From ab468b8e359606014a241daf2564d90ce6fea14d Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Tue, 20 Feb 2024 15:05:23 -0500 Subject: [PATCH 1/2] feat(metamorpheus-converter): Create converter for Metamorpheus to MSstatsPTM format --- DESCRIPTION | 2 +- NAMESPACE | 4 +- R/converters.R | 130 ++++++++ inst/extdata/metamorpheus_fasta.fasta | 217 +++++++++++++ .../Metamorpheus/AllQuantifiedPeaks.tsv | 293 ++++++++++++++++++ .../Metamorpheus/ExperimentalDesign.tsv | 7 + inst/tinytest/test_converters.R | 18 ++ man/MSstatsPTM.Rd | 21 ++ man/MetamorpheusToMSstatsPTMFormat.Rd | 94 ++++++ 9 files changed, 783 insertions(+), 3 deletions(-) create mode 100644 inst/extdata/metamorpheus_fasta.fasta create mode 100644 inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv create mode 100644 inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv create mode 100644 man/MetamorpheusToMSstatsPTMFormat.Rd diff --git a/DESCRIPTION b/DESCRIPTION index e5639e7..e6d3316 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,4 +32,4 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.0 diff --git a/NAMESPACE b/NAMESPACE index 62dd0e6..e94057b 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ export(DIANNtoMSstatsPTMFormat) export(FragPipetoMSstatsPTMFormat) export(MSstatsPTMSiteLocator) export(MaxQtoMSstatsPTMFormat) +export(MetamorpheusToMSstatsPTMFormat) export(PDtoMSstatsPTMFormat) export(PStoMSstatsPTMFormat) export(ProgenesistoMSstatsPTMFormat) @@ -37,6 +38,7 @@ importFrom(MSstats,theme_msstats) importFrom(MSstatsConvert,MSstatsBalancedDesign) importFrom(MSstatsConvert,MSstatsLogsSettings) importFrom(MSstatsConvert,MSstatsSaveSessionInfo) +importFrom(MSstatsConvert,MetamorpheusToMSstatsFormat) importFrom(MSstatsTMT,MaxQtoMSstatsTMTFormat) importFrom(MSstatsTMT,PDtoMSstatsTMTFormat) importFrom(MSstatsTMT,PhilosophertoMSstatsTMTFormat) @@ -47,8 +49,6 @@ importFrom(checkmate,assertCharacter) importFrom(checkmate,assertChoice) importFrom(checkmate,assertLogical) importFrom(checkmate,assertNumeric) -importFrom(data.table,`%like%`) -importFrom(data.table,`:=`) importFrom(data.table,as.data.table) importFrom(data.table,copy) importFrom(data.table,data.table) diff --git a/R/converters.R b/R/converters.R index 791c59f..49bb7de 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1405,4 +1405,134 @@ SpectronauttoMSstatsPTMFormat = function( } return(msstats_input) +} + +#' Import Metamorpheus files into PTM format +#' +#' @author Anthony Wu +#' +#' @param input name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output. +#' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate. +#' @param fasta_path string containing path to the corresponding fasta file for +#' the modified peptide dataset. +#' @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_id Character that indicates the modification of interest. Default +#' is `Common Biological:Phosphorylation on S`. +#' 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 max(default) or sum - 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 MetamorpheusToMSstatsFormat +#' @export +#' +#' @examples +#' input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", +#' package = "MSstatsPTM") +#' input = data.table::fread(input) +#' annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", +#' package = "MSstatsPTM") +#' annot = data.table::fread(annot) +#' fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", +#' package="MSstatsPTM") +#' metamorpheus_imported = MetamorpheusToMSstatsPTMFormat( +#' input, +#' annot, +#' fasta_path=fasta_path, +#' use_unmod_peptides=TRUE, +#' mod_id = "\\[Common Fixed:Carbamidomethyl on C\\]" +#' ) +#' head(metamorpheus_imported$PTM) +#' head(metamorpheus_imported$PROTEIN) +MetamorpheusToMSstatsPTMFormat = function(input, + annotation, + fasta_path, + use_unmod_peptides = FALSE, + mod_id = "\\[Common Biological:Phosphorylation on S\\]", + useUniquePeptide = TRUE, + removeFewMeasurements = TRUE, + removeProtein_with1Feature = FALSE, + summaryforMultipleRows = max, + 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_") + + input = as.data.table(input) + + ## Check input parameters + checkmate::assertTRUE(!is.null(input)) + .checkAnnotation(annotation, "LF") + + fasta = MSstatsPTM::tidyFasta(fasta_path) + + protein_id_col = "Protein Group" + input = MSstatsPTMSiteLocator(input, + protein_name_col=protein_id_col, + unmod_pep_col="Base Sequence", + mod_pep_col="Full Sequence", + fasta_file=fasta, + mod_id=mod_id, + fasta_protein_name="uniprot_iso") + + if (use_unmod_peptides){ + protein_input = input[input[,..protein_id_col][[1]] == input$ProteinNameUnmod] + annotation_protein = annotation + } else { + input = input[input[,..protein_id_col][[1]] != input$ProteinNameUnmod] + } + + ptm_input = MetamorpheusToMSstatsFormat(input, + annotation, + useUniquePeptide, + removeFewMeasurements, + removeProtein_with1Feature, + summaryforMultipleRows, + use_log_file, + append, + verbose, + log_file_path) + + msstats_format = list(PTM = ptm_input, PROTEIN = NULL) + + if (use_unmod_peptides) { + protein_input = MetamorpheusToMSstatsFormat(protein_input, + annotation_protein, + useUniquePeptide, + removeFewMeasurements, + removeProtein_with1Feature, + summaryforMultipleRows, + use_log_file, + append, + verbose, + log_file_path) + + msstats_format = list(PTM = ptm_input, PROTEIN = protein_input) + } + + return(msstats_format) + } \ No newline at end of file diff --git a/inst/extdata/metamorpheus_fasta.fasta b/inst/extdata/metamorpheus_fasta.fasta new file mode 100644 index 0000000..f27114e --- /dev/null +++ b/inst/extdata/metamorpheus_fasta.fasta @@ -0,0 +1,217 @@ +>sp|O14950|ML12B_HUMAN Myosin regulatory light chain 12B OS=Homo sapiens OX=9606 GN=MYL12B PE=1 SV=2 +MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLAS +LGKNPTDAYLDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQE +DYLRELLTTMGDRFTDEEVDELYREAPIDKKGNFNYIEFTRILKHGAKDKDD +>sp|O95817|BAG3_HUMAN BAG family molecular chaperone regulator 3 OS=Homo sapiens OX=9606 GN=BAG3 PE=1 SV=3 +MSAATHSPMMQVASGNGDRDPLPPGWEIKIDPQTGWPFFVDHNSRTTTWNDPRVPSEGPK +ETPSSANGPSREGSRLPPAREGHPVYPQLRPGYIPIPVLHEGAENRQVHPFHVYPQPGMQ +RFRTEAAAAAPQRSQSPLRGMPETTQPDKQCGQVAAAAAAQPPASHGPERSQSPAASDCS +SSSSSASLPSSGRSSLGSHQLPRGYISIPVIHEQNVTRPAAQPSFHQAQKTHYPAQQGEY +QTHQPVYHKIQGDDWEPRPLRAASPFRSSVQGASSREGSPARSSTPLHSPSPIRVHTVVD +RPQQPMTHRETAPVSQPENKPESKPGPVGPELPPGHIPIQVIRKEVDSKPVSQKPPPPSE +KVEVKVPPAPVPCPPPSPGPSAVPSSPKSVATEERAAPSTAPAEATPPKPGEAEAPPKHP +GVLKVEAILEKVQGLEQAVDNFEGKKTDKKYLMIEEYLTKELLALDSVDPEGRADVRQAR +RDGVRKVQTILEKLEQKAIDVPGQVQVYELQPSNLEADQPLQAIMEMGAVAADKGKKNAG +NAEDPHTETQQPEATAAATSNPSSMTDTPGNPAAP +>sp|P04406|G3P_HUMAN Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens OX=9606 GN=GAPDH PE=1 SV=3 +MGKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTV +KAENGKLVINGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVI +ISAPSADAPMFVMGVNHEKYDNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHA +ITATQKTVDGPSGKLWRDGRGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANV +SVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQVVSSDFNSDTHSSTFDAGAG +IALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE +>sp|P06493|CDK1_HUMAN Cyclin-dependent kinase 1 OS=Homo sapiens OX=9606 GN=CDK1 PE=1 SV=3 +MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRH +PNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCH +SRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSAR +YSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNT +FPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM +>sp|P06748|NPM_HUMAN Nucleophosmin OS=Homo sapiens OX=9606 GN=NPM1 PE=1 SV=2 +MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIV +EAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVE +EDAESEDEEEEDVKLLSISGKRSAPGGGSKVPQKKVKLAADEDDDDDDEEDDDEDDDDDD +FDDEEAEEKAPVKKSIRDTPAKNAQKSNQNGKDSKPSSTPRSKGQESFKKQEKTPKTPKG +PSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL +>sp|P07355|ANXA2_HUMAN Annexin A2 OS=Homo sapiens OX=9606 GN=ANXA2 PE=1 SV=2 +MSTVHEILCKLSLEGDHSTPPSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNIL +TNRSNAQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKG +LGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRA +EDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDM +LESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDM +LKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD +>sp|P08670|VIME_HUMAN Vimentin OS=Homo sapiens OX=9606 GN=VIM PE=1 SV=4 +MSTRSVSSSSYRRMFGGPGTASRPSSSRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGV +YATRSSAVRLRSSVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDK +VRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAE +DIMRLREKLQEEMLQREEAENTLQSFRQDVDNASLARLDLERKVESLQEEIAFLKKLHEE +EIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSE +AANRNNDALRQAKQESTEYRRQVQSLTCEVDALKGTNESLERQMREMEENFAVEAANYQD +TIGRLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSS +LNLRETNLDSLPLVDTHSKRTLLIKTVETRDGQVINETSQHHDDLE +>sp|P19105|ML12A_HUMAN Myosin regulatory light chain 12A OS=Homo sapiens OX=9606 GN=MYL12A PE=1 SV=2 +MSSKRTKTKTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASL +GKNPTDEYLDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQED +YLRELLTTMGDRFTDEEVDELYREAPIDKKGNFNYIEFTRILKHGAKDKDD +>sp|P24844|MYL9_HUMAN Myosin regulatory light polypeptide 9 OS=Homo sapiens OX=9606 GN=MYL9 PE=1 SV=4 +MSSKRAKAKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLAS +LGKNPTDEYLEGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHE +DHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNFNYVEFTRILKHGAKDKDD +>sp|P24941|CDK2_HUMAN Cyclin-dependent kinase 2 OS=Homo sapiens OX=9606 GN=CDK2 PE=1 SV=2 +MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH +PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS +HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY +STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF +PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL +>sp|P35579|MYH9_HUMAN Myosin-9 OS=Homo sapiens OX=9606 GN=MYH9 PE=1 SV=4 +MAQQAADKYLYVDKNFINNPLAQADWAAKKLVWVPSDKSGFEPASLKEEVGEEAIVELVE +NGKKVKVNKDDIQKMNPPKFSKVEDMAELTCLNEASVLHNLKERYYSGLIYTYSGLFCVV +INPYKNLPIYSEEIVEMYKGKKRHEMPPHIYAITDTAYRSMMQDREDQSILCTGESGAGK +TENTKKVIQYLAYVASSHKSKKDQGELERQLLQANPILEAFGNAKTVKNDNSSRFGKFIR +INFDVNGYIVGANIETYLLEKSRAIRQAKEERTFHIFYYLLSGAGEHLKTDLLLEPYNKY +RFLSNGHVTIPGQQDKDMFQETMEAMRIMGIPEEEQMGLLRVISGVLQLGNIVFKKERNT +DQASMPDNTAAQKVSHLLGINVTDFTRGILTPRIKVGRDYVQKAQTKEQADFAIEALAKA +TYERMFRWLVLRINKALDKTKRQGASFIGILDIAGFEIFDLNSFEQLCINYTNEKLQQLF +NHTMFILEQEEYQREGIEWNFIDFGLDLQPCIDLIEKPAGPPGILALLDEECWFPKATDK +SFVEKVMQEQGTHPKFQKPKQLKDKADFCIIHYAGKVDYKADEWLMKNMDPLNDNIATLL 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+GPLGSPPKRGPLPTEEQRVYRRKELEEVSPETPVVPATTQRTLARPGPEPAPATDERDRV +QKKTFTKWVNKHLIKAQRHISDLYEDLRDGHNLISLLEVLSGDSLPREKGRMRFHKLQNV +QIALDYLRHRQVKLVNIRNDDIADGNPKLTLGLIWTIILHFQISDIQVSGQSEDMTAKEK +LLLWSQRMVEGYQGLRCDNFTSSWRDGRLFNAIIHRHKPLLIDMNKVYRQTNLENLDQAF +SVAERDLGVTRLLDPEDVDVPQPDEKSIITYVSSLYDAMPRVPDVQDGVRANELQLRWQE +YRELVLLLLQWMRHHTAAFEERRFPSSFEEIEILWSQFLKFKEMELPAKEADKNRSKGIY +QSLEGAVQAGQLKVPPGYHPLDVEKEWGKLHVAILEREKQLRSEFERLECLQRIVTKLQM +EAGLCEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGR +HPQGEQMYRRVYRLHERLVAIRTEYNLRLKAGVAAPATQVAQVTLQSVQRRPELEDSTLR +YLQDLLAWVEENQHRVDGAEWGVDLPSVEAQLGSHRGLHQSIEEFRAKIERARSDEGQLS +PATRGAYRDCLGRLDLQYAKLLNSSKARLRSLESLHSFVAAATKELMWLNEKEEEEVGFD +WSDRNTNMTAKKESYSALMRELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQ +WSWMLQLCCCIEAHLKENAAYFQFFSDVREAEGQLQKLQEALRRKYSCDRSATVTRLEDL +LQDAQDEKEQLNEYKGHLSGLAKRAKAVVQLKPRHPAHPMRGRLPLLAVCDYKQVEVTVH +KGDECQLVGPAQPSHWKVLSSSGSEAAVPSVCFLVPPPNQEAQEAVTRLEAQHQALVTLW +HQLHVDMKSLLAWQSLRRDVQLIRSWSLATFRTLKPEEQRQALHSLELHYQAFLRDSQDA 