From d29ad06255cd751a64a1a2f1c93c76e3e094884d Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 16 Sep 2024 11:35:42 -0400 Subject: [PATCH 1/5] feature(protein-prospector): Add new MSstatsPTM converter for protein prospector --- NAMESPACE | 2 + R/converters.R | 150 ++++++++++++++ .../raw_data/ProteinProspector/Annotation.csv | 193 ++++++++++++++++++ .../Prospector_PhosphoTMT.txt | 182 +++++++++++++++++ inst/tinytest/test_converters.R | 71 ++++++- man/PDtoMSstatsPTMFormat.Rd | 30 +++ man/ProteinProspectortoMSstatsPTMFormat.Rd | 103 ++++++++++ 7 files changed, 730 insertions(+), 1 deletion(-) create mode 100644 inst/tinytest/raw_data/ProteinProspector/Annotation.csv create mode 100644 inst/tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt create mode 100644 man/ProteinProspectortoMSstatsPTMFormat.Rd diff --git a/NAMESPACE b/NAMESPACE index d821291..7d1cf00 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,6 +8,7 @@ export(MetamorpheusToMSstatsPTMFormat) export(PDtoMSstatsPTMFormat) export(PStoMSstatsPTMFormat) export(ProgenesistoMSstatsPTMFormat) +export(ProteinProspectortoMSstatsPTMFormat) export(SkylinetoMSstatsPTMFormat) export(SpectronauttoMSstatsPTMFormat) export(annotSite) @@ -36,6 +37,7 @@ importFrom(MSstatsConvert,MaxQtoMSstatsFormat) importFrom(MSstatsConvert,MetamorpheusToMSstatsFormat) importFrom(MSstatsConvert,PDtoMSstatsFormat) importFrom(MSstatsConvert,ProgenesistoMSstatsFormat) +importFrom(MSstatsConvert,ProteinProspectortoMSstatsTMTFormat) importFrom(MSstatsConvert,SkylinetoMSstatsFormat) importFrom(MSstatsConvert,SpectronauttoMSstatsFormat) importFrom(MSstatsTMT,MaxQtoMSstatsTMTFormat) diff --git a/R/converters.R b/R/converters.R index 1d610fc..9826643 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1612,4 +1612,154 @@ MetamorpheusToMSstatsPTMFormat = function(input, return(msstats_format) +} + + +#' Generate MSstatsPTM required input format from Protein Prospector output +#' +#' @author Anthony Wu +#' +#' @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. +#' @param input_protein same as `input` for global profiling run. Default is NULL. +#' @param annotation_protein same as `annotation` for global profiling run. Default is NULL. +#' @param use_unmod_peptides If `protein_input` is not provided, +#' unmodified peptides can be extracted from `input` to be used in place of a +#' global profiling run. Default is `FALSE`. +#' @param mod_ids List of modifications of interest. Default +#' is a list with only `\\(Phospho\\)`. +#' Please note that the 'mod_ids' parameter currently supports lists of size 1 only. +#' Future updates aim to extend its functionality to accommodate lists of greater sizes. +#' Note `\\` must be included before special characters. +#' @param useUniquePeptide TRUE (default) removes peptides that are assigned for +#' more than one proteins. We assume to use unique peptide for each protein. +#' @param removeFewMeasurements TRUE (default) will remove the features that +#' have 1 or 2 measurements across runs. +#' @param 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. +#' @param summaryforMultipleRows sum(default) or max - when there are multiple +#' measurements for certain feature and certain run, use highest or sum of +#' multiple intensities. +#' @param use_log_file logical. If TRUE, information about data processing will +#' be saved to a file. +#' @param append logical. If TRUE, information about data processing will be +#' added to an existing log file. +#' @param verbose logical. If TRUE, information about data processing wil be +#' printed to the console. +#' @param 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 'append = TRUE', has to be a valid path to a file. +#' @return a list of two data.tables named 'PTM' and 'PROTEIN' in the format +#' required by MSstatsPTM. +#' @importFrom MSstatsConvert ProteinProspectortoMSstatsTMTFormat +#' +#' @export +#' +#' @examples +#' input = system.file("tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt", +#' package = "MSstatsPTM") +#' input = data.table::fread(input) +#' annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", +#' package = "MSstatsPTM") +#' annot = data.table::fread(annot) +#' input_protein = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", +#' package = "MSstatsConvert") +#' input_protein = data.table::fread(input_protein) +#' annot_protein = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", +#' package = "MSstatsConvert") +#' annot_protein = data.table::fread(annot_protein) +#' output <- ProteinProspectortoMSstatsPTMFormat( +#' input, +#' annot, +#' input_protein, +#' annot_protein +#' ) +#' head(output) +#' +ProteinProspectortoMSstatsPTMFormat = function( + input, + annotation, + input_protein = NULL, + annotation_protein = NULL, + use_unmod_peptides = FALSE, + mod_ids = c("\\(Phospho\\)"), + 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 = "MSstatsPTM_converter_log_") + + mod_id = mod_ids[[1]] + input = as.data.table(input) + + ## Check input parameters + checkmate::assertTRUE(!is.null(input)) + .checkAnnotation(annotation, "TMT") + if (!is.null(input_protein)) { + checkmate::assertTRUE(!is.null(annotation_protein)) + } + + input$Peptide = gsub("TMT[0-9]*plex-", "", input$Peptide) # remove TMT tags + input = input[!grepl("\\|", input$`Protein Mods`),] # filter out rows with uncertainty in protein mods + + protein_id_col = "Acc #" + input = MSstatsPTMSiteLocator(input, + protein_name_col=protein_id_col, + unmod_pep_col = "DB Peptide", + mod_pep_col = "Peptide", + clean_mod=FALSE, + mod_id=mod_id, + remove_other_mods = TRUE, + bracket = "(" + ) + + if (use_unmod_peptides){ + input_protein = input[input[,..protein_id_col][[1]] == input$ProteinNameUnmod] + annotation_protein = annotation + } else { + input = input[input[,..protein_id_col][[1]] != input$ProteinNameUnmod] + } + + input[["DB Peptide"]] = input[[colnames(input)[grepl("new_peptide_col", colnames(input))][[1]]]] + ptm_input = ProteinProspectortoMSstatsTMTFormat(input, + annotation, + useUniquePeptide, + removeFewMeasurements, + removeProtein_with1Feature, + summaryforMultipleRows, + use_log_file, + append, + verbose, + log_file_path) + + msstats_format = list(PTM = ptm_input, PROTEIN = NULL) + + if (!is.null(input_protein)) { + protein_input = ProteinProspectortoMSstatsTMTFormat(input_protein, + annotation_protein, + useUniquePeptide, + removeFewMeasurements, + removeProtein_with1Feature, + summaryforMultipleRows, + use_log_file, + append, + verbose, + log_file_path) + + ptm_input = ptm_input[grepl(mod_id, ptm_input$PeptideSequence),] + + msstats_format = list(PTM = ptm_input, PROTEIN = protein_input) + } + + return(msstats_format) } \ 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 0000000..a1fb0c1 --- /dev/null +++ b/inst/tinytest/raw_data/ProteinProspector/Annotation.csv @@ -0,0 +1,193 @@ +Run,Fraction,TechRepMixture,Channel,Condition,Mixture,BioReplicate +Z20180612-04_FTMSms2hcd,1,1,Int 126,Young,Mixture1,S1 +Z20180612-05_FTMSms2hcd,2,1,Int 126,Young,Mixture1,S1 +Z20180612-06_FTMSms2hcd,3,1,Int 126,Young,Mixture1,S1 +Z20180612-29_FTMSms2hcd,4,1,Int 126,Young,Mixture1,S1 +Z20180612-30_FTMSms2hcd,5,1,Int 126,Young,Mixture1,S1 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130,Old,Mixture1,S5 +Z20180619-03_FTMSms2hcd,22,1,Int 130,Old,Mixture1,S5 +Z20180612-11_FTMSms2hcd,23,1,Int 130,Old,Mixture1,S5 +Z20180612-10_FTMSms2hcd,24,1,Int 130,Old,Mixture1,S5 +Z20180619-02_FTMSms2hcd,25,1,Int 130,Old,Mixture1,S5 +Z20180612-26_FTMSms2hcd,26,1,Int 130,Old,Mixture1,S5 +Z20180612-24_FTMSms2hcd,27,1,Int 130,Old,Mixture1,S5 +Z20180612-25_FTMSms2hcd,28,1,Int 130,Old,Mixture1,S5 +Z20180612-22_FTMSms2hcd,29,1,Int 130,Old,Mixture1,S5 +Z20180612-23_FTMSms2hcd,30,1,Int 130,Old,Mixture1,S5 +Z20180612-19_FTMSms2hcd,31,1,Int 130,Old,Mixture1,S5 +Z20180612-28_FTMSms2hcd,32,1,Int 130,Old,Mixture1,S5 +Z20180612-04_FTMSms2hcd,1,1,Int 131,Old,Mixture1,S6 +Z20180612-05_FTMSms2hcd,2,1,Int 131,Old,Mixture1,S6 +Z20180612-06_FTMSms2hcd,3,1,Int 131,Old,Mixture1,S6 +Z20180612-29_FTMSms2hcd,4,1,Int 131,Old,Mixture1,S6 +Z20180612-30_FTMSms2hcd,5,1,Int 131,Old,Mixture1,S6 +Z20180612-20_FTMSms2hcd,6,1,Int 131,Old,Mixture1,S6 +Z20180612-13_FTMSms2hcd,7,1,Int 131,Old,Mixture1,S6 +Z20180612-15_FTMSms2hcd,8,1,Int 131,Old,Mixture1,S6 +Z20180612-33_FTMSms2hcd,9,1,Int 