43 LIDKEVISPDTR TMT6plex-LIDK(TMT6plex)EVISPDTR Z20180606-05_FTMSms2hcd 123.333 1 50522 353271 359141 410776 441094 456423 454753 37.8 2.1e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 801.4251 2 -0.13 MSQYLENMK TMT6plex-MSQYLENMK(TMT6plex) Z20180606-08_FTMSms2hcd 136.350 7 56662 43909 39041 53972 56203 44154 47325 29.4 2.5e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 667.9264 2 0.53 GFVDLVVK TMT6plex-GFVDLVVK(TMT6plex) Z20180606-09_FTMSms2hcd 153.867 6 64570 199082 142694 189549 177034 142824 146929 32.2 3.5e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 500.8032 4 0.36 LIDKEVISPDTRR TMT6plex-LIDK(TMT6plex)EVISPDTRR Z20180606-07_FTMSms2hcd 110.183 1 44076 54026 88645 84440 115526 115833 121097 32.5 4.5e-7 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 545.2823 3 -0.30 MSQYLENMK TMT6plex-M(Oxidation)SQYLENM(Oxidation)K(TMT6plex) Oxidation@127;Oxidation@134 Z20180606-02_FTMSms2hcd 95.183 7 36513 17422 14461 19527 20570 18280 20299 23.7 8.6e-6 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 590.3323 2 0.25 IGDTIEFR TMT6plex-IGDTIEFR Z20180606-02_FTMSms2hcd 128.317 2 51937 217046 180073 218970 219230 189245 208423 31.9 1.0e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 575.6746 3 -0.97 DILLRPELEELR TMT6plex-DILLRPELEELR Z20180606-02_FTMSms2hcd 146.067 7 60132 103119 82124 115322 114894 102774 107063 38.6 1.3e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 863.0081 2 -1.1 DILLRPELEELR TMT6plex-DILLRPELEELR Z20180606-02_FTMSms2hcd 146.217 2 60197 14490 12342 14130 17157 13235 13156 26.9 1.4e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 450.7770 2 0.41 SNPVVR TMT6plex-SNPVVR Z20180606-03_FTMSms2hcd 64.567 7 22193 503037 440529 538371 605475 499790 563186 23.8 3.8e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 691.9078 2 -0.091 LWYTVDK TMT6plex-LWYTVDK(TMT6plex) Z20180606-10_FTMSms2hcd 145.867 2 60871 230262 120946 202121 140565 126462 131735 24.8 4.4e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 573.3221 2 0.45 EVISPDTR TMT6plex-EVISPDTR Z20180606-11_FTMSms2hcd 84.283 3 34955 248198 203349 263747 245719 195150 214466 25.0 5.1e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 575.6754 3 0.53 DILLRPELEELR TMT6plex-DILLRPELEELR Z20180606-02_FTMSms2hcd 146.650 5 60399 4993 6525 6181 7392 5964 7704 26.2 5.4e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 575.6747 3 -0.76 DILLRPELEELR TMT6plex-DILLRPELEELR Z20180606-01_FTMSms2hcd 148.817 4 58064 7441 8731 7735 11861 4991 5549 28.7 7.2e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 854.7997 3 1.2 IDGNLVIRPYTPVSSDDDK TMT6plex-IDGNLVIRPYTPVSSDDDK(TMT6plex) Z20180606-05_FTMSms2hcd 142.217 7 59460 33844 33879 34046 38742 37583 38234 21.8 8.9e-5 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 +[792] Q9DCN2 Cyb5r3 21 55.5 8.82 1.0e-15 721.4003 3 -0.56 SVGMIAGGTGITPMLQVIR TMT6plex-SVGM(Oxidation)IAGGTGITPM(Oxidation)LQVIR Oxidation@177;Oxidation@187 Z20180606-09_FTMSms2hcd 150.433 4 62963 16690 20374 23680 21842 16630 21236 21.4 1.1e-4 1 34128.0 MOUSE NADH-cytochrome b5 reductase 3 diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd index d74ccba2..74591b17 100644 --- a/man/MSstatsClean.Rd +++ b/man/MSstatsClean.Rd @@ -14,6 +14,7 @@ \alias{MSstatsClean,MSstatsPhilosopherFiles-method} \alias{MSstatsClean,MSstatsDIANNFiles-method} \alias{MSstatsClean,MSstatsMetamorpheusFiles-method} +\alias{MSstatsClean,MSstatsProteinProspectorFiles-method} \title{Clean files generated by a signal processing tools.