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+YLQLLERCVEDPETGLCLLPLTDKAAKGGELVYTDSEARDVFEKATVSAPFGKFQGKTVT +IWEIINSEYFTAEQRRDLLRQFRTGRITVEKIIKIIITVVEEQEQKGRLCFEGLRSLVPA +AELLESRVIDRELYQQLQRGERSVRDVAEVDTVRRALRGANVIAGVWLEEAGQKLSIYNA +LKKDLLPSDMAVALLEAQAGTGHIIDPATSARLTVDEAVRAGLVGPEFHEKLLSAEKAVT +GYRDPYTGQSVSLFQALKKGLIPREQGLRLLDAQLSTGGIVDPSKSHRVPLDVACARGCL +DEETSRALSAPRADAKAYSDPSTGEPATYGELQQRCRPDQLTGLSLLPLSEKAARARQEE +LYSELQARETFEKTPVEVPVGGFKGRTVTVWELISSEYFTAEQRQELLRQFRTGKVTVEK +VIKILITIVEEVETLRQERLSFSGLRAPVPASELLASGVLSRAQFEQLKDGKTTVKDLSE +LGSVRTLLQGSGCLAGIYLEDTKEKVSIYEAMRRGLLRATTAALLLEAQAATGFLVDPVR +NQRLYVHEAVKAGVVGPELHEQLLSAEKAVTGYRDPYSGSTISLFQAMQKGLVLRQHGIR +LLEAQIATGGIIDPVHSHRVPVDVAYQRGYFSEEMNRVLADPSDDTKGFFDPNTHENLTY +RQLLERCVEDPETGLRLLPLKGAEKAEVVETTQVYTEEETRRAFEETQIDIPGGGSHGGS +TMSLWEVMQSDLIPEEQRAQLMADFQAGRVTKERMIIIIIEIIEKTEIIRQQGLASYDYV +RRRLTAEDLFEARIISLETYNLLREGTRSLREALEAESAWCYLYGTGSVAGVYLPGSRQT +LSIYQALKKGLLSAEVARLLLEAQAATGFLLDPVKGERLTVDEAVRKGLVGPELHDRLLS +AERAVTGYRDPYTEQTISLFQAMKKELIPTEEALRLLDAQLATGGIVDPRLGFHLPLEVA +YQRGYLNKDTHDQLSEPSEVRSYVDPSTDERLSYTQLLRRCRRDDGTGQLLLPLSDARKL +TFRGLRKQITMEELVRSQVMDEATALQLREGLTSIEEVTKNLQKFLEGTSCIAGVFVDAT +KERLSVYQAMKKGIIRPGTAFELLEAQAATGYVIDPIKGLKLTVEEAVRMGIVGPEFKDK +LLSAERAVTGYKDPYSGKLISLFQAMKKGLILKDHGIRLLEAQIATGGIIDPEESHRLPV +EVAYKRGLFDEEMNEILTDPSDDTKGFFDPNTEENLTYLQLMERCITDPQTGLCLLPLKE +KKRERKTSSKSSVRKRRVVIVDPETGKEMSVYEAYRKGLIDHQTYLELSEQECEWEEITI +SSSDGVVKSMIIDRRSGRQYDIDDAIAKNLIDRSALDQYRAGTLSITEFADMLSGNAGGF +RSRSSSVGSSSSYPISPAVSRTQLASWSDPTEETGPVAGILDTETLEKVSITEAMHRNLV +DNITGQRLLEAQACTGGIIDPSTGERFPVTDAVNKGLVDKIMVDRINLAQKAFCGFEDPR +TKTKMSAAQALKKGWLYYEAGQRFLEVQYLTGGLIEPDTPGRVPLDEALQRGTVDARTAQ +KLRDVGAYSKYLTCPKTKLKISYKDALDRSMVEEGTGLRLLEAAAQSTKGYYSPYSVSGS +GSTAGSRTGSRTGSRAGSRRGSFDATGSGFSMTFSSSSYSSSGYGRRYASGSSASLGGPE +SAVA +>sp|Q8N3V7|SYNPO_HUMAN Synaptopodin OS=Homo sapiens OX=9606 GN=SYNPO PE=1 SV=2 +MLGPHLPPPPLAPSEGRPTPCAFQIPDGSYRCLALEAEESSGEEGLQGEVGPTDLEEDEG +VSRSGDDSACRVTQGTPQLPKALGIQPPSCSREEQGASQHDDRASQDWDVVKAGQMMTAS +PSPGPGPRVAQKPALGRSTSLTEKDLKEAKARSQQIAAQLTTPPSSNSRGVQLFNRRRQR +VNEFTLESHGQRGQKPSQESLRVLPSSLPGHAPGLSLSSTSLPEPGPPRHPSPQSPDRGV +PGHSMEGYSEEASLLRHLEKVASEEEEVPLVVYLKENAALLTANGLHLSQNREAQQSSPA +PPPAEVHSPAADVNQNLASPSATLTTPTSNSSHNPPATDVNQNPPATVVPQSLPLSSIQQ +NSSEAQLPSNGTGPASKPSTLCADGQPQAPAEEVRCSTLLIDKVSTPATTTSTFSREATL +IPSSRPPASDFMSSSLLIDIQPNTLVVSADQEMSGRAAATTPTKVYSEVHFTLAKPPSVV +NRTARPFGIQAPGGTSQMERSPMLERRHFGEKAPAPQPPSLPDRSPRPQRHIMSRSPMVE +RRMMGQRSPASERRPLGNFTAPPTYTETLSTAPLASWVRSPPSYSVLYPSSDPKSSHLKG +QAVPASKTGILEESMARRGSRKSMFTFVEKPKVTPNPDLLDLVQTADEKRRQRDQGEVGV +EEEPFALGAEASNFQQEPAPRDRASPAAAEEVVPEWASCLKSPRIQAKPKPKPNQNLSEA +SGKGAELYARRQSRMEKYVIESSSHTPELARCPSPTMSLPSSWKYPTNAPGAFRVASRSP +ARTPPASLYHGYLPENGVLRPEPTKQPPYQLRPSLFVLSPIKEPAKVSPRAASPAKPSSL +DLVPNLPKGALPPSPALPRPSRSSPGLYTSPGQDSLQPTAVSPPYGGDISPVSPSRAWSP +RAKQAPRPSFSTRNAGIEAQVWKPSFCFK diff --git a/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv b/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv new file mode 100644 index 0000000..3fcc382 --- /dev/null +++ b/inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv @@ -0,0 +1,293 @@ +File Name Base Sequence Full Sequence Protein Group Peptide Monoisotopic Mass MS2 Retention Time Precursor Charge Theoretical MZ Peak intensity Peak RT Start Peak RT Apex Peak RT End Peak MZ Peak Charge Num Charge States Observed Peak Detection Type MBR Score PSMs Mapped Base Sequences Mapped Full Sequences Mapped Peak Split Valley RT Peak Apex Mass Error (ppm) +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 50.397666666666666 2 1140.4577332313788 514664.08591409435 50.252475 50.42875166666666 50.510398333333335 1140.9592170625633 2 2 MSMS 1 1 1 0 0.087875825 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 201052.45584649045 54.139628333333334 54.50228833333333 54.78205 719.8097832775803 2 1 MBR 1.7336595330500857 1 1 1 0 -0.311308359 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 2 1140.4577332313788 496019.5469859136 50.199040000000004 50.302225 50.42404833333333 1140.9595414912699 2 1 MBR 9.237016638440622 4 1 1 0 0.37247443285717907 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 209822.54186753198 54.17451 54.392965000000004 54.88590333333333 719.8097491 2 1 MBR 1.422384388178278 1 1 1 0 -0.358883303 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 50.485704999999996 2 1140.4577332313788 539475.7012 50.434225 50.520723333333336 50.60698166666666 1140.959128847675 2 2 MSMS 1 1 1 0 0.010491075055972502 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 189233.38037109375 54.25706666666666 54.50651166666667 54.86478666666667 719.8098241563564 2 1 MBR 2.4282804908957543 1 1 1 0 -0.254437713 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 50.24521666666667 2 1140.4577332313788 459901.17559790844 50.14263166666667 50.26945666666666 50.430398333333336 1140.9589278462745 2 2 MSMS 1 1 1 0 -0.165833392 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 183782.10978723018 53.806178333333335 54.028675 54.510915000000004 719.8098787441593 2 1 MBR 2.168093031859773 1 1 1 0 -0.178495037 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 2 1140.4577332313788 444473.2927530834 49.849804999999996 50.00181666666667 50.114315000000005 1140.9588663284128 2 1 MBR 10.628773655532353 4 1 1 0 -0.219798708 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 53.68306 2 719.810007 189586.42210977216 53.60731 53.89033833333333 54.396258333333336 719.8099571080513 2 1 MSMS 1 1 1 0 -0.069475011 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib SQSPAASDCSSSSSSASLPSSGR SQS[UniProt:Phosphoserine on S]PAASDC[Common Fixed:Carbamidomethyl on C]SSSSSSASLPSSGR O95817 2278.900914 50.46595666666666 2 1140.4577332313788 457509.04289748595 50.35503333333333 50.481355 50.5779 1140.9589799857106 2 2 MSMS 1 1 1 0 -0.120095112 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib SSTPLHSPSPIR SST[UniProt:Phosphothreonine on T]PLHS[UniProt:Phosphoserine on S]PSPIR O95817 1437.605461 2 719.810007 188819.1301057861 54.11136166666667 54.372384999999994 55.001846666666665 719.8100047536697 2 1 MBR 2.0350377595656686 1 1 1 0 -0.003190318 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib VIHDNFGIVEGLMTTVHAITATQK VIHDNFGIVEGLM[Common Variable:Oxidation on M]TTVHAITATQK P04406 2610.347573 98.31652333333332 3 871.123134 1702536.1320496653 98.28782666666667 98.32741166666666 98.360585 653.8446076628446 4 2 MSMS 1 1 1 0 -0.429702408 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 2 882.404826 95820.55094827108 93.01209666666666 93.110345 93.17617166666666 882.4051769967726 2 1 MBR 1.3844209718432765 2 1 1 0 0.39819533623516207 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 2 917.4635038718791 57073.40135267524 68.91320166666667 68.95002833333334 69.061615 917.4641235146242 2 1 MBR 3.544002054421164 4 1 1 0 0.6761291227241661 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib VIHDNFGIVEGLMTTVHAITATQK VIHDNFGIVEGLMTTVHAITATQK P04406 2594.352658 98.74340666666666 3 865.7914958082124 815201.3073146566 98.71828333333333 98.71828333333333 98.71828333333333 649.8463982326466 4 2 MSMS 1 1 1 0 0.36788625755414295 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 2 882.404826 72270.30850735056 92.89875333333333 93.006125 93.10159333333334 882.4049859757685 2 1 MBR 0.4513434646036635 1 1 1 0 0.18147019979785753 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 2 917.4635038718791 54425.40501713606 68.891375 68.94847333333333 69.00958 917.4665113509099 2 1 MBR 2.991679342894218 4 1 1 0 3.2816395816011608 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib VIHDNFGIVEGLMTTVHAITATQK VIHDNFGIVEGLMTTVHAITATQK P04406 2594.352658 98.593295 3 865.7914958082124 1215513.5208333333 98.5787 98.59860166666667 98.62301 866.1252851711644 3 2 MSMS 2 1 1 0 -0.580326881 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 69.54576999999999 2 917.4635038718791 174026.61323525844 69.415515 69.56714333333333 69.75951166666667 917.4637105142335 2 1 MSMS 1 1 1 0 0.2254797863215394 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 2 882.404826 83212.58009091942 93.25224666666666 93.33665833333333 93.62745666666666 882.4051356 2 1 MBR 1.7943852080916343 3 1 1 0 0.3512743905036857 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 69.55684000000001 2 917.4635038718791 192936.39195841277 69.43142666666667 69.56289333333334 69.73079333333334 917.4653036266075 2 1 MSMS 1 1 1 0 1.9638196287493792 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 93.6715 2 882.404826 58596.690864839715 93.62020166666667 93.724005 93.87557166666667 882.4037472150617 2 1 MSMS 1 1 1 0 -1.223980391 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 69.47715166666667 2 917.4635038718791 367699.6554610786 69.43728 69.56315833333333 69.793805 917.4633891549909 2 1 MSMS 1 1 1 0 -0.125174433 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 94.02937166666666 2 882.404826 84532.11190517797 93.88877166666667 93.98134666666667 94.10935333333333 882.4045280785009 2 1 MSMS 1 1 1 0 -0.338042553 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IISNASCTTNCLAPLAK IISNASC[Common Fixed:Carbamidomethyl on C]TTNC[Common Fixed:Carbamidomethyl on C]LAPLAK P04406 1832.912455 70.08695999999999 2 917.4635038718791 350856.5977285622 70.002 70.17507333333333 70.43004499999999 917.4635070818939 2 1 MSMS 1 1 1 0 0.003502638 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib VIHDNFGIVEGLMTTVHAITATQK VIHDNFGIVEGLMTTVHAITATQK P04406 2594.352658 98.73205666666667 3 865.7914958082124 131577.98028759114 98.69229 98.71633 98.71633 649.8449416712751 4 2 MSMS 1 1 1 0 -1.876987485 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib LISWYDNEFGYSNR LISWYDNEFGYSNR P04406 1762.795099 94.15219333333333 2 882.404826 71098.44557431604 94.05792 94.21552 94.38573000000001 882.4051187043918 2 1 MSMS 1 1 1 0 0.33205902711031177 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 62.24373166666666 4 1062.393097385379 3828526.379 61.59261166666667 62.311673333333324 62.752480000000006 1062.8944646659804 4 2 MSMS 1 1 1 0 -0.068680686 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib CGSGPVHISGQHLVAVEEDAESEDEEEEDVK C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK P06748 3459.429734 71.57300833333333 3 1154.1505210652124 224148.3621753267 71.375275 71.52819833333332 71.77767833333333 1154.4851800721635 3 2 MSMS 1 1 1 0 0.31938580542822653 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 3 1241.738965164879 124040.74252710001 64.12654166666667 64.14200833333334 64.32642666666668 1242.0725076420179 3 1 MBR 1.3565358778983123 2 1 1 64.369135 -0.627621066 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 3 1317.4600908082123 27389.023508129154 67.225645 67.32419666666667 67.32419666666667 1318.1285234390814 3 1 MBR 1.4107984594378558 1 1 1 0 -0.115889578 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 3 1241.738965164879 8151514.291 64.54514499999999 65.3379 66.52528833333334 1242.0775380269372 3 1 MBR 0.9866542585816164 1 1 1 0 3.4256564220608574 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 4 1062.393097385379 3175122.8476175754 61.364106666666665 62.07816999999999 62.34558166666667 1062.8960183931679 4 1 MBR 5.245144159843528 3 1 1 0 1.3944945906304627 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 66.80918333333334 3 1317.4600908082123 975613.2146145281 66.48338333333334 66.71437666666667 67.53541166666668 1318.1326781757534 3 1 MSMS 1 1 1 0 3.038517201223087 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 65.05399333333334 3 1241.738965164879 7640216.75 64.682815 65.47546 66.72676666666666 1242.0722537468441 3 1 MSMS 1 1 1 0 -0.832199365 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 62.34090333333333 