131,Old,Mixture1,S6 +Z20180612-12_FTMSms2hcd,10,1,Int 131,Old,Mixture1,S6 +Z20180612-31_FTMSms2hcd,11,1,Int 131,Old,Mixture1,S6 +Z20180612-32_FTMSms2hcd,12,1,Int 131,Old,Mixture1,S6 +Z20180612-21_FTMSms2hcd,13,1,Int 131,Old,Mixture1,S6 +Z20180612-18_FTMSms2hcd,14,1,Int 131,Old,Mixture1,S6 +Z20180612-16_FTMSms2hcd,15,1,Int 131,Old,Mixture1,S6 +Z20180612-34_FTMSms2hcd,16,1,Int 131,Old,Mixture1,S6 +Z20180612-35_FTMSms2hcd,17,1,Int 131,Old,Mixture1,S6 +Z20180612-07_FTMSms2hcd,18,1,Int 131,Old,Mixture1,S6 +Z20180612-08_FTMSms2hcd,19,1,Int 131,Old,Mixture1,S6 +Z20180612-09_FTMSms2hcd,20,1,Int 131,Old,Mixture1,S6 +Z20180612-14_FTMSms2hcd,21,1,Int 131,Old,Mixture1,S6 +Z20180619-03_FTMSms2hcd,22,1,Int 131,Old,Mixture1,S6 +Z20180612-11_FTMSms2hcd,23,1,Int 131,Old,Mixture1,S6 +Z20180612-10_FTMSms2hcd,24,1,Int 131,Old,Mixture1,S6 +Z20180619-02_FTMSms2hcd,25,1,Int 131,Old,Mixture1,S6 +Z20180612-26_FTMSms2hcd,26,1,Int 131,Old,Mixture1,S6 +Z20180612-24_FTMSms2hcd,27,1,Int 131,Old,Mixture1,S6 +Z20180612-25_FTMSms2hcd,28,1,Int 131,Old,Mixture1,S6 +Z20180612-22_FTMSms2hcd,29,1,Int 131,Old,Mixture1,S6 +Z20180612-23_FTMSms2hcd,30,1,Int 131,Old,Mixture1,S6 +Z20180612-19_FTMSms2hcd,31,1,Int 131,Old,Mixture1,S6 +Z20180612-28_FTMSms2hcd,32,1,Int 131,Old,Mixture1,S6 \ No newline at end of file diff --git a/inst/tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt b/inst/tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt new file mode 100644 index 0000000..70acccf --- /dev/null +++ b/inst/tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt @@ -0,0 +1,182 @@ +Search Name: Z20180612_YvA_Phospho/SW190408RC_10_30ppm_2mc3mm_phospho + Z20180612_YvA_Phospho/SW190408RC_10_30ppm_2mc3mm_phospho + Uniq Pep Acc # Gene Num Unique % Cov Best Disc Score Best Expect Val M+H m/z z ppm Prev AA DB Peptide Peptide Next AA Protein Mods Composition M Cl Fraction RT Spectrum MSMS Info Int 126 Int 127 Int 128 Int 129 Int 130 Int 131 Start Score Expect # in DB Protein MW Species Protein Name +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8260 598.2802 3 0.56 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=11;Oxidation@78 1 0 Z20180612-04_FTMSms2hcd 56.533 5 13419 22052 24866 23685 27973 17492 24048 66 47.6 7.0e-11 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8260 598.2802 3 0.56 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=14;Oxidation@78 1 0 Z20180612-04_FTMSms2hcd 57.050 1 13634 30005 39865 62579 54998 40223 63535 66 50.8 1.2e-12 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8245 598.2797 3 -0.26 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=11;Oxidation@78 1 0 Z20180612-05_FTMSms2hcd 52.383 3 14193 28867 40236 41200 41164 21304 33142 66 34.0 1.3e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8269 896.9171 2 1.0 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=13;Oxidation@78 1 0 Z20180612-05_FTMSms2hcd 52.600 3 14281 5308 8466 9011 9498 5131 10197 66 20.5 1.1e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8266 598.2804 3 0.88 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=12;Oxidation@78 1 0 Z20180612-05_FTMSms2hcd 52.900 5 14413 34443 42969 47845 45850 41835 44949 66 46.3 7.9e-10 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8251 598.2799 3 -0.038 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSM(Oxidation)HR KQELDS Phospho@75=12;Oxidation@78 1 0 Z20180612-06_FTMSms2hcd 52.067 4 13587 17248 22011 18389 23124 17093 19713 66 31.1 1.5e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1776.8300 592.9482 3 0.0096 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSMHR KQELDS Phospho@75=25 1 0 Z20180612-05_FTMSms2hcd 60.033 5 17565 72828 80934 90459 78753 76561 94021 66 69.8 1.2e-14 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1776.8293 888.9183 2 -0.43 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSMHR KQELDS Phospho@75|77 1 0 Z20180612-05_FTMSms2hcd 60.083 3 17586 18387 24072 27314 23031 19265 29095 66 33.7 8.9e-11 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1776.8300 592.9482 3 -0.092 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAES(Phospho)PSMHR KQELDS Phospho@75=24 1 0 Z20180612-06_FTMSms2hcd 59.750 2 16933 33996 41440 42646 44973 30960 32494 66 62.0 2.9e-12 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1792.8263 598.2803 3 0.77 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAESPS(Phospho)M(Oxidation)HR KQELDS Phospho@77=10;Oxidation@78 1 0 Z20180612-05_FTMSms2hcd 53.550 5 14688 65974 76727 82841 80603 59127 74477 66 33.1 1.2e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1776.8297 592.9481 3 -0.19 AQGLPK GSVPAAAAESPSMHR TMT6plex-GSVPAAAAESPS(Phospho)MHR KQELDS Phospho@77=11 1 0 Z20180612-05_FTMSms2hcd 61.533 5 18252 57687 76093 68325 80734 34869 65923 66 40.4 7.5e-12 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2073.9755 691.9967 3 -0.78 QHGLSK SRTTDTFRSEQK TMT6plex-S(Phospho)RTT(Phospho)DTFRSEQK(TMT6plex) LPGRSP Phospho&Phospho@((110&(113|115))|(112&(113|115))) 1 2 Z20180612-29_FTMSms2hcd 36.683 6 10975 22247 23934 30508 24599 16610 26507 110 18.4 6.0e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6219 431.5455 3 1.6 QHGLSK SRTTDTFR TMT6plex-S(Phospho)RTTDTFR SEQKLP Phospho@110|112 1 1 Z20180612-04_FTMSms2hcd 50.717 2 11049 34051 35471 49987 47808 36538 42785 110 25.1 2.4e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6192 431.5446 3 -0.41 QHGLSK SRTTDTFR TMT6plex-S(Phospho)RTTDTFR SEQKLP Phospho@110|112 1 1 Z20180612-04_FTMSms2hcd 51.733 2 11448 70625 104056 134550 124591 99920 120529 110 28.2 2.7e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6201 431.5449 3 0.36 QHGLSK SRTTDTFR TMT6plex-S(Phospho)RTTDTFR SEQKLP Phospho@110|112 1 1 Z20180612-05_FTMSms2hcd 43.217 5 10354 141460 188459 228248 206306 194475 201153 110 27.3 2.7e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6204 431.5450 3 0.63 QHGLSK SRTTDTFR TMT6plex-S(Phospho)RTTDTFR SEQKLP Phospho@110|112 1 1 Z20180612-05_FTMSms2hcd 43.733 3 10560 12219 13718 20648 18201 13978 18830 110 24.1 3.0e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6198 431.5448 3 0.15 QHGLSK SRTTDTFR TMT6plex-S(Phospho)RTTDTFR SEQKLP Phospho@110|112|113 1 1 Z20180612-06_FTMSms2hcd 42.583 1 9665 18613 24668 27242 29755 22785 25568 110 21.6 1.5e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6213 431.5453 3 1.1 QHGLSK SRTTDTFR TMT6plex-SRT(Phospho)TDTFR SEQKLP Phospho@110|112 1 1 Z20180612-04_FTMSms2hcd 45.650 5 9122 7706 9611 9875 10161 9868 10146 110 19.5 2.0e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6201 431.5449 3 0.22 QHGLSK SRTTDTFR TMT6plex-SRT(Phospho)TDTFR SEQKLP Phospho@110|112 1 1 Z20180612-04_FTMSms2hcd 51.233 2 11260 206956 281984 331047 322746 260410 324361 110 26.7 6.7e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6186 431.5444 3 -0.78 QHGLSK SRTTDTFR TMT6plex-SRT(Phospho)TDTFR SEQKLP Phospho@112=10 1 1 Z20180612-04_FTMSms2hcd 52.267 3 11662 28628 32874 38196 35274 26482 28653 110 22.5 3.3e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6201 431.5449 3 0.29 QHGLSK SRTTDTFR TMT6plex-SRT(Phospho)TDTFR SEQKLP Phospho@110|112 1 1 Z20180612-05_FTMSms2hcd 42.717 2 10149 28493 37366 40986 40890 30855 38023 110 25.1 2.5e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1292.6207 431.5451 3 0.70 QHGLSK SRTTDTFR TMT6plex-SRT(Phospho)TDTFR SEQKLP Phospho@110|112 1 1 Z20180612-05_FTMSms2hcd 44.250 3 10768 11081 12009 12803 16967 13623 15054 110 18.5 2.3e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2575.3886 644.6026 4 0.81 TTDTFR SEQKLPGRSPSTISLK TMT6plex-SEQK(TMT6plex)LPGRS(Phospho)PSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@126=8;Phospho@131=13 1 2 Z20180612-30_FTMSms2hcd 67.667 3 23787 27374 36066 45088 43403 35079 41550 118 21.7 2.3e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2575.3841 859.1329 3 -0.87 TTDTFR SEQKLPGRSPSTISLK TMT6plex-SEQK(TMT6plex)LPGRS(Phospho)PSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@126=8;Phospho@131=29 1 2 Z20180612-30_FTMSms2hcd 68.400 3 24118 79078 109026 126574 112539 108233 118963 118 26.1 8.6e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1794.0299 598.6815 3 0.43 FRSEQK LPGRSPSTISLK TMT6plex-LPGRSPS(Phospho)TISLK(TMT6plex) ESKSRT Phospho@128=11 1 1 Z20180612-20_FTMSms2hcd 75.083 6 27501 36736 41448 40465 45374 27285 34630 122 26.3 5.0e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1450.7363 