} \usage{ MSstatsClean(msstats_object, ...) @@ -64,6 +65,8 @@ MSstatsClean(msstats_object, ...) ) \S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object) + +\S4method{MSstatsClean}{MSstatsProteinProspectorFiles}(msstats_object) } \arguments{ \item{msstats_object}{object that inherits from \code{MSstatsInputFiles} class.} @@ -138,6 +141,8 @@ data.table data.table +data.table + data.table } \description{ @@ -166,6 +171,8 @@ Clean Philosopher files Clean DIA-NN files Clean Metamorpheus files + +Clean Protein Prospector files } \examples{ evidence_path = system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", diff --git a/man/MSstatsInputFiles.Rd b/man/MSstatsInputFiles.Rd index d849567b..e09fff8d 100644 --- a/man/MSstatsInputFiles.Rd +++ b/man/MSstatsInputFiles.Rd @@ -16,6 +16,7 @@ \alias{MSstatsDIANNFiles-class} \alias{MSstatsFragPipeFiles-class} \alias{MSstatsMetamorpheusFiles-class} +\alias{MSstatsProteinProspectorFiles-class} \title{Class to model files that describe a single MS dataset.} \description{ Class to model files that describe a single MS dataset. @@ -45,6 +46,8 @@ MSstatsDIANNFiles: class for DIA-NN files. MSstatsFragPipeFiles: class for FragPipe files. MSstatsMetamorpheusFiles: class for Metamorpheus files. + +MSstatsProteinProspectorFiles: class for ProteinProspector files. } \section{Slots}{ diff --git a/man/ProteinProspectortoMSstatsTMTFormat.Rd b/man/ProteinProspectortoMSstatsTMTFormat.Rd new file mode 100644 index 00000000..927cced9 --- /dev/null +++ b/man/ProteinProspectortoMSstatsTMTFormat.Rd @@ -0,0 +1,67 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in +% R/converters_ProteinProspectortoMSstatsTMTFormat.R +\name{ProteinProspectortoMSstatsTMTFormat} +\alias{ProteinProspectortoMSstatsTMTFormat} +\title{Generate MSstatsTMT required input format from Protein Prospector output} +\usage{ +ProteinProspectortoMSstatsTMTFormat( + input, + annotation, + useUniquePeptide = TRUE, + removeFewMeasurements = TRUE, + removeProtein_with1Feature = FALSE, + summaryforMultipleRows = sum, + use_log_file = TRUE, + append = FALSE, + verbose = TRUE, + log_file_path = NULL +) +} +\arguments{ +\item{input}{txt report file from Protein Prospector with +\verb{Keep Replicates} option selected.} + +\item{annotation}{data frame which contains column Run, Fraction, +TechRepMixture, Mixture, Channel, BioReplicate, Condition.} + +\item{useUniquePeptide}{TRUE (default) removes peptides that are assigned for more than one proteins. +We assume to use unique peptide for each protein.} + +\item{removeFewMeasurements}{TRUE (default) will remove the features that have 1 or 2 measurements across runs.} + +\item{removeProtein_with1Feature}{TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.} + +\item{summaryforMultipleRows}{max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.} + +\item{use_log_file}{logical. If TRUE, information about data processing +will be saved to a file.} + +\item{append}{logical. If TRUE, information about data processing will be added +to an existing log file.} + +\item{verbose}{logical. If TRUE, information about data processing wil be printed +to the console.} + +\item{log_file_path}{character. Path to a file to which information about +data processing will be saved. +If not provided, such a file will be created automatically. +If \code{append = TRUE}, has to be a valid path to a file.