4 1062.393097385379 2562752.359 61.662213333333334 62.416016666666664 62.587185 1062.894004993213 4 2 MSMS 1 1 1 0 -0.501563521 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 3 1317.4600908082123 600031.1041666666 66.75977166666667 67.06987166666667 67.55813333333333 1318.1286211716163 3 1 MBR 3.9975644789440015 2 1 1 0 -0.041687963 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TVSLGAGAKDELHIVEAEAMNYEGSPIK TVSLGAGAKDELHIVEAEAM[Common Variable:Oxidation on M]NYEGS[UniProt:Phosphoserine on S]PIK P06748 3024.415134 3 1009.1456544032123 32055.758457437998 95.471815 95.471815 95.63726833333334 1009.4814188400666 3 1 MBR 0.057673747 1 1 1 0 1.453566998 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 3 1241.738965164879 7612781.590571441 64.87349666666667 65.37143333333334 66.37052333333332 1242.0728085894466 3 1 MBR 2.044434448744727 1 1 1 0 -0.385129992 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 4 1062.393097385379 2184533.877659601 61.441030000000005 62.222301666666674 62.450075 1062.894477570744 4 1 MBR 6.648971525516906 3 1 1 0 -0.056528018 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 3 1317.4600908082123 588555.3167733714 66.77379 66.96889 67.59217833333334 1318.1286798862668 3 1 MBR 4.001827708874124 2 1 1 0 0.002890047 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib CGSGPVHISGQHLVAVEEDAESEDEEEEDVK C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK P06748 3459.429734 97.281425 3 1154.1505210652124 251253.66139122547 88.61551999999999 97.34548166666667 99.00334333333333 866.1144526353784 4 2 MSMS 3 1 1 0 -1.127295123 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib TVSLGAGAKDELHIVEAEAMNYEGSPIK TVSLGAGAKDELHIVEAEAM[Common Variable:Oxidation on M]NYEGS[UniProt:Phosphoserine on S]PIK P06748 3024.415134 3 1009.1456544032123 25827.188634101076 96.68346333333334 96.79141666666666 96.86326666666666 1009.4784913163431 3 1 MBR 0.4237647320026436 2 1 1 0 -1.449361154 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 61.96016333333333 4 1062.393097385379 1381157.8467948118 61.66204666666667 62.097976666666675 62.39145833333334 1062.8944196391628 4 2 MSMS 1 1 1 0 -0.111083321 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 3 1317.4600908082123 546781.0070405641 66.72023333333334 66.87286333333333 67.265065 1318.1282916890661 3 1 MBR 4.015359301127534 2 1 1 0 -0.29184148 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib CGSGPVHISGQHLVAVEEDAESEDEEEEDVK C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK P06748 3459.429734 107.25628833333333 3 1154.1505210652124 188734.70995233112 105.40791000000002 107.19122166666665 107.71720833333333 1154.4865039493407 3 2 MSMS 1 1 1 0 1.467112689331376 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 3 1241.738965164879 141902.5423227326 63.10910666666666 64.00052833333334 64.19556833333334 1242.072646640539 3 1 MBR 1.534464948801613 2 1 1 64.20931666666667 -0.515621768 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib CGSGPVHISGQHLVAVEEDAESEDEEEEDVK C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK P06748 3459.429734 74.29393333333334 3 1154.1505210652124 136103.23339083142 74.00593333333333 74.22844333333333 74.68629666666666 1154.4837728927976 3 2 MSMS 1 1 1 0 -0.90055938 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib TVSLGAGAKDELHIVEAEAMNYEGSPIK TVSLGAGAKDELHIVEAEAM[Common Variable:Oxidation on M]NYEGS[UniProt:Phosphoserine on S]PIK P06748 3024.415134 97.44361500000001 3 1009.1456544032123 124887.1000048296 97.31922833333333 97.436065 97.58785333333333 1009.4787446742971 3 2 MSMS 1 1 1 0 -1.198131785 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3722.195066 3 1241.738965164879 7821598.912193158 65.481155 65.62898666666668 66.53702 1242.0731925130774 3 1 MBR 2.5353262253726645 2 1 1 0 -0.075780105 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK LAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKK P06748 4245.543284 4 1062.393097385379 1290245.4832056588 62.041035 62.775018333333335 63.00713666666667 1062.894962643144 4 1 MBR 5.6261680195199535 3 1 1 0 0.40027414699482927 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK VKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEK P06748 3949.358443 67.32117166666667 3 1317.4600908082123 530513.7237438716 67.02881666666666 67.34437 67.87788666666667 1318.1287520569288 3 1 MSMS 1 1 1 0 0.057684284 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib TVSLGAGAKDELHIVEAEAMNYEGSPIK TVSLGAGAKDELHIVEAEAM[Common Variable:Oxidation on M]NYEGS[UniProt:Phosphoserine on S]PIK P06748 3024.415134 97.570825 3 1009.1456544032123 165130.9058 97.51400333333333 97.57832666666667 97.63441833333333 1009.4776141948445 3 2 MSMS 1 1 1 0 -2.319113522 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib TNQELQEINR TNQELQEINR P07355 1243.615678 53.409859999999995 2 622.8151156 293626.0848640621 53.37154666666667 53.47935833333334 53.661485 622.8151774321178 2 1 MSMS 1 1 1 0 0.099487712 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib DIISDTSGDFRK DIISDTSGDFRK P07355 1352.657209 70.03022833333333 2 677.3358808003791 119267.83990378719 69.914665 70.08326166666667 70.23728333333334 677.3366649658856 2 2 MSMS 1 1 1 0 1.1594445386331598 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 3 688.9992686642123 53492.340795920834 82.53516 82.62957833333333 82.748755 689.3329740598625 3 1 MBR 2.165982366527348 1 1 1 0 -0.84431567 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib TNQELQEINR TNQELQEINR P07355 1243.615678 53.47882833333333 2 622.8151156 321253.0465609691 53.38734833333333 53.573535 53.721059999999994 622.8151062221024 2 1 MSMS 1 1 1 0 -0.015033224 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 82.59347666666667 3 688.9992686642123 57495.12288351632 82.48725166666667 82.585285 82.69194833333333 689.3333268093431 3 1 MSMS 