725.8718 2 0.27 QKLPGR SPSTISLK TMT6plex-S(Phospho)PSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@131=28;Phospho@126|128 1 0 Z20180612-13_FTMSms2hcd 75.300 1 26725 56588 53507 67045 56435 35639 49935 126 14.0 1.1e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2024.0687 675.3611 3 0.092 QKLPGR SPSTISLKESK TMT6plex-S(Phospho)PSTIS(Phospho)LK(TMT6plex)ESK(TMT6plex) SRTDFK Phospho@131=9;Phospho@126|128 1 1 Z20180612-15_FTMSms2hcd 69.533 3 24430 28430 35259 41236 44558 37008 51240 126 19.7 2.7e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1370.7695 685.8884 2 -0.14 QKLPGR SPSTISLK TMT6plex-SPS(Phospho)TISLK(TMT6plex) ESKSRT Phospho@128=8 1 0 Z20180612-33_FTMSms2hcd 68.650 1 24003 74020 84756 84232 81831 57146 67194 126 27.6 1.0e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1450.7373 725.8723 2 0.94 QKLPGR SPSTISLK TMT6plex-SPST(Phospho)IS(Phospho)LK(TMT6plex) ESKSRT Phospho@131=25;Phospho@126|128|129 1 0 Z20180612-12_FTMSms2hcd 76.117 2 27500 60218 59328 75395 64309 50746 57693 126 15.1 2.8e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1370.7698 457.5948 3 0.18 QKLPGR SPSTISLK TMT6plex-SPSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@131=14 1 0 Z20180612-31_FTMSms2hcd 65.017 1 22238 18445 21808 27893 24551 23956 23432 126 21.5 5.2e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1370.7699 685.8886 2 0.21 QKLPGR SPSTISLK TMT6plex-SPSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@131=9 1 0 Z20180612-31_FTMSms2hcd 65.050 6 22259 233957 238535 357265 268053 262127 280330 126 27.7 5.1e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1370.7691 685.8882 2 -0.33 QKLPGR SPSTISLK TMT6plex-SPSTIS(Phospho)LK(TMT6plex) ESKSRT Phospho@131=22 1 0 Z20180612-32_FTMSms2hcd 65.067 2 21413 30734 31476 39808 33803 31229 34367 126 19.9 3.1e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2970.4433 990.8193 3 1.4 FKEEYK SSMMPGFFSDVNPLSAVSSVVNK TMT6plex-SS(Phospho)M(Oxidation)M(Oxidation)PGFFSDVNPLSAVSSVVNK(TMT6plex) FNPFDL Oxidation@149;Oxidation@150;Phospho@147|148|155 1 0 Z20180612-21_FTMSms2hcd 134.700 3 53994 2218 3657 5104 4576 2469 4059 147 24.5 1.4e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2954.4446 985.4864 3 0.038 FKEEYK SSMMPGFFSDVNPLSAVSSVVNK TMT6plex-SSM(Oxidation)MPGFFS(Phospho)DVNPLSAVSSVVNK(TMT6plex) FNPFDL Oxidation&Phospho@((149&(155|161))|(150&(155|161))) 1 0 Z20180612-21_FTMSms2hcd 141.683 1 56920 3760 3481 3010 3014 2492 3495 147 18.3 3.2e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2954.4527 985.4891 3 2.8 FKEEYK SSMMPGFFSDVNPLSAVSSVVNK TMT6plex-SSM(Oxidation)MPGFFSDVNPLSAVSS(Phospho)VVNK(TMT6plex) FNPFDL Phospho@165=7;Oxidation@149|150 1 0 Z20180612-18_FTMSms2hcd 132.850 6 53950 5762 7863 8234 8677 4811 6377 147 44.5 1.4e-13 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2938.4573 980.1573 3 2.6 FKEEYK SSMMPGFFSDVNPLSAVSSVVNK TMT6plex-SSMMPGFFSDVNPLSAVSS(Phospho)VVNK(TMT6plex) FNPFDL Phospho@165=6 1 0 Z20180612-21_FTMSms2hcd 140.117 6 56264 5135 5607 3937 4364 2594 3114 147 37.0 1.0e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2708.3246 903.4464 3 5.0 SSVVNK FNPFDLISDSEAVQEETTK TMT6plex-FNPFDLIS(Phospho)DSEAVQEETTK(TMT6plex) KQKVAQ Phospho@177|179 1 0 Z20180612-15_FTMSms2hcd 133.067 6 52671 6188 7036 7245 8006 5568 4777 170 33.3 9.8e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2708.3156 903.4434 3 1.8 SSVVNK FNPFDLISDSEAVQEETTK TMT6plex-FNPFDLIS(Phospho)DSEAVQEETTK(TMT6plex) KQKVAQ Phospho@177=7 1 0 Z20180612-16_FTMSms2hcd 133.350 5 52655 11785 15112 15933 13880 11916 13206 170 39.5 1.3e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2708.3039 903.4395 3 -2.5 SSVVNK FNPFDLISDSEAVQEETTK TMT6plex-FNPFDLISDS(Phospho)EAVQEETTK(TMT6plex) KQKVAQ Phospho@179=6 1 0 Z20180612-31_FTMSms2hcd 125.500 2 49170 5357 9176 10395 8729 5227 11059 170 35.0 1.7e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 3065.5738 767.1489 4 1.6 SSVVNK FNPFDLISDSEAVQEETTKK TMT6plex-FNPFDLISDS(Phospho)EAVQEETTK(TMT6plex)K(TMT6plex) QKVAQK Phospho@177|179 1 1 Z20180612-34_FTMSms2hcd 114.217 2 43671 5320 7635 6225 9130 3540 8116 170 30.1 2.6e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 3021.6794 605.1417 5 0.0085 QKVAQK DQGKSEGITKPSLQQPSPK TMT6plex-DQGK(TMT6plex)SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=39 1 1 Z20180612-34_FTMSms2hcd 63.467 5 21246 25103 37207 42873 42307 40001 44746 196 31.7 2.5e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 3021.6789 605.1416 5 -0.091 QKVAQK DQGKSEGITKPSLQQPSPK TMT6plex-DQGK(TMT6plex)SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=34 1 1 Z20180612-35_FTMSms2hcd 63.317 1 20712 43809 58956 76681 66692 82919 77978 196 36.1 7.8e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2364.3166 591.8346 4 0.95 QKDQGK SEGITKPSLQQPSPK TMT6plex-SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=38 1 0 Z20180612-34_FTMSms2hcd 65.617 6 22182 37715 37284 47498 38339 28866 39553 200 29.5 9.4e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2364.3140 788.7762 3 -0.13 QKDQGK SEGITKPSLQQPSPK TMT6plex-SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=24 1 0 Z20180612-35_FTMSms2hcd 65.683 1 21756 59892 55796 89693 62793 62563 67739 200 33.3 1.1e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2364.3146 591.8341 4 0.035 QKDQGK SEGITKPSLQQPSPK TMT6plex-SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=30 1 0 Z20180612-35_FTMSms2hcd 65.700 4 21767 38213 33580 43622 31673 32259 36376 200 36.7 4.3e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2364.3129 473.6684 5 -0.53 QKDQGK SEGITKPSLQQPSPK TMT6plex-SEGITK(TMT6plex)PSLQQPS(Phospho)PK(TMT6plex) LIPKQQ Phospho@212=21 1 0 Z20180612-35_FTMSms2hcd 65.983 8 21895 13559 16787 25183 16857 16661 19321 200 34.0 1.2e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2837.5298 710.1379 4 1.2 QQGPGK EVIPQDIPSKSVSSQQAEK TMT6plex-EVIPQDIPS(Phospho)K(TMT6plex)SVSSQQAEK(TMT6plex) TKPQAP Phospho@233|235|238 1 1 Z20180612-15_FTMSms2hcd 75.117 1 26912 29425 28293 22522 31975 17986 28662 225 33.2 8.9e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2837.5289 946.5145 3 0.84 QQGPGK EVIPQDIPSKSVSSQQAEK TMT6plex-EVIPQDIPSK(TMT6plex)S(Phospho)VSSQQAEK(TMT6plex) TKPQAP Phospho@235=8 1 1 Z20180612-15_FTMSms2hcd 75.200 1 26949 30719 32962 26548 35883 25994 31855 225 43.3 3.4e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7645 751.3859 2 -1.2 QDIPSK SVSSQQAEK TMT6plex-SVS(Phospho)SQQAEK(TMT6plex) TKPQAP Phospho@235|237 1 0 Z20180612-07_FTMSms2hcd 51.217 6 13810 35111 37458 41220 36219 32416 34501 235 28.3 1.8e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7647 751.3860 2 -1.0 QDIPSK SVSSQQAEK TMT6plex-SVS(Phospho)SQQAEK(TMT6plex) TKPQAP Phospho@235|237 1 0 Z20180612-07_FTMSms2hcd 53.233 1 14662 47859 59795 50791 53742 38592 49391 235 27.9 2.3e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7681 751.3877 2 1.2 QDIPSK SVSSQQAEK TMT6plex-SVS(Phospho)SQQAEK(TMT6plex) TKPQAP Phospho@237=12 1 0 Z20180612-08_FTMSms2hcd 51.750 5 13582 24503 23789 29818 24642 23918 22867 235 25.2 1.6e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7663 751.3868 2 -0.051 QDIPSK SVSSQQAEK TMT6plex-SVS(Phospho)SQQAEK(TMT6plex) TKPQAP Phospho@237|238 1 0 Z20180612-08_FTMSms2hcd 53.667 4 14371 40658 42692 38947 47910 32862 37910 235 26.5 1.4e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7661 751.3867 2 -0.21 QDIPSK SVSSQQAEK TMT6plex-SVSS(Phospho)QQAEK(TMT6plex) TKPQAP Phospho@238=9 1 0 Z20180612-08_FTMSms2hcd 52.450 5 13871 32482 32183 41125 35346 33958 36180 235 22.0 1.2e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1501.7671 751.3872 2 0.52 QDIPSK SVSSQQAEK TMT6plex-SVSS(Phospho)QQAEK(TMT6plex) TKPQAP Phospho@237|238 1 0 Z20180612-09_FTMSms2hcd 54.433 6 13986 17205 20279 20117 19094 14094 19389 235 21.1 1.3e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2658.4618 665.3709 4 1.3 QPGPAK ATVQQPGPAKSPAQPAGTGK TMT6plex-ATVQQPGPAK(TMT6plex)S(Phospho)PAQPAGTGK(TMT6plex) SPAQPP Phospho@289=20 1 1 Z20180612-32_FTMSms2hcd 51.733 2 15663 5112 6876 6456 9866 5502 7183 279 26.7 5.0e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2272.2377 758.0841 3 0.96 NCQMQR ALGGELAAIPSSPQPTPK TMT6plex-ALGGELAAIPSS(Phospho)PQPTPK(TMT6plex) AASVQP Phospho@599=9 1 0 Z20180612-30_FTMSms2hcd 88.050 4 32959 39471 48551 62397 54429 35338 49178 588 44.5 8.1e-10 