} +} +\value{ +data.frame of class "MSstatsTMT" +} +\description{ +Generate MSstatsTMT required input format from Protein Prospector output +} +\examples{ +input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", + package = "MSstatsConvert") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsConvert") +annot = data.table::fread(annot) +output <- ProteinProspectortoMSstatsTMTFormat(input, annot) +head(output) + +} From f1f04fb5be655aaf6c9f91298610537494950d0b Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 29 Jul 2024 14:44:00 -0400 Subject: [PATCH 2/7] modify parameter description and annotation file --- ...ters_ProteinProspectortoMSstatsTMTFormat.R | 4 +- .../raw_data/ProteinProspector/Annotation.csv | 144 +++++++++--------- 2 files changed, 74 insertions(+), 74 deletions(-) diff --git a/R/converters_ProteinProspectortoMSstatsTMTFormat.R b/R/converters_ProteinProspectortoMSstatsTMTFormat.R index 12d6a438..ae372fc0 100644 --- a/R/converters_ProteinProspectortoMSstatsTMTFormat.R +++ b/R/converters_ProteinProspectortoMSstatsTMTFormat.R @@ -1,8 +1,8 @@ #' Generate MSstatsTMT required input format from Protein Prospector output #' #' @inheritParams .sharedParametersAmongConverters -#' @param input txt report file from Protein Prospector with -#' `Keep Replicates` option selected. +#' @param input Input txt peptide report file from Protein Prospector with +#' "Keep Replicates", "Mods in Peptide", and "Protein Mods" options selected. #' @param annotation data frame which contains column Run, Fraction, #' TechRepMixture, Mixture, Channel, BioReplicate, Condition. #' diff --git a/inst/tinytest/raw_data/ProteinProspector/Annotation.csv b/inst/tinytest/raw_data/ProteinProspector/Annotation.csv index 1f95da55..1a609184 100644 --- a/inst/tinytest/raw_data/ProteinProspector/Annotation.csv +++ b/inst/tinytest/raw_data/ProteinProspector/Annotation.csv @@ -1,73 +1,73 @@ Run,Fraction,TechRepMixture,Channel,Condition,Mixture,BioReplicate -Z20180606-01_FTMSms2hcd,1,1,Int 126,Control,Mixture1,S1 -Z20180606-02_FTMSms2hcd,2,1,Int 126,Control,Mixture1,S1 -Z20180606-03_FTMSms2hcd,3,1,Int 126,Control,Mixture1,S1 -Z20180606-04_FTMSms2hcd,4,1,Int 126,Control,Mixture1,S1 -Z20180606-05_FTMSms2hcd,5,1,Int 126,Control,Mixture1,S1 -Z20180606-06_FTMSms2hcd,6,1,Int 126,Control,Mixture1,S1 -Z20180606-07_FTMSms2hcd,7,1,Int 126,Control,Mixture1,S1 -Z20180606-08_FTMSms2hcd,8,1,Int 126,Control,Mixture1,S1 -Z20180606-09_FTMSms2hcd,9,1,Int 126,Control,Mixture1,S1 -Z20180606-10_FTMSms2hcd,10,1,Int 126,Control,Mixture1,S1 -Z20180606-11_FTMSms2hcd,11,1,Int 126,Control,Mixture1,S1 -Z20180606-12_FTMSms2hcd,12,1,Int 126,Control,Mixture1,S1 -Z20180606-01_FTMSms2hcd,1,1,Int 127,Control,Mixture1,S2 -Z20180606-02_FTMSms2hcd,2,1,Int 127,Control,Mixture1,S2 -Z20180606-03_FTMSms2hcd,3,1,Int 127,Control,Mixture1,S2 -Z20180606-04_FTMSms2hcd,4,1,Int 127,Control,Mixture1,S2 -Z20180606-05_FTMSms2hcd,5,1,Int 127,Control,Mixture1,S2 -Z20180606-06_FTMSms2hcd,6,1,Int 127,Control,Mixture1,S2 -Z20180606-07_FTMSms2hcd,7,1,Int 127,Control,Mixture1,S2 -Z20180606-08_FTMSms2hcd,8,1,Int 127,Control,Mixture1,S2 -Z20180606-09_FTMSms2hcd,9,1,Int 127,Control,Mixture1,S2 -Z20180606-10_FTMSms2hcd,10,1,Int 127,Control,Mixture1,S2 -Z20180606-11_FTMSms2hcd,11,1,Int 127,Control,Mixture1,S2 -Z20180606-12_FTMSms2hcd,12,1,Int 127,Control,Mixture1,S2 -Z20180606-01_FTMSms2hcd,1,1,Int 128,Control,Mixture1,S3 -Z20180606-02_FTMSms2hcd,2,1,Int 128,Control,Mixture1,S3 -Z20180606-03_FTMSms2hcd,3,1,Int 128,Control,Mixture1,S3 -Z20180606-04_FTMSms2hcd,4,1,Int 128,Control,Mixture1,S3 -Z20180606-05_FTMSms2hcd,5,1,Int 128,Control,Mixture1,S3 -Z20180606-06_FTMSms2hcd,6,1,Int 128,Control,Mixture1,S3 -Z20180606-07_FTMSms2hcd,7,1,Int 128,Control,Mixture1,S3 -Z20180606-08_FTMSms2hcd,8,1,Int 128,Control,Mixture1,S3 -Z20180606-09_FTMSms2hcd,9,1,Int 128,Control,Mixture1,S3 -Z20180606-10_FTMSms2hcd,10,1,Int 128,Control,Mixture1,S3 -Z20180606-11_FTMSms2hcd,11,1,Int 128,Control,Mixture1,S3 -Z20180606-12_FTMSms2hcd,12,1,Int 128,Control,Mixture1,S3 -Z20180606-01_FTMSms2hcd,1,1,Int 129,Disease,Mixture1,S4 -Z20180606-02_FTMSms2hcd,2,1,Int 129,Disease,Mixture1,S4 -Z20180606-03_FTMSms2hcd,3,1,Int 129,Disease,Mixture1,S4 -Z20180606-04_FTMSms2hcd,4,1,Int 129,Disease,Mixture1,S4 -Z20180606-05_FTMSms2hcd,5,1,Int 129,Disease,Mixture1,S4 -Z20180606-06_FTMSms2hcd,6,1,Int 129,Disease,Mixture1,S4 -Z20180606-07_FTMSms2hcd,7,1,Int 129,Disease,Mixture1,S4 -Z20180606-08_FTMSms2hcd,8,1,Int 129,Disease,Mixture1,S4 -Z20180606-09_FTMSms2hcd,9,1,Int 129,Disease,Mixture1,S4 -Z20180606-10_FTMSms2hcd,10,1,Int 129,Disease,Mixture1,S4 -Z20180606-11_FTMSms2hcd,11,1,Int 129,Disease,Mixture1,S4 -Z20180606-12_FTMSms2hcd,12,1,Int 129,Disease,Mixture1,S4 -Z20180606-01_FTMSms2hcd,1,1,Int 130,Disease,Mixture1,S5 -Z20180606-02_FTMSms2hcd,2,1,Int 130,Disease,Mixture1,S5 -Z20180606-03_FTMSms2hcd,3,1,Int 130,Disease,Mixture1,S5 -Z20180606-04_FTMSms2hcd,4,1,Int 130,Disease,Mixture1,S5 -Z20180606-05_FTMSms2hcd,5,1,Int 130,Disease,Mixture1,S5 -Z20180606-06_FTMSms2hcd,6,1,Int 130,Disease,Mixture1,S5 -Z20180606-07_FTMSms2hcd,7,1,Int 130,Disease,Mixture1,S5 -Z20180606-08_FTMSms2hcd,8,1,Int 130,Disease,Mixture1,S5 -Z20180606-09_FTMSms2hcd,9,1,Int 130,Disease,Mixture1,S5 -Z20180606-10_FTMSms2hcd,10,1,Int 130,Disease,Mixture1,S5 -Z20180606-11_FTMSms2hcd,11,1,Int 130,Disease,Mixture1,S5 -Z20180606-12_FTMSms2hcd,12,1,Int 130,Disease,Mixture1,S5 -Z20180606-01_FTMSms2hcd,1,1,Int 131,Disease,Mixture1,S6 -Z20180606-02_FTMSms2hcd,2,1,Int 131,Disease,Mixture1,S6 -Z20180606-03_FTMSms2hcd,3,1,Int 131,Disease,Mixture1,S6 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+Z20180606-03_FTMSms2hcd,3,1,Int 131,Aged,Mixture1,S6 +Z20180606-04_FTMSms2hcd,4,1,Int 131,Aged,Mixture1,S6 +Z20180606-05_FTMSms2hcd,5,1,Int 131,Aged,Mixture1,S6 +Z20180606-06_FTMSms2hcd,6,1,Int 131,Aged,Mixture1,S6 +Z20180606-07_FTMSms2hcd,7,1,Int 131,Aged,Mixture1,S6 +Z20180606-08_FTMSms2hcd,8,1,Int 131,Aged,Mixture1,S6 +Z20180606-09_FTMSms2hcd,9,1,Int 131,Aged,Mixture1,S6 +Z20180606-10_FTMSms2hcd,10,1,Int 131,Aged,Mixture1,S6 +Z20180606-11_FTMSms2hcd,11,1,Int 131,Aged,Mixture1,S6 +Z20180606-12_FTMSms2hcd,12,1,Int 131,Aged,Mixture1,S6 \ No newline at end of file From 5c40362a40fbed308169819626070eb28c12e9ae Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 5 Aug 2024 14:27:00 -0400 Subject: [PATCH 3/7] remove zero to NA conversion in the clean function --- R/clean_ProteinProspector.R | 5 ----- 1 file changed, 5 deletions(-) diff --git a/R/clean_ProteinProspector.R b/R/clean_ProteinProspector.R index 7dbf8e4b..391573d2 100644 --- a/R/clean_ProteinProspector.R +++ b/R/clean_ProteinProspector.R @@ -34,11 +34,6 @@ protein_prospector_input$Channel = .standardizeColnames( protein_prospector_input$Channel ) - protein_prospector_input$Intensity = ifelse( - protein_prospector_input$Intensity == 0, - NA, - protein_prospector_input$Intensity - ) .logSuccess("ProteinProspector", "clean") protein_prospector_input From 14e7bd9d64f8c6072d5c01805bff24f302080dde Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 5 Aug 2024 