1 1 1 0 -0.331841438 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TNQELQEINR TNQELQEINR P07355 1243.615678 53.78603666666667 2 622.8151156 227646.3203 53.734991666666666 53.87881166666667 53.999085 622.8148067576057 2 1 MSMS 1 1 1 0 -0.496636185 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 3 688.9992686642123 51876.320963541664 83.34227333333332 83.46090833333334 83.55463833333333 689.3336304929181 3 1 MBR 0.9105138750098349 1 1 1 0 0.10934987503976555 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib TNQELQEINR TNQELQEINR P07355 1243.615678 53.36815833333334 2 622.8151156 220774.2828677135 53.315868333333334 53.461209999999994 53.64058333333334 622.8148439774691 2 1 MSMS 1 1 1 0 -0.436778684 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 3 688.9992686642123 51738.55883369802 83.47615666666667 83.63195 83.76141833333334 689.3338160679297 3 1 MBR 1.0711740676277475 2 1 1 0 0.37895313915342727 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib TNQELQEINR TNQELQEINR P07355 1243.615678 53.32922833333333 2 622.8151156 210567.19592012276 53.22441166666667 53.421958333333336 53.60731 622.8150368379345 2 1 MSMS 1 1 1 0 -0.126617806 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 3 688.9992686642123 50244.336182049345 84.097115 84.1589 84.22501666666666 689.3322454128679 3 1 MBR 1.4620267726011749 1 1 1 0 -1.902893581 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib TNQELQEINR TNQELQEINR P07355 1243.615678 54.03211999999999 2 622.8151156 208791.9747044664 53.93490500000001 54.0925 54.338858333333334 622.8149478558563 2 1 MSMS 1 1 1 0 -0.26972002 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib DIISDTSGDFRK DIISDTSGDFRK P07355 1352.657209 71.42292333333333 2 677.3358808003791 96372.60792200496 71.28926333333332 71.54221666666666 71.747675 677.335937 2 2 MSMS 1 1 1 0 0.083128434 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib RAEDGSVIDYELIDQDAR RAEDGSVIDYELIDQDAR P07355 2063.975977 84.59378666666667 3 688.9992686642123 51164.86153968635 84.51616999999999 84.62269 84.729275 689.3339813197667 3 1 MSMS 1 1 1 0 0.6190309077010498 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 54.67231833333334 2 918.9033758 11923220.545955326 54.536035 54.917078333333336 55.19004833333333 612.9378821 3 2 MSMS 1 1 1 54.52146833333334 -0.20797805 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR P08670 1507.670824 67.164955 2 754.8426885733791 2971656.1569561223 66.59203666666667 67.09621166666668 67.40263333333334 754.8421226532008 2 1 MSMS 1 1 1 0 -0.750721138 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ETNLDSLPLVDTHSK ETNLDS[UniProt:Phosphoserine on S]LPLVDTHSK P08670 1747.802961 82.55944666666667 2 874.9087568 498801.5697426063 82.44200166666667 82.86474333333334 83.085895 583.6079758475307 3 2 MSMS 1 1 1 0 -0.493442948 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 3 808.3738343 344599.3316010586 56.898295 57.898215 58.38771333333333 606.7828512030862 4 2 MBR 2.0382534548852047 1 1 1 0 -0.078651402 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib FADLSEAANR FADLSEAANR P08670 1092.519987 60.13047333333333 2 547.2672699 235147.37634176345 60.01007833333333 60.197433333333336 60.38621666666666 547.2670722099014 2 1 MSMS 1 1 1 0 -0.361942079 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 55.36218833333333 2 918.9033758 12165726.910863927 54.769796666666664 55.118543333333335 55.63744333333334 612.9376871616101 3 2 MSMS 2 1 1 54.66875166666667 -0.526467978 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR P08670 1507.670824 67.18200333333333 2 754.8426885733791 2802237.541129825 66.591985 67.09714666666667 67.40177666666668 754.8453931277502 2 2 MSMS 1 1 1 0 3.587725288154751 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib VELQELNDR VELQELNDR P08670 1114.561852 61.714884999999995 2 558.2882023 806741.3606802425 61.69145166666667 61.843756666666664 62.07816999999999 558.2888946450739 2 1 MSMS 1 1 1 0 1.242307358418891 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 57.249315 2 918.9033758 570782.5842569149 57.076480000000004 57.259721666666664 57.460435 612.9374548658901 3 2 MSMS 1 1 1 56.901669999999996 -0.906079113 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib FADLSEAANR FADLSEAANR P08670 1092.519987 60.02697833333333 2 547.2672699 250457.22341185776 59.94582833333333 60.147013333333334 60.37049833333333 547.2673852964591 2 1 MSMS 1 1 1 0 0.21120360544985364 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib NLQEAEEWYK NLQEAEEWYK P08670 1308.598631 75.316265 2 655.306592 90373.16650041322 75.26004333333333 75.33546333333334 75.70825333333333 655.3056723 2 1 MSMS 1 1 1 0 -1.405689306 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib QVQSLTCEVDALK QVQSLTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1489.744644 78.42318166666666 2 745.8795984 66751.93129154011 78.33764333333333 78.46879 78.65774 745.8799215516271 2 1 MSMS 1 1 1 0 0.4337793721154183 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 3 808.3738343 19008.50880623686 58.624631666666666 58.707135 58.77771 606.7831626 4 2 MBR 1.1459950326518928 2 1 1 0 0.43536904397760634 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 55.56326333333333 2 918.9033758 8290700.625 55.342626666666675 55.761316666666666 56.396551666666674 612.9377463434079 3 2 MSMS 2 1 1 0 -0.429754748 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR P08670 1507.670824 67.35012833333333 2 754.8426885733791 2988975.047 66.75977166666667 67.324735 67.57417833333334 754.8428825237851 2 2 MSMS 1 1 1 0 0.2572848169505518 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib QVQSLTCEVDALK QVQS[UniProt:Phosphoserine on S]LTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1569.710975 84.72293499999999 2 785.8627639413791 1302574.805 84.60730500000001 84.83188666666668 85.03784666666667 