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2272.2386 568.8151 4 1.3 NCQMQR ALGGELAAIPSSPQPTPK TMT6plex-ALGGELAAIPSS(Phospho)PQPTPK(TMT6plex) AASVQP Phospho@598|599 1 0 Z20180612-31_FTMSms2hcd 88.300 7 32617 6559 5463 7953 7691 4368 7805 588 40.9 1.7e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2272.2356 758.0834 3 0.060 NCQMQR ALGGELAAIPSSPQPTPK TMT6plex-ALGGELAAIPSS(Phospho)PQPTPK(TMT6plex) AASVQP Phospho@599=9 1 0 Z20180612-31_FTMSms2hcd 88.383 6 32655 23984 27471 36962 32674 25647 33495 588 51.3 2.4e-11 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1568.8455 784.9264 2 0.36 PQPTPK AASVQPATASK TMT6plex-AAS(Phospho)VQPATASK(TMT6plex) SPVPSQ Phospho@608=46 1 0 Z20180612-12_FTMSms2hcd 46.833 3 14537 35677 39390 31921 42021 23273 34693 606 24.6 1.2e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5429 597.7144 5 -1.2 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATAS(Phospho)K(TMT6plex)SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=20;Phospho@613|615|617 1 1 Z20180612-15_FTMSms2hcd 60.467 4 20408 27534 28081 45422 39826 28021 37425 606 43.0 1.3e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2904.5831 968.8659 3 1.1 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATAS(Phospho)K(TMT6plex)SPVPSQQASPK(TMT6plex) KELPSK Phospho@613|615|617 1 1 Z20180612-33_FTMSms2hcd 56.650 4 18779 4608 5120 9073 6180 6370 6460 606 17.3 3.7e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5526 995.5224 3 2.2 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)S(Phospho)PVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=13;Phospho@615|617 1 1 Z20180612-14_FTMSms2hcd 60.783 6 20829 12181 13813 23620 19933 15500 20221 606 34.5 1.7e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5438 746.8914 4 -0.80 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)S(Phospho)PVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@617=7;Phospho@625=29 1 1 Z20180612-14_FTMSms2hcd 60.800 6 20838 32103 45075 65793 53048 43588 49907 606 41.6 1.6e-10 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5486 746.8926 4 0.76 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)S(Phospho)PVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=37;Phospho@615|617 1 1 Z20180612-15_FTMSms2hcd 60.333 6 20351 42722 48655 72666 62062 58632 60172 606 49.1 2.4e-12 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5478 995.5208 3 0.55 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)S(Phospho)PVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=14;Phospho@615|617 1 1 Z20180612-15_FTMSms2hcd 60.350 3 20354 19734 24636 37787 27086 27183 28460 606 36.7 3.2e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2984.5481 995.5209 3 0.61 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)S(Phospho)PVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=11;Phospho@615|617 1 1 Z20180612-16_FTMSms2hcd 60.283 4 20263 11191 10742 19471 13851 14322 13445 606 32.0 9.5e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2904.5758 726.8994 4 -1.4 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=31 1 1 Z20180612-35_FTMSms2hcd 58.200 3 18482 11003 24600 23359 29631 32580 26484 606 52.2 6.7e-11 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2904.5814 726.9008 4 0.45 PQPTPK AASVQPATASKSPVPSQQASPK TMT6plex-AASVQPATASK(TMT6plex)SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=27 1 1 Z20180612-35_FTMSms2hcd 58.833 2 18756 10792 13499 15362 12229 9227 9892 606 39.9 1.2e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8827 555.2991 3 0.36 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=32 1 0 Z20180612-14_FTMSms2hcd 47.633 5 15066 71007 64702 85276 68057 57499 68513 617 41.6 6.0e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8839 832.4456 2 1.1 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=18 1 0 Z20180612-14_FTMSms2hcd 48.117 2 15274 30692 31447 35683 33693 31102 35452 617 36.8 5.6e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8824 555.2990 3 0.25 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=29 1 0 Z20180612-15_FTMSms2hcd 47.133 4 14627 110067 108569 129873 108131 107446 101541 617 41.2 2.5e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8829 832.4451 2 0.56 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=28 1 0 Z20180612-15_FTMSms2hcd 47.600 1 14824 73451 69715 98877 79049 77695 81938 617 40.7 9.7e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8811 832.4442 2 -0.62 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=28 1 0 Z20180612-15_FTMSms2hcd 48.683 4 15295 19418 27005 32700 28950 22897 28248 617 30.3 2.7e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8843 832.4458 2 1.4 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=11 1 0 Z20180612-16_FTMSms2hcd 46.900 3 14393 25910 30190 37083 35609 22780 44364 617 24.7 4.2e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8824 555.2990 3 0.25 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=35 1 0 Z20180612-16_FTMSms2hcd 46.933 3 14408 57173 56668 74904 66848 60723 58297 617 36.8 6.7e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8823 832.4448 2 0.11 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=31 1 0 Z20180612-20_FTMSms2hcd 48.317 4 15471 17868 16969 22605 22314 18409 16712 617 33.1 5.7e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1663.8848 555.2998 3 1.7 PATASK SPVPSQQASPK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex) KELPSK Phospho@625=36 1 0 Z20180612-30_FTMSms2hcd 46.917 4 14629 24298 29378 33254 32562 19660 28107 617 31.1 2.1e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2021.1389 674.3845 3 -0.47 PATASK SPVPSQQASPKK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex)K(TMT6plex) ELPSKQ Phospho@625=21 1 1 Z20180612-34_FTMSms2hcd 46.250 2 13771 53404 52476 62672 57006 48006 54185 617 36.1 6.3e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2021.1407 674.3851 3 0.35 PATASK SPVPSQQASPKK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex)K(TMT6plex) ELPSKQ Phospho@625=14 1 1 Z20180612-35_FTMSms2hcd 46.283 6 13552 50080 53975 59170 55089 41496 45321 617 30.6 2.0e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2021.1394 506.0403 4 -0.39 PATASK SPVPSQQASPKK TMT6plex-SPVPSQQAS(Phospho)PK(TMT6plex)K(TMT6plex) ELPSKQ Phospho@625=26 1 1 Z20180612-35_FTMSms2hcd 46.500 4 13644 24960 20458 29394 27968 23712 24336 617 32.3 3.6e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2253.3018 564.0809 4 -0.29 QQASPK KELPSKQDSPK TMT6plex-K(TMT6plex)ELPSK(TMT6plex)QDS(Phospho)PK(TMT6plex) APESKK Phospho@636=24 1 2 Z20180619-03_FTMSms2hcd 50.000 3 15561 44399 46672 55586 52200 38990 46493 628 19.2 1.3e-4 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 1853.9972 618.6706 3 -0.26 KELPSK QDSPKAPESK TMT6plex-QDS(Phospho)PK(TMT6plex)APESK(TMT6plex) KPPPLV Phospho@636=44 1 1 Z20180612-11_FTMSms2hcd 39.583 5 11860 67959 56744 80015 64970 60874 65219 634 22.9 2.6e-5 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2249 810.7465 3 1.8 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TS(Phospho)QSFPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-13_FTMSms2hcd 93.467 2 34884 17863 23102 24545 28581 16775 21764 745 37.5 5.5e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2243 810.7463 3 1.6 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-12_FTMSms2hcd 90.717 6 34073 26506 29224 33084 33908 28300 33863 745 53.9 8.8e-10 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2219 810.7455 3 0.62 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-12_FTMSms2hcd 91.500 7 34426 31113 36316 47347 40123 37276 39808 745 42.5 5.9e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2234 810.7460 3 1.2 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-12_FTMSms2hcd 92.383 3 34818 26691 34293 40551 35325 33125 38777 745 41.3 3.0e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2249 810.7465 3 1.8 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-12_FTMSms2hcd 93.683 3 35406 28437 30820 40838 35581 28651 36856 745 41.6 2.9e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2192 810.7446 3 -0.58 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-14_FTMSms2hcd 90.050 4 33932 18855 27029 29755 29179 23230 27956 745 37.8 2.2e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2243 810.7463 3 1.6 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-14_FTMSms2hcd 91.317 4 