14:52:16 -0400 Subject: [PATCH 4/7] add initial unit tests for protein prospector --- ...MSstatsProteinProspectorFilesObjectTMT.rds | Bin 0 -> 12121 bytes inst/tinytest/test_clean_ProteinProspector.R | 23 ++++++++++++++++++ ...ters_ProteinProspectortoMSstatsTMTFormat.R | 21 ++++++++++++++++ 3 files changed, 44 insertions(+) create mode 100644 inst/tinytest/processed_data/ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds create mode 100644 inst/tinytest/test_clean_ProteinProspector.R create mode 100644 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a/inst/tinytest/test_clean_ProteinProspector.R b/inst/tinytest/test_clean_ProteinProspector.R new file mode 100644 index 00000000..948e23a2 --- /dev/null +++ b/inst/tinytest/test_clean_ProteinProspector.R @@ -0,0 +1,23 @@ +.testHappyPath = function(input) { + output = MSstatsConvert:::.cleanRawProteinProspector(input) + expect_equal(ncol(output), 7) + expect_equal(nrow(output), 966) + expected_column_names = c( + "ProteinName", + "PeptideSequence", + "PrecursorCharge", + "Run", + "PSM", + "Channel", + "Intensity" + ) + missing_columns = setdiff(expected_column_names, colnames(output)) + expect_equal(length(missing_columns), 0) +} + +# Test PD .cleanRawPDTMT --------------------------- + +file_path = system.file("tinytest/processed_data/ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds", package="MSstatsConvert") +input = readRDS(file_path) +.testHappyPath(input) + diff --git a/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R new file mode 100644 index 00000000..8f2875b1 --- /dev/null +++ b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R @@ -0,0 +1,21 @@ +# Test ProteinProspectortoMSstatsTMTFormat --------------------------- +input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", + package = "MSstatsConvert") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsConvert") +annot = data.table::fread(annot) +output = ProteinProspectortoMSstatsTMTFormat(input, annot) +expect_equal(ncol(output), 11) +expect_equal(nrow(output), 528) +expect_true("Run" %in% colnames(output)) +expect_true("ProteinName" %in% colnames(output)) +expect_true("PeptideSequence" %in% colnames(output)) +expect_true("PrecursorCharge" %in% colnames(output)) +expect_true("Intensity" %in% colnames(output)) +expect_true("TechRepMixture" %in% colnames(output)) +expect_true("PSM" %in% colnames(output)) +expect_true("Mixture" %in% colnames(output)) +expect_true("Condition" %in% colnames(output)) +expect_true("BioReplicate" %in% colnames(output)) +expect_true("Channel" %in% colnames(output)) \ No newline at end of file From 69d3a4c8d110e5fd1edd18b6ccad6e960d6196e5 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 12 Aug 2024 14:13:43 -0400 Subject: [PATCH 5/7] fix column name: PrecursorCharge -> Charge --- R/converters_ProteinProspectortoMSstatsTMTFormat.R | 1 + .../test_converters_ProteinProspectortoMSstatsTMTFormat.R | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/R/converters_ProteinProspectortoMSstatsTMTFormat.R b/R/converters_ProteinProspectortoMSstatsTMTFormat.R index ae372fc0..bce44f7b 100644 --- a/R/converters_ProteinProspectortoMSstatsTMTFormat.R +++ b/R/converters_ProteinProspectortoMSstatsTMTFormat.R @@ -48,6 +48,7 @@ ProteinProspectortoMSstatsTMTFormat = function( ) input = MSstatsConvert::MSstatsBalancedDesign(input, feature_columns, fix_missing = "zero_to_na") + data.table::setnames(input, "PrecursorCharge", "Charge", skip_absent = TRUE) msg_final = paste("** Finished