785.8626425323893 2 1 MSMS 1 1 1 0 -0.154689611 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 3 808.3738343 459900.5156 58.67742 59.09032666666667 59.31414833333333 606.7826898502587 4 2 MBR 2.474516590860718 2 1 1 0 -0.345008815 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TNEKVELQELNDR TNEKVELQELNDR P08670 1586.790014 62.08141666666666 3 529.937281 238871.61979166666 61.90172333333333 62.13038833333333 62.36918333333334 529.9371077145122 3 2 MSMS 1 1 1 0 -0.32770568 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib LQEEMLQREEAENTLQSFR LQEEM[Common Variable:Oxidation on M]LQREEAENTLQSFR P08670 2366.117238 3 789.7130225842125 82043.08042921766 81.34713833333333 81.45731833333333 81.62876833333334 790.0485398392312 3 1 MBR 0.16232870211918607 1 1 1 0 1.5732555738313747 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib QVQSLTCEVDALK QVQSLTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1489.744644 79.63821999999999 2 745.8795984 79257.24409896725 79.39058333333334 79.56565166666667 79.72932 745.8797248502449 2 1 MSMS 1 1 1 0 0.16970541412003365 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib NLQEAEEWYK NLQEAEEWYK P08670 1308.598631 76.39223166666666 2 655.306592 73259.3584 76.15695166666667 76.47383166666667 76.67510833333334 655.3063383105208 2 1 MSMS 2 1 1 0 -0.387799364 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR P08670 1507.670824 67.23156666666667 2 754.8426885733791 2999799.673277415 66.647645 67.20399 67.49137833333333 754.8427405860376 2 2 MSMS 1 1 1 0 0.068997367 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 57.47134499999999 2 918.9033758 607399.8269 57.369168333333334 57.58266999999999 57.73153333333334 612.9386882084941 3 2 MSMS 1 1 1 56.98481999999999 1.109414696802762 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 59.088975 3 808.3738343 411305.8976031086 58.77804166666666 59.11274 59.36740666666667 606.7835253449824 4 2 MSMS 1 1 1 0 1.0342060176033885 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR P08670 1507.670824 67.08177666666667 2 754.8426885733791 3196149.109 66.48455666666666 67.07172666666668 67.365235 754.8425920018885 2 2 MSMS 1 1 1 0 -0.128106864 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib QVQSLTCEVDALK QVQS[UniProt:Phosphoserine on S]LTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1569.710975 84.630085 2 785.8627639413791 1376694.0333622799 84.57993666666667 84.75573833333333 84.96073666666668 785.8618659928494 2 1 MSMS 1 1 1 0 -1.144094096 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib VELQELNDR VELQELNDR P08670 1114.561852 61.83998666666667 2 558.2882023 762637.9876662452 61.806635 61.99084166666666 62.26399 558.2880937371053 2 1 MSMS 1 1 1 0 -0.194863611 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 3 808.3738343 389607.1926 58.97770500000001 59.273833333333336 59.47289 606.7831480073015 4 2 MBR 2.0984121600410286 2 1 1 0 0.41130594212844074 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib QVQSLTCEVDALK QVQSLTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1489.744644 80.42311166666667 2 745.8795984 74013.16961959568 80.17788833333333 80.337885 80.541895 745.8801492 2 1 MSMS 1 1 1 0 0.73937341 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib LQEEMLQREEAENTLQSFR LQEEM[Common Variable:Oxidation on M]LQREEAENTLQSFR P08670 2366.117238 3 789.7130225842125 49615.556941282455 82.49901166666668 82.49901166666668 82.49901166666668 790.0456647559945 3 1 MBR 2.5761193247823915 1 1 1 0 -2.070518071 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 56.942976666666674 2 918.9033758 7228723.811243412 56.299565 56.82920333333333 57.36232833333333 612.9381941862601 3 2 MSMS 2 1 1 55.54246833333333 0.3020974507850446 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib SLYASSPGGVYATR SLYASS[UniProt:Phosphoserine on S]PGGVYATR|S[UniProt:Phosphoserine on S]LYASSPGGVYATR P08670 1507.670824 67.53363666666667 2 754.8426885733791 2830871.0126044992 66.9443 67.482365 67.79890333333333 754.8430134663269 2 1 MSMS 2 1 2 0 0.43098658217690977 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib QVQSLTCEVDALK QVQS[UniProt:Phosphoserine on S]LTC[Common Fixed:Carbamidomethyl on C]EVDALK P08670 1569.710975 85.00732333333333 2 785.8627639413791 1222979.7802536252 84.95679333333334 85.16807166666666 85.38755333333333 785.8632498357354 2 1 MSMS 1 1 1 0 0.619087672 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ETNLDSLPLVDTHSK ETNLDS[UniProt:Phosphoserine on S]LPLVDTHSK P08670 1747.802961 83.77011999999999 2 874.9087568 892360.0670781406 83.153035 83.60996666666666 83.90356333333332 583.6092294151781 3 2 MSMS 1 1 1 0 1.6582314840439962 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib VELQELNDR VELQELNDR P08670 1114.561852 62.51511166666667 2 558.2882023 728742.3622450937 62.4379 62.651026666666674 62.871408333333335 558.2882979 2 1 MSMS 1 1 1 0 0.1714212859344834 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib DGQVINETSQHHDDLE DGQVINETSQHHDDLE P08670 1835.792199 58.035095 2 918.9033758 667085.0747119802 57.92331166666667 58.11685333333333 58.289345 612.9378406063223 3 2 MSMS 1 1 1 57.661384999999996 -0.275712943 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib TVETRDGQVINETSQHHDDLE TVETRDGQVINETSQHHDDLE P08670 2422.099674 59.91911666666666 3 808.3738343 392742.1849586587 59.63836833333333 59.930705 60.11649666666667 606.7829074808143 4 3 MSMS 1 1 1 0 0.014250533581689661 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib LQEEMLQREEAENTLQSFR LQEEM[Common Variable:Oxidation on M]LQREEAENTLQSFR P08670 2366.117238 82.84422666666667 3 789.7130225842125 89215.64308 82.73693666666667 82.89806333333333 82.98305500000001 790.0487008426423 3 1 MSMS 1 1 1 0 1.7773053133923193 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 48.87096666666667 3 752.3042964215457 