34501 27873 30597 35646 35118 28495 26573 745 42.3 2.8e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2252 810.7466 3 1.9 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-14_FTMSms2hcd 92.150 1 34870 26145 28283 30177 26682 22827 29675 745 40.5 1.3e-7 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2207 810.7451 3 0.10 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-14_FTMSms2hcd 93.200 3 35336 27458 28105 33860 31419 26612 32310 745 36.2 3.8e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2237 810.7461 3 1.4 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-15_FTMSms2hcd 89.717 3 33427 32793 34696 37463 36746 33176 32406 745 40.2 6.1e-8 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2237 810.7461 3 1.3 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748|752 1 0 Z20180612-15_FTMSms2hcd 90.350 3 33713 30193 34325 37975 37556 28413 31161 745 38.1 1.5e-6 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2225 810.7457 3 0.86 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-15_FTMSms2hcd 91.150 1 34072 31305 40863 44887 39526 35374 38473 745 51.5 9.7e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2210 810.7452 3 0.18 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-15_FTMSms2hcd 91.733 5 34338 34276 34089 43813 44483 40571 41697 745 52.1 4.4e-10 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2225 810.7457 3 0.86 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-15_FTMSms2hcd 92.617 4 34736 38046 39122 45853 41112 37849 38213 745 52.5 1.0e-9 1 550838.8 MOUSE Protein piccolo +[1] Q9QYX7 Pclo 496 33.4 12.23 4.9e-22 2430.2243 810.7463 3 1.5 KTDSAK TSQSFPPTGDTITPLDSK TMT6plex-TSQS(Phospho)FPPTGDTITPLDSK(TMT6plex) AMPRPA Phospho@745|746|748 1 0 Z20180612-15_FTMSms2hcd 94.367 1 35517 22439 25397 30344 32723 23957 23609 745 47.9 5.2e-9 1 550838.8 MOUSE Protein piccolo +[16-3] 78 Q6PFD5 Dlgap3 81 37.5 9.47 6.2e-17 2614.2233 872.0793 3 -0.0098 RAASFR HSSATESADSIEIYIPEAQTR TMT6plex-HSSATESADS(Phospho)IEIYIPEAQTR L- Phospho@965=14 1 0 Z20180612-14_FTMSms2hcd 78.500 3 28748 25756 33050 30903 32438 25555 31425 956 44.3 7.8e-8 1 105873.9 MOUSE Disks large-associated protein 3 +[16-3] 78 Q6PFD5 Dlgap3 81 37.5 9.47 6.2e-17 2727.3122 909.7756 3 1.7 RAASFR HSSATESADSIEIYIPEAQTRL TMT6plex-HSSATESADS(Phospho)IEIYIPEAQTRL - Phospho@965=13 1 1 Z20180612-06_FTMSms2hcd 110.017 3 40086 37368 44992 50119 49058 47124 47436 956 48.7 2.1e-11 1 105873.9 MOUSE Disks large-associated protein 3 +[16-3] 78 Q6PFD5 Dlgap3 81 37.5 9.47 6.2e-17 2727.2999 909.7715 3 -2.8 RAASFR HSSATESADSIEIYIPEAQTRL TMT6plex-HSSATESADS(Phospho)IEIYIPEAQTRL - Phospho@965=9 1 1 Z20180612-14_FTMSms2hcd 91.900 2 34757 23756 23936 33322 34727 29493 32879 956 39.4 4.5e-8 1 105873.9 MOUSE Disks large-associated protein 3 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1531.8173 511.2773 3 0.50 DPSGVK VLETAEDIQER TMT6plex-VLETAEDIQER RQQVLD 0 0 Z20180612-05_FTMSms2hcd 86.383 2 29617 9156 10150 12724 14605 7482 11708 8 38.4 1.5e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1531.8137 766.4105 2 -1.9 DPSGVK VLETAEDIQER TMT6plex-VLETAEDIQER RQQVLD 0 0 Z20180612-05_FTMSms2hcd 86.433 2 29639 62039 67432 80066 77501 57991 71642 8 33.6 5.1e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1531.8181 766.4127 2 1.1 DPSGVK VLETAEDIQER TMT6plex-VLETAEDIQER RQQVLD 0 0 Z20180612-06_FTMSms2hcd 86.367 3 29237 76083 93186 124121 103857 74505 89683 8 26.5 1.0e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1531.8161 511.2769 3 -0.32 DPSGVK VLETAEDIQER TMT6plex-VLETAEDIQER RQQVLD 0 0 Z20180612-06_FTMSms2hcd 86.400 4 29254 12575 18743 25555 19606 11217 14910 8 37.7 7.0e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2707.4878 677.6274 4 0.27 KWIQEK LQVASDENYKDPTNLQGK TMT6plex-LQVASDENYK(TMT6plex)DPTNLQGK(TMT6plex) LQKHQA 0 1 Z20180612-35_FTMSms2hcd 72.700 6 24840 20478 22050 20933 19021 18749 21063 64 26.4 4.1e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2707.4897 903.1681 3 1.1 KWIQEK LQVASDENYKDPTNLQGK TMT6plex-LQVASDENYK(TMT6plex)DPTNLQGK(TMT6plex) LQKHQA 0 1 Z20180619-02_FTMSms2hcd 72.533 6 25321 26903 34948 47344 38203 32874 34803 64 43.4 5.2e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2027.9456 676.6534 3 0.068 LVQYLR ECEDVMDWINDK TMT6plex-EC(Carbamidomethyl)EDVM(Oxidation)DWINDK(TMT6plex) EAIVTS Oxidation@162 0 0 Z20180612-09_FTMSms2hcd 109.717 1 39321 40535 40117 43916 48777 37221 38914 157 27.1 8.4e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2011.9493 671.3213 3 -0.61 LVQYLR ECEDVMDWINDK TMT6plex-EC(Carbamidomethyl)EDVMDWINDK(TMT6plex) EAIVTS 0 0 Z20180612-12_FTMSms2hcd 99.783 2 38133 26124 22228 29243 28790 22770 22928 157 29.6 1.1e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2011.9493 671.3213 3 -0.61 LVQYLR ECEDVMDWINDK TMT6plex-EC(Carbamidomethyl)EDVMDWINDK(TMT6plex) EAIVTS 0 0 Z20180612-13_FTMSms2hcd 99.583 4 37617 22991 22417 26504 27654 23254 20163 157 28.7 1.3e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2824.5374 706.8898 4 1.0 DWINDK EAIVTSEELGQDLEHVEVLQK TMT6plex-EAIVTSEELGQDLEHVEVLQK(TMT6plex) KFEEFQ 0 0 Z20180612-11_FTMSms2hcd 108.883 4 42495 7146 6900 9534 9186 6745 6551 169 48.3 1.1e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2824.5358 706.8894 4 0.48 DWINDK EAIVTSEELGQDLEHVEVLQK TMT6plex-EAIVTSEELGQDLEHVEVLQK(TMT6plex) KFEEFQ 0 0 Z20180612-12_FTMSms2hcd 108.317 1 41929 5528 6949 6458 5191 4565 5086 169 45.3 4.5e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2308.1974 577.8048 4 0.012 VEVLQK KFEEFQTDLAAHEER TMT6plex-K(TMT6plex)FEEFQTDLAAHEER VNEVSQ 0 1 Z20180612-30_FTMSms2hcd 68.433 4 24134 26985 25855 34312 36355 28569 28139 190 55.3 7.6e-11 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2308.2014 577.8058 4 1.7 VEVLQK KFEEFQTDLAAHEER TMT6plex-K(TMT6plex)FEEFQTDLAAHEER VNEVSQ 0 1 Z20180612-31_FTMSms2hcd 69.217 6 24111 11380 14421 14623 16815 9838 12495 190 41.4 4.4e-11 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1550.8955 775.9514 2 0.84 AAHEER VNEVSQFAAK TMT6plex-VNEVSQFAAK(TMT6plex) LIQEQH 0 0 Z20180612-18_FTMSms2hcd 69.117 6 25543 50677 53002 60950 55745 47704 56487 205 35.4 1.3e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1904.0438 635.3528 3 2.6 EEELIK TKQDEVNAAWQR TMT6plex-TK(TMT6plex)QDEVNAAWQR LKGLAL 0 1 Z20180612-34_FTMSms2hcd 49.150 1 15010 38006 46732 45851 57926 36384 40186 228 35.8 6.5e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1219.6999 610.3536 2 0.20 LQRQGK LFGAAEVQR TMT6plex-LFGAAEVQR FNRDVD 0 0 Z20180612-22_FTMSms2hcd 66.450 1 24563 99565 109099 127449 131276 102339 95844 251 19.7 1.3e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1633.9208 545.3118 3 0.49 VQRFNR DVDETIGWIK TMT6plex-DVDETIGWIK(TMT6plex) EKEQLM 0 0 Z20180612-31_FTMSms2hcd 89.550 5 33177 11078 11608 13723 13349 8561 11139 263 25.3 2.1e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1394.7595 697.8834 2 -0.83 SDDFGR DLASVQALLR TMT6plex-DLAS(Phospho)VQALLR KHEGLE Phospho@289 1 0 Z20180612-30_FTMSms2hcd 99.683 4 38161 14510 20882 22037 20808 15400 19311 286 24.3 3.1e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1789.1045 597.0397 3 0.36 HEGLER DLAALEDKVK TMT6plex-DLAALEDK(TMT6plex)VK(TMT6plex) ALCAEA 0 1 Z20180619-03_FTMSms2hcd 80.533 1 28874 35504 44021 42109 45286 32652 36269 303 19.5 9.4e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2202.2042 734.7396 3 -0.30 CAEADR LQQSHPLSASQIQVK TMT6plex-LQQS(Phospho)HPLSASQIQVK(TMT6plex) REELIT Phospho@324=31 1 0 Z20180612-35_FTMSms2hcd 69.367 3 23376 17696 20819 26085 27945 21373 25470 321 39.1 1.7e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2202.2051 734.7399 3 0.20 CAEADR LQQSHPLSASQIQVK TMT6plex-LQQSHPLSAS(Phospho)QIQVK(TMT6plex) REELIT Phospho@330=9 1 0 Z20180612-34_FTMSms2hcd 71.433 2 24698 69061 67346 103392 86397 87316 81399 321 59.8 7.4e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2202.2069 734.7405 3 0.95 CAEADR LQQSHPLSASQIQVK TMT6plex-LQQSHPLSAS(Phospho)QIQVK(TMT6plex) REELIT Phospho@330=13 1 0 Z20180612-35_FTMSms2hcd 71.550 3 24329 28537 36537 38822 36336 35054 32638 321 43.9 4.0e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2122.2416 708.0854 3 1.5 CAEADR LQQSHPLSASQIQVK TMT6plex-LQQSHPLSASQIQVK(TMT6plex) REELIT 0 0 Z20180612-23_FTMSms2hcd 68.767 3 24900 28906 33424 36065 39792 31242 29944 321 53.8 6.6e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1815.9926 