preprocessing. The dataset is ready", "to be processed by the proteinSummarization function.") diff --git a/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R index 8f2875b1..764ec5da 100644 --- a/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R +++ b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R @@ -11,7 +11,7 @@ expect_equal(nrow(output), 528) expect_true("Run" %in% colnames(output)) expect_true("ProteinName" %in% colnames(output)) expect_true("PeptideSequence" %in% colnames(output)) -expect_true("PrecursorCharge" %in% colnames(output)) +expect_true("Charge" %in% colnames(output)) expect_true("Intensity" %in% colnames(output)) expect_true("TechRepMixture" %in% colnames(output)) expect_true("PSM" %in% colnames(output)) From 3d51aad5835d5390851d74873b87b88e129c723d Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 12 Aug 2024 15:05:13 -0400 Subject: [PATCH 6/7] modified file paths and added unit tests for 0 value --- .../MSstatsProtProspectorFilesObjectTMT.rds} | Bin .../ProteinProspector/Prospector_TotalTMT.txt | 2 +- inst/tinytest/test_clean_ProteinProspector.R | 2 +- ...converters_ProteinProspectortoMSstatsTMTFormat.R | 8 +++++++- 4 files changed, 9 insertions(+), 3 deletions(-) rename inst/tinytest/processed_data/{ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds => ProtProspector/MSstatsProtProspectorFilesObjectTMT.rds} (100%) diff --git a/inst/tinytest/processed_data/ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds b/inst/tinytest/processed_data/ProtProspector/MSstatsProtProspectorFilesObjectTMT.rds similarity index 100% rename from inst/tinytest/processed_data/ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds rename to inst/tinytest/processed_data/ProtProspector/MSstatsProtProspectorFilesObjectTMT.rds diff --git a/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt b/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt index c129bba1..912c7201 100644 --- a/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt +++ b/inst/tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt @@ -61,7 +61,7 @@ Search Name: Z20180606_YvA_TotalRPLC/SW201948rc2mc2mm [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 859.6717 4 1.2 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLMAEEVQAVQQQEVYGAMPR Z20180606-10_FTMSms2hcd 193.917 5 83128 3401 2862 4007 5905 3350 3113 63.1 1.4e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1151.2245 3 0.88 VAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-VAEDLESEGLM(Oxidation)AEEVQAVQQQEVYGAMPR Oxidation@1163=118 Z20180606-09_FTMSms2hcd 177.550 4 75472 1786 1896 3445 3085 1896 2213 72.1 1.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1091.0525 2 -0.37 SSLSSAQADFNQLAELDR TMT6plex-SSLSSAQADFNQLAELDR Z20180606-01_FTMSms2hcd 158.583 6 62499 12705 10385 16191 13560 11680 14529 67.6 1.8e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 -[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1038.5217 4 -0.63 DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-DINK(TMT6plex)VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=122 Z20180606-11_FTMSms2hcd 188.333 4 92786 7876 7542 8204 10578 9828 11855 65.4 2.6e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[1] P16546 Sptan1 272 77.3 10.57 5.7e-19 1038.5217 4 -0.63 DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR TMT6plex-DINK(TMT6plex)VAEDLESEGLMAEEVQAVQQQEVYGAM(Oxidation)PR Oxidation@1179=122 Z20180606-11_FTMSms2hcd 188.333 4 92786 0 7542 8204 10578 9828 