68315457.76311593 48.131031666666665 48.556805 49.44005666666666 752.6378952656409 3 2 MSMS 4 1 1 48.113793333333334 -0.917322376 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 49.58517333333334 2 1127.952806398879 10688140.457952555 49.49241666666667 49.664645 50.188109999999995 752.6381071740986 3 2 MSMS 1 1 1 49.4688 -0.635390988 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.58450166666667 2 1247.090621700879 3396933.345472178 98.54785 98.56307833333334 98.56307833333334 1247.591577077115 2 3 MSMS 2 1 1 0 -0.38898342 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib GAGDGSDEEVDGKADGAEAK GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAK P35579 1956.758589 43.01915666666667 2 979.386571 855892.7801804077 42.962265 43.09008166666666 43.257958333333335 653.2599487538001 3 2 MSMS 1 1 1 0 -0.292463383 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 89.083625 2 1236.5904545248789 752452.4059560716 89.03570333333333 89.20090833333333 89.41860333333334 1237.0917458452195 2 2 MSMS 2 1 1 0 -0.124417168 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ELEDATETADAMNR ELEDATETADAM[Common Variable:Oxidation on M]NR P35579 1580.66243 50.97417333333333 2 791.3384917 350539.01204009337 50.929851666666664 51.053684999999994 51.191318333333335 791.3384834852636 2 2 MSMS 1 1 1 0 -0.010380604 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IAQLEEQLDNETK IAQLEEQLDNETK P35579 1529.757317 68.16933833333333 2 765.8859347833791 260429.5958485172 68.09045333333333 68.24055166666668 68.41502666666668 765.8853323108274 2 1 MSMS 1 1 1 0 -0.787670757 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib KLEEEQIILEDQNCK KLEEEQIILEDQNC[Common Fixed:Carbamidomethyl on C]K P35579 1887.924793 67.74724333333333 3 630.3155408472123 218294.59499507118 67.67853000000001 67.89290666666666 67.89290666666666 630.3150205974616 3 2 MSMS 1 1 1 0 -0.826700967 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib QAQQERDELADEIANSSGK QAQQERDELADEIANSS[UniProt:Phosphoserine on S]GK P35579 2167.938285 63.7108 3 723.6533714135458 146567.56944894415 63.65119333333333 63.77691 63.9097 723.9870531495428 3 2 MSMS 1 1 1 0 -0.813138513 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 90.10311666666666 3 783.6885426762124 123890.6811169704 89.97222 90.10908166666667 90.23833333333334 784.0227957399337 3 2 MSMS 1 1 1 0 -0.03624707 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 2 827.3963322908791 85092.88651030231 73.34119333333334 73.53518333333334 73.59928333333333 827.3951454294618 2 1 MBR 0.1804164846158333 1 1 1 0 -1.436201761 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 2 783.3410344 63952.47945757114 61.080665 61.118995 61.237678333333335 783.3408098091257 2 1 MBR 2.3296339643335218 1 1 1 0 -0.287051723 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib NMDPLNDNIATLLHQSSDK NM[Common Variable:Oxidation on M]DPLNDNIATLLHQSSDK P35579 2141.005897 90.48785 3 714.6759087992124 56896.05061044871 90.38343666666667 90.53764833333332 90.726835 715.0101845039209 3 1 MSMS 1 1 1 0 0.00019468 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 2 617.2776972 48587.50520547346 45.93292 46.04391666666667 46.123176666666666 617.2774132977214 2 1 MBR 2.779038031533121 1 1 1 0 -0.460706287 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib NSFREQLEEEEEAK NSFREQLEEEEEAK P35579 1736.785322 2 869.3999376 15085.172552493286 67.49190833333334 67.49190833333334 67.49190833333334 579.9358432889162 3 1 MBR 1.015617232392543 1 1 1 0 0.21774775909416758 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 46.844229999999996 2 1127.952806398879 2571771.690555933 46.67724333333334 47.01228833333334 47.313543333333335 752.6380861 3 2 MSMS 2 1 1 47.336126666666665 -0.663417058 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib RQAQQERDELADEIANSSGK RQAQQERDELADEIANSSGK P35579 2244.073065 65.65452333333333 3 749.0316314215457 2387182.118383664 65.02735333333334 65.50427833333333 66.30908833333334 562.2780034380498 4 3 MSMS 1 1 1 0 3.1528977870457866 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.65955833333334 3 831.7295066228791 1877620.8450795359 98.64503333333333 98.64503333333333 98.64503333333333 1247.593776862739 2 2 MSMS 2 1 1 0 1.3756664054785486 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib GAGDGSDEEVDGKADGAEAK GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAK P35579 1956.758589 42.96040333333333 2 979.386571 903460.5376002868 42.89036 43.03131833333333 43.205940000000005 653.2598573260093 3 2 MSMS 1 1 1 0 -0.432635693 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 89.169785 2 1236.5904545248789 654003.7671911259 89.06413833333333 89.22363 89.47295833333334 1237.0962359309315 2 2 MSMS 2 1 1 0 3.508089561701245 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib RQLEEAEEEAQR RQLEEAEEEAQR P35579 1486.701199 49.72875833333333 2 744.3578758 540564.5729 49.459215 49.68226333333334 49.86024166666667 496.5742651906515 3 2 MSMS 2 1 1 0 -0.156430009 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib NSFREQLEEEEEAK NSFREQLEEEEEAK P35579 1736.785322 67.80629 2 869.3999376 303631.2693109452 67.667575 67.81219333333334 68.01837333333333 579.9380381139501 3 2 MSMS 1 1 1 0 4.008933127447426 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ELEDATETADAMNR ELEDATETADAM[Common Variable:Oxidation on M]NR P35579 1580.66243 50.918525 2 791.3384917 288289.85588234616 50.876718333333336 50.99120166666667 51.171305 791.3387126213372 2 2 MSMS 1 1 1 0 0.27954350524863725 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib IAQLEEQLDNETK IAQLEEQLDNETK P35579 1529.757317 68.30286333333333 2 765.8859347833791 275014.54371490993 68.20886166666666 68.36891666666666 68.57093666666667 765.8883144358147 2 1 MSMS 1 1 1 0 3.1111502587146624 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DLEAHIDSANK DLEAHIDSANK