606.0024 3 0.72 SQIQVK REELITNWEQIR TMT6plex-REELITNWEQIR TLAAER 0 1 Z20180612-30_FTMSms2hcd 72.933 6 26155 18662 29010 27317 35997 19919 24618 336 34.4 1.0e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1077.4813 539.2443 2 -0.15 AERHAR LDDSYR TMT6plex-LDDSY(Phospho)R LQRFLA Phospho@360|361 1 0 Z20180612-25_FTMSms2hcd 36.483 2 10773 37942 39470 46229 49202 39163 44674 357 16.7 1.0e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1683.9053 561.9733 3 1.6 FLADFR DLTSWVTEMK TMT6plex-DLTSWVTEM(Oxidation)K(TMT6plex) ALINAD Oxidation@380 0 0 Z20180612-22_FTMSms2hcd 89.367 1 34923 9678 10955 8910 11510 7340 7174 372 18.4 5.2e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1667.9087 834.4580 2 0.53 FLADFR DLTSWVTEMK TMT6plex-DLTSWVTEMK(TMT6plex) ALINAD 0 0 Z20180612-22_FTMSms2hcd 104.383 4 41669 27694 34347 30514 33201 30268 32591 372 38.0 7.1e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2383.2698 795.0948 3 1.3 WVTEMK ALINADELANDVAGAEALLDR TMT6plex-ALINADELANDVAGAEALLDR HQEHKG 0 0 Z20180612-14_FTMSms2hcd 133.500 1 53208 4303 3619 4485 5629 4636 5625 382 60.3 1.1e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1175.6853 588.3463 2 1.7 DEVREK LSILSEER TMT6plex-LSILSEER TALLEL 0 0 Z20180619-02_FTMSms2hcd 66.483 3 22642 44295 50244 62757 57807 40936 48840 442 24.4 2.4e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1175.6845 588.3459 2 1.0 DEVREK LSILSEER TMT6plex-LSILSEER TALLEL 0 0 Z20180619-03_FTMSms2hcd 66.717 1 22822 15761 17237 15994 18887 13642 17855 442 18.5 1.9e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1906.8677 636.2941 3 0.97 LQLFYR DTEQVDNWMSK TMT6plex-DTEQVDNWM(Oxidation)S(Phospho)K(TMT6plex) QEAFLL Oxidation@483;Phospho@484=56 1 0 Z20180612-05_FTMSms2hcd 81.667 4 27397 54431 58256 60176 67648 50893 62789 475 25.5 1.1e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1890.8723 630.9623 3 0.73 LQLFYR DTEQVDNWMSK TMT6plex-DTEQVDNWMS(Phospho)K(TMT6plex) QEAFLL Phospho@484=90 1 0 Z20180612-09_FTMSms2hcd 97.600 1 33551 72649 69923 82825 96140 62012 91102 475 30.7 3.0e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1810.9076 604.3074 3 1.6 LQLFYR DTEQVDNWMSK TMT6plex-DTEQVDNWMSK(TMT6plex) QEAFLL 0 0 Z20180612-16_FTMSms2hcd 73.117 3 25949 23695 28623 30729 32970 29025 33504 475 24.8 1.2e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2877.5531 959.8559 3 1.2 DNWMSK QEAFLLNEDLGDSLDSVEALLK TMT6plex-QEAFLLNEDLGDSLDSVEALLK(TMT6plex) KHEDFE 0 0 Z20180612-31_FTMSms2hcd 143.267 6 56951 7974 7156 10799 10173 9473 9578 486 57.9 3.0e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1429.7361 715.3717 2 1.5 HEDFEK SLSAQEEK TMT6plex-SLS(Phospho)AQEEK(TMT6plex) ITALDE Phospho@515|517 1 0 Z20180612-06_FTMSms2hcd 65.533 4 19534 107602 113518 126999 132287 102618 114955 515 22.3 7.1e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1429.7351 715.3712 2 0.82 HEDFEK SLSAQEEK TMT6plex-SLS(Phospho)AQEEK(TMT6plex) ITALDE Phospho@515|517 1 0 Z20180612-07_FTMSms2hcd 64.933 4 19698 122027 136043 150744 148985 140333 148525 515 25.2 1.4e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1349.7679 675.3876 2 0.23 HEDFEK SLSAQEEK TMT6plex-SLSAQEEK(TMT6plex) ITALDE 0 0 Z20180612-15_FTMSms2hcd 40.317 2 11646 52974 55758 65680 60165 54617 55166 515 30.3 3.1e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1566.9149 522.9765 3 0.39 SAQEEK ITALDEFATK TMT6plex-ITALDEFATK(TMT6plex) LIQNNH 0 0 Z20180612-18_FTMSms2hcd 91.300 4 35486 25126 25725 32813 26397 24183 25971 523 31.9 1.2e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2004.0155 668.6767 3 -0.74 DEFATK LIQNNHYAMEDVATR TMT6plex-LIQNNHYAMEDVATR RDALLS 0 0 Z20180612-33_FTMSms2hcd 62.067 4 21115 13913 18303 16233 21019 11076 23331 533 29.7 1.4e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 983.5127 492.2600 2 0.38 DVATRR DALLSR TMT6plex-DALLS(Phospho)R RNALHE Phospho@553 1 0 Z20180612-04_FTMSms2hcd 71.483 3 20043 140924 147982 219516 187403 175154 175012 549 15.5 2.3e-5 3 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2016.9926 673.0024 3 1.6 RAMHRR AQLADSFHLQQFFR TMT6plex-AQLADS(Phospho)FHLQQFFR DSDELK Phospho@572 1 0 Z20180619-02_FTMSms2hcd 104.100 3 39307 10241 16523 17101 16818 12515 14038 567 31.8 1.0e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2217.1382 739.7176 3 -1.1 LQQFFR DSDELKSWVNEK TMT6plex-DSDELK(TMT6plex)S(Phospho)WVNEK(TMT6plex) MKTATD Phospho@587=25 1 1 Z20180612-14_FTMSms2hcd 84.433 5 31411 107793 107894 136424 137355 133689 131555 581 32.9 4.5e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2425.3154 809.1100 3 -0.97 VNEKMK TATDEAYKDPSNLQGK TMT6plex-TATDEAYK(TMT6plex)DPSNLQGK(TMT6plex) VQKHQA 0 1 Z20180612-30_FTMSms2hcd 57.583 6 19315 63858 64915 83838 71686 65759 63120 595 38.5 5.4e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1816.9139 606.3095 3 0.020 QGKVQK HQAFEAELSANQSR TMT6plex-HQAFEAELSANQSR IDALEK 0 0 Z20180612-13_FTMSms2hcd 46.400 4 13971 26449 29126 32385 35546 19542 28966 614 39.8 1.2e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1816.9136 606.3094 3 -0.079 QGKVQK HQAFEAELSANQSR TMT6plex-HQAFEAELSANQSR IDALEK 0 0 Z20180612-14_FTMSms2hcd 45.650 5 14200 28569 35635 37942 38900 25483 36873 614 35.3 2.0e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1816.9160 606.3102 3 1.1 QGKVQK HQAFEAELSANQSR TMT6plex-HQAFEAELSANQSR IDALEK 0 0 Z20180612-14_FTMSms2hcd 46.250 4 14462 16411 20272 26516 26476 19892 20157 614 29.2 3.9e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1530.9038 510.9728 3 -0.36 EKAGQK LIDVNHYAK TMT6plex-LIDVNHYAK(TMT6plex) EEVAAR 0 0 Z20180612-22_FTMSms2hcd 69.650 2 26006 20113 18252 22936 24249 19358 19303 638 24.8 5.4e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1530.9038 510.9728 3 -0.31 EKAGQK LIDVNHYAK TMT6plex-LIDVNHYAK(TMT6plex) EEVAAR 0 0 Z20180612-22_FTMSms2hcd 70.200 1 26246 23771 28583 33451 34441 25280 27221 638 25.9 8.2e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1760.9357 587.6501 3 0.21 ELKGIK LREANQQQQFNR TMT6plex-LREANQQQQFNR NVEDIE 0 1 Z20180619-02_FTMSms2hcd 33.233 2 8350 11487 12209 12037 15514 9796 12794 674 24.9 8.8e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7505 497.9217 3 0.23 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-07_FTMSms2hcd 40.583 4 9464 11134 12786 14761 15977 12118 15733 676 26.0 3.9e-6 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7521 746.3797 2 1.3 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-07_FTMSms2hcd 40.850 1 9567 76808 71259 91402 82460 80479 77602 676 43.4 3.4e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7519 746.3796 2 1.1 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-08_FTMSms2hcd 41.650 5 9525 23508 20260 28918 23152 23702 24100 676 37.3 1.4e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7502 497.9216 3 0.052 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-08_FTMSms2hcd 41.700 2 9542 11783 12690 13222 15398 10172 13098 676 27.6 1.5e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7527 746.3800 2 1.7 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-08_FTMSms2hcd 42.183 3 9741 258648 244556 324972 292705 273059 269668 676 44.1 1.8e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7517 497.9221 3 1.1 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-08_FTMSms2hcd 42.217 4 9756 52413 59549 70819 174856 62767 67047 676 28.6 1.2e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7505 746.3789 2 0.25 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-08_FTMSms2hcd 42.717 1 9953 22608 21354 34259 24464 23267 23977 676 37.9 1.9e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7514 497.9220 3 0.80 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-09_FTMSms2hcd 42.717 4 9254 8865 9614 11239 9832 7319 8965 676 23.7 8.2e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7507 746.3790 2 0.33 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-09_FTMSms2hcd 43.083 1 9397 33026 28748 36537 35992 30980 30900 676 38.4 2.1e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7514 497.9220 3 0.86 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-09_FTMSms2hcd 43.250 2 9468 11619 11735 13069 18916 9968 10543 676 26.3 5.4e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1491.7505 746.3789 2 0.17 KGIKLR EANQQQQFNR TMT6plex-EANQQQQFNR NVEDIE 0 0 Z20180612-09_FTMSms2hcd 43.600 1 9610 11990 11226 14553 14171 12055 13609 676 