11855 65.4 2.6e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 839.4818 3 1.3 IAALQAFADQLIAVDHYAK TMT6plex-IAALQAFADQLIAVDHYAK(TMT6plex) Z20180606-12_FTMSms2hcd 206.150 3 85642 26874 26781 34611 25013 34561 31381 88.3 2.6e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 802.7302 3 1.0 SADESGQALLAASHYASDEVR TMT6plex-SADESGQALLAASHYASDEVR Z20180606-10_FTMSms2hcd 116.300 4 46352 48578 47944 52354 59709 60174 60190 71.0 2.7e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 [1] P16546 Sptan1 272 77.3 10.57 5.7e-19 984.5354 3 1.3 QETFDAGLQAFQQEGIANITALK TMT6plex-QETFDAGLQAFQQEGIANITALK(TMT6plex) Z20180606-06_FTMSms2hcd 196.750 3 86053 29667 21042 28738 25489 24756 20230 68.2 3.0e-14 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 diff --git a/inst/tinytest/test_clean_ProteinProspector.R b/inst/tinytest/test_clean_ProteinProspector.R index 948e23a2..6c7f6af6 100644 --- a/inst/tinytest/test_clean_ProteinProspector.R +++ b/inst/tinytest/test_clean_ProteinProspector.R @@ -17,7 +17,7 @@ # Test PD .cleanRawPDTMT --------------------------- -file_path = system.file("tinytest/processed_data/ProteinProspector/MSstatsProteinProspectorFilesObjectTMT.rds", package="MSstatsConvert") +file_path = system.file("tinytest/processed_data/ProtProspector/MSstatsProtProspectorFilesObjectTMT.rds", package="MSstatsConvert") input = readRDS(file_path) .testHappyPath(input) diff --git a/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R index 764ec5da..0d0823ff 100644 --- a/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R +++ b/inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R @@ -18,4 +18,10 @@ expect_true("PSM" %in% colnames(output)) expect_true("Mixture" %in% colnames(output)) expect_true("Condition" %in% colnames(output)) expect_true("BioReplicate" %in% colnames(output)) -expect_true("Channel" %in% colnames(output)) \ No newline at end of file +expect_true("Channel" %in% colnames(output)) + +# Test ProteinProspectortoMSstatsTMTFormat with missing value ------------ +zero_value_entry = + output[output$PeptideSequence == "DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR" + & output$BioReplicate == "S1",]$Intensity +expect_true(is.na(zero_value_entry)) \ No newline at end of file From 4e8c3965d74e505dc03e35f9fe0e9cce8c8c29da Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 19 Aug 2024 10:55:02 -0400 Subject: [PATCH 7/7] modify code to add PSM column to use := --- R/clean_ProteinProspector.R | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/R/clean_ProteinProspector.R b/R/clean_ProteinProspector.R index 391573d2..b597822e 100644 --- a/R/clean_ProteinProspector.R +++ b/R/clean_ProteinProspector.R @@ -4,6 +4,7 @@ #' @keywords internal #' @noRd .cleanRawProteinProspector = function(msstats_object) { + PSM = PeptideSequence = PrecursorCharge = NULL protein_prospector_input = getInputFile(msstats_object, "input") protein_prospector_input = data.table::as.data.table(protein_prospector_input) @@ -16,11 +17,8 @@ c("AccX", "DBPeptide", "z", "Fraction"), c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run"), skip_absent = TRUE) - protein_prospector_input$PSM = paste( - protein_prospector_input$PeptideSequence, - protein_prospector_input$PrecursorCharge, - 1:nrow(protein_prospector_input), sep = "_" - ) + protein_prospector_input[, PSM := paste(PeptideSequence, PrecursorCharge, + 1:nrow(protein_prospector_input), sep = "_")] protein_prospector_input = melt(protein_prospector_input, measure.vars = channels,