30.5 2.4e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2132.1984 427.2455 5 0.37 VQNLQK KHALLEADVAAHQDR TMT6plex-K(TMT6plex)HALLEADVAAHQDR IDGITI 0 1 Z20180619-02_FTMSms2hcd 44.133 1 12936 13298 12054 12375 10299 10814 9216 719 23.5 2.4e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2132.1964 427.2451 5 -0.62 VQNLQK KHALLEADVAAHQDR TMT6plex-K(TMT6plex)HALLEADVAAHQDR IDGITI 0 1 Z20180619-03_FTMSms2hcd 44.017 6 13017 13801 11587 14033 13203 9261 12001 719 36.8 7.8e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1774.9406 444.4906 4 0.39 QNLQKK HALLEADVAAHQDR TMT6plex-HALLEADVAAHQDR IDGITI 0 0 Z20180612-13_FTMSms2hcd 44.300 4 13073 19795 23761 24090 24273 16293 25736 720 36.8 1.7e-8 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1215.7259 608.3666 2 0.025 AAHQDR IDGITIQAR TMT6plex-IDGITIQAR QFQDAG 0 0 Z20180612-18_FTMSms2hcd 65.300 5 23844 85120 87821 92006 93719 64650 74675 734 31.7 7.2e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2435.3306 609.5881 4 0.85 ITIQAR QFQDAGHFDAENIKK TMT6plex-QFQDAGHFDAENIK(TMT6plex)K(TMT6plex) KQEALV 0 1 Z20180612-34_FTMSms2hcd 65.083 3 21947 29892 32662 39315 38119 32446 33712 743 51.9 7.6e-12 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1765.0112 589.0086 3 1.7 EALVAR YEALKEPMVAR TMT6plex-YEALK(TMT6plex)EPMVAR KQKLAD 0 1 Z20180612-20_FTMSms2hcd 68.917 1 24703 47654 50684 68809 56516 54470 61145 766 18.0 1.4e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1753.9259 585.3135 3 0.62 EETWIR EKEPIAASTNR TMT6plex-EK(TMT6plex)EPIAAS(Phospho)TNR GKDLIG Phospho@809=14 1 1 Z20180612-10_FTMSms2hcd 42.250 2 12285 31963 30481 39043 36968 26465 33886 802 20.9 2.8e-5 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1673.9576 558.6574 3 -0.58 EETWIR EKEPIAASTNR TMT6plex-EK(TMT6plex)EPIAASTNR GKDLIG 0 1 Z20180612-30_FTMSms2hcd 34.550 2 9457 88883 90159 101436 87985 90154 87876 802 36.0 3.3e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2124 429.4483 5 -0.65 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-02_FTMSms2hcd 40.983 1 11591 15241 15173 17212 16467 12046 13487 825 36.0 2.9e-7 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2134 536.5588 4 -0.16 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-02_FTMSms2hcd 41.183 6 11684 18572 24446 28838 25870 19778 23424 825 47.6 3.9e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2129 429.4484 5 -0.37 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-02_FTMSms2hcd 41.533 2 11825 13819 14614 14226 15780 12316 12033 825 35.5 2.1e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2149 429.4488 5 0.49 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-03_FTMSms2hcd 40.283 4 11430 20911 19195 25314 25178 16667 22742 825 51.9 7.1e-11 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2146 536.5591 4 0.40 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-03_FTMSms2hcd 40.350 5 11458 16890 18328 24048 24175 12806 22386 825 48.6 6.7e-11 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2139 429.4486 5 0.071 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-03_FTMSms2hcd 40.950 1 11707 14443 13512 14192 17140 13538 13593 825 39.2 2.5e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 2143.2118 536.5584 4 -0.85 VQNLLK KHQALQAEIAGHEPR TMT6plex-K(TMT6plex)HQALQAEIAGHEPR IKAVTQ 0 1 Z20180619-03_FTMSms2hcd 40.950 6 11712 19418 23092 27758 23908 20706 24162 825 20.8 3.4e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1785.9582 447.2450 4 1.4 QNLLKK HQALQAEIAGHEPR TMT6plex-HQALQAEIAGHEPR IKAVTQ 0 0 Z20180612-14_FTMSms2hcd 42.750 6 12973 12032 16020 13695 15056 10226 13247 826 38.7 8.4e-10 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 1798.0454 600.0200 3 0.59 AAEDVK AKLSELNQK TMT6plex-AK(TMT6plex)LS(Phospho)ELNQK(TMT6plex) WEALKA Phospho@866 1 1 Z20180612-35_FTMSms2hcd 63.550 7 20820 21352 20708 24370 27013 21308 26018 863 14.1 1.6e-4 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 3246.4970 1082.8372 3 0.31 AKASQR RQDLEDSLQAQQYFADANEAESWMR TMT6plex-RQDLEDSLQAQQYFADANEAESWM(Oxidation)R EKEPIV Oxidation@906 0 1 Z20180612-10_FTMSms2hcd 98.617 2 37204 13919 19109 24112 21988 15967 19783 883 53.6 1.9e-9 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 +[17] P16546 Sptan1 133 46.8 8.90 7.2e-16 3230.5136 1077.5094 3 3.9 AKASQR RQDLEDSLQAQQYFADANEAESWMR TMT6plex-RQDLEDSLQAQQYFADANEAESWMR EKEPIV 0 1 Z20180612-12_FTMSms2hcd 106.150 4 40971 9705 11476 14967 15908 10646 13526 883 59.9 6.8e-11 1 284599.7 MOUSE Spectrin alpha chain, non-erythrocytic 1 diff --git a/inst/tinytest/test_converters.R b/inst/tinytest/test_converters.R index da3db10..86122d0 100644 --- a/inst/tinytest/test_converters.R +++ b/inst/tinytest/test_converters.R @@ -523,4 +523,73 @@ fragpipe_input = FragPipetoMSstatsPTMFormat(input, .validateProteinId(fragpipe_input$PTM, "sp|O13563|RPN13_YEAST_S132", 4) .validatePtmSubstring( fragpipe_input$PTM, "\\*", - length(fragpipe_input$PTM$PeptideSequence)) \ No newline at end of file + length(fragpipe_input$PTM$PeptideSequence)) + + +## Protein Prospector + +#### Setup +input = system.file("tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt", + package = "MSstatsPTM") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +input_protein = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", + package = "MSstatsConvert") +input_protein = data.table::fread(input_protein) +annot_protein = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsConvert") +annot_protein = data.table::fread(annot_protein) + +#### Happy Case +expect_silent(ProteinProspectortoMSstatsPTMFormat( + input, + annot, + input_protein, + annot_protein +)) + +#### Global profiling run removed +expect_silent(ProteinProspectortoMSstatsPTMFormat( + input, + annot +)) + +#### Global profiling run removed with use_unmod_peptides = TRUE +expect_silent(ProteinProspectortoMSstatsPTMFormat( + input, + annot, + use_unmod_peptides = TRUE +)) + +#### Annotation missing +expect_error(ProteinProspectortoMSstatsPTMFormat( + input, + input_protein, + annot_protein +)) + +#### Annotation global profiling missing +expect_error(ProteinProspectortoMSstatsPTMFormat( + input, + annot, + input_protein +)) + +#### Output validation tests +protein_prospector_imported = ProteinProspectortoMSstatsPTMFormat( + input, + annot, + input_protein, + annot_protein +) +.validatePositiveNumberOfRows(protein_prospector_imported) +.validateProteinId(protein_prospector_imported$PROTEIN, "P16546", 234) +.validateProteinId(protein_prospector_imported$PTM, "P16546_S572", 6) +.validateProteinId(protein_prospector_imported$PTM, "P16546", 0) +.validatePtmSubstring( + protein_prospector_imported$PTM, "\\(Phospho\\)", + length(protein_prospector_imported$PTM$PeptideSequence)) +.validatePtmSubstring( + protein_prospector_imported$PROTEIN, "\\(Phospho\\)", 0) \ No newline at end of file diff --git a/man/PDtoMSstatsPTMFormat.Rd b/man/PDtoMSstatsPTMFormat.Rd index f997d11..43b60f6 100644 --- a/man/PDtoMSstatsPTMFormat.Rd +++ b/man/PDtoMSstatsPTMFormat.Rd @@ -117,6 +117,36 @@ automatically. If 'append = TRUE', has to be a valid path to a file.} Import Proteome Discoverer files, identify modification site location. } \examples{ +# Global profiling example +input = system.file("tinytest/raw_data/PD/pd-ptm-input.csv", +package = "MSstatsPTM") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/PD/pd-ptm-annot.csv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +input_protein = system.file("tinytest/raw_data/PD/protein-input.csv", + package = "MSstatsPTM") +input_protein = data.table::fread(input_protein) +annot_protein = system.file("tinytest/raw_data/PD/protein-annot.csv", + package = "MSstatsPTM") +annot_protein = data.table::fread(annot_protein) +fasta_path=system.file("extdata", "pd_with_proteome.fasta", + package="MSstatsPTM") +pd_imported = PDtoMSstatsPTMFormat( + input, + annotation = annot, + protein_input = input_protein, + annotation_protein = annot_protein, + fasta_path = fasta_path, + mod_id = "\\\\(GG\\\\)", + labeling_type = "TMT", + use_localization_cutoff = FALSE, + which_proteinid = "Master.Protein.Accessions") + +head(pd_imported$PTM) +head(pd_imported$PROTEIN) + +# No global profiling example head(pd_psm_input) head(pd_annotation) diff --git a/man/ProteinProspectortoMSstatsPTMFormat.Rd b/man/ProteinProspectortoMSstatsPTMFormat.Rd new file mode 100644 index 0000000..0604519 --- /dev/null +++ b/man/ProteinProspectortoMSstatsPTMFormat.Rd @@ -0,0 +1,103 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/converters.R +\name{ProteinProspectortoMSstatsPTMFormat} +\alias{ProteinProspectortoMSstatsPTMFormat} +\title{Generate MSstatsPTM required input format from Protein Prospector output} +\usage{ +ProteinProspectortoMSstatsPTMFormat( + input, + annotation, + input_protein = NULL, + annotation_protein = NULL, + use_unmod_peptides = FALSE, + mod_ids = c("\\\\(Phospho\\\\)"), + useUniquePeptide = TRUE, + removeFewMeasurements = TRUE, + removeProtein_with1Feature = FALSE, + summaryforMultipleRows = sum, + use_log_file = TRUE, + append = FALSE, + verbose = TRUE, + log_file_path = NULL +) +} +\arguments{ +\item{input}{Input txt peptide report file from Protein Prospector with +"Keep Replicates", "Mods in Peptide", and "Protein Mods" options selected.} + +\item{annotation}{data frame which contains column Run, Fraction, +TechRepMixture, Mixture, Channel, BioReplicate, Condition.} + +\item{input_protein}{same as \code{input} for global profiling run. Default is NULL.} + +\item{annotation_protein}{same as \code{annotation} for global profiling run. Default is NULL.} + +\item{use_unmod_peptides}{If \code{protein_input} is not provided, +unmodified peptides can be extracted from \code{input} to be used in place of a +global profiling run. Default is \code{FALSE}.} + +\item{mod_ids}{List of modifications of interest. Default +is a list with only \verb{\\\\(Phospho\\\\)}. +Please note that the 'mod_ids' parameter currently supports lists of size 1 only. +Future updates aim to extend its functionality to accommodate lists of greater sizes. +Note \verb{\\\\} must be included before special characters.} + +\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}{sum(default) or max - 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 'append = TRUE', has to be a valid path to a file.} +} +\value{ +a list of two data.tables named 'PTM' and 'PROTEIN' in the format +required by MSstatsPTM. +} +\description{ +Generate MSstatsPTM required input format from Protein Prospector output +} +\examples{ +input = system.file("tinytest/raw_data/ProteinProspector/Prospector_PhosphoTMT.txt", + package = "MSstatsPTM") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +input_protein = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt", + package = "MSstatsConvert") +input_protein = data.table::fread(input_protein) +annot_protein = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv", + package = "MSstatsConvert") +annot_protein = data.table::fread(annot_protein) +output <- ProteinProspectortoMSstatsPTMFormat( + input, + annot, + input_protein, + annot_protein +) +head(output) + +} +\author{ +Anthony Wu +} From 5298cd121835a5282de6c8cf7885239eb2a44db8 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 16 Sep 2024 17:09:28 -0400 Subject: [PATCH 2/5] set replace_text = TRUE for MSstats PTM site locator --- R/converters.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/converters.R b/R/converters.R index 9826643..484ad43 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1720,7 +1720,8 @@ ProteinProspectortoMSstatsPTMFormat = function( clean_mod=FALSE, mod_id=mod_id, remove_other_mods = TRUE, - bracket = "(" + bracket = "(", + replace_text = TRUE ) if (use_unmod_peptides){ From f2fbdb3e908236f6e8b868bbde13832e77d689e8 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 16 Sep 2024 18:26:02 -0400 Subject: [PATCH 3/5] set remove_other_mods to FALSE --- R/converters.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/converters.R b/R/converters.R index 484ad43..dd92f30 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1719,7 +1719,6 @@ ProteinProspectortoMSstatsPTMFormat = function( mod_pep_col = "Peptide", clean_mod=FALSE, mod_id=mod_id, - remove_other_mods = TRUE, bracket = "(", replace_text = TRUE ) From 98e637243ec6ce0733663e221b3108f515a9e1e9 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Fri, 1 Nov 2024 16:50:29 -0400 Subject: [PATCH 4/5] fixed bug related to multiple modifications --- R/converters.R | 5 +++-- inst/tinytest/test_converters.R | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/R/converters.R b/R/converters.R index dd92f30..ace8574 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1685,7 +1685,7 @@ ProteinProspectortoMSstatsPTMFormat = function( input_protein = NULL, annotation_protein = NULL, use_unmod_peptides = FALSE, - mod_ids = c("\\(Phospho\\)"), + mod_ids = c("Phospho"), useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, @@ -1711,6 +1711,7 @@ ProteinProspectortoMSstatsPTMFormat = function( input$Peptide = gsub("TMT[0-9]*plex-", "", input$Peptide) # remove TMT tags input = input[!grepl("\\|", input$`Protein Mods`),] # filter out rows with uncertainty in protein mods + input$Peptide = gsub(paste0("\\((?!", mod_id, "\\)).*?\\)"), "", input$Peptide, perl=TRUE) # filter out other modifications protein_id_col = "Acc #" input = MSstatsPTMSiteLocator(input, @@ -1718,7 +1719,7 @@ ProteinProspectortoMSstatsPTMFormat = function( unmod_pep_col = "DB Peptide", mod_pep_col = "Peptide", clean_mod=FALSE, - mod_id=mod_id, + mod_id=paste0("\\(", mod_id, "\\)"), bracket = "(", replace_text = TRUE ) diff --git a/inst/tinytest/test_converters.R b/inst/tinytest/test_converters.R index 86122d0..52d9089 100644 --- a/inst/tinytest/test_converters.R +++ b/inst/tinytest/test_converters.R @@ -587,6 +587,7 @@ protein_prospector_imported = ProteinProspectortoMSstatsPTMFormat( .validatePositiveNumberOfRows(protein_prospector_imported) .validateProteinId(protein_prospector_imported$PROTEIN, "P16546", 234) .validateProteinId(protein_prospector_imported$PTM, "P16546_S572", 6) +.validateProteinId(protein_prospector_imported$PTM, "Q9QYX7_S617_S625", 6) .validateProteinId(protein_prospector_imported$PTM, "P16546", 0) .validatePtmSubstring( protein_prospector_imported$PTM, "\\(Phospho\\)", From e6651d9407f8cea8251990dd2548eaa1669f8176 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Fri, 1 Nov 2024 17:09:02 -0400 Subject: [PATCH 5/5] fixed tests --- R/converters.R | 3 +-- man/ProteinProspectortoMSstatsPTMFormat.Rd | 7 +++---- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/R/converters.R b/R/converters.R index ace8574..ebd1849 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1629,10 +1629,9 @@ MetamorpheusToMSstatsPTMFormat = function(input, #' unmodified peptides can be extracted from `input` to be used in place of a #' global profiling run. Default is `FALSE`. #' @param mod_ids List of modifications of interest. Default -#' is a list with only `\\(Phospho\\)`. +#' is a list with only `Phospho`. #' Please note that the 'mod_ids' parameter currently supports lists of size 1 only. #' Future updates aim to extend its functionality to accommodate lists of greater sizes. -#' Note `\\` must be included before special characters. #' @param useUniquePeptide TRUE (default) removes peptides that are assigned for #' more than one proteins. We assume to use unique peptide for each protein. #' @param removeFewMeasurements TRUE (default) will remove the features that diff --git a/man/ProteinProspectortoMSstatsPTMFormat.Rd b/man/ProteinProspectortoMSstatsPTMFormat.Rd index 0604519..ef25b78 100644 --- a/man/ProteinProspectortoMSstatsPTMFormat.Rd +++ b/man/ProteinProspectortoMSstatsPTMFormat.Rd @@ -10,7 +10,7 @@ ProteinProspectortoMSstatsPTMFormat( input_protein = NULL, annotation_protein = NULL, use_unmod_peptides = FALSE, - mod_ids = c("\\\\(Phospho\\\\)"), + mod_ids = c("Phospho"), useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, @@ -37,10 +37,9 @@ unmodified peptides can be extracted from \code{input} to be used in place of a global profiling run. Default is \code{FALSE}.} \item{mod_ids}{List of modifications of interest. Default -is a list with only \verb{\\\\(Phospho\\\\)}. +is a list with only \code{Phospho}. Please note that the 'mod_ids' parameter currently supports lists of size 1 only. -Future updates aim to extend its functionality to accommodate lists of greater sizes. -Note \verb{\\\\} must be included before special characters.} +Future updates aim to extend its functionality to accommodate lists of greater sizes.} \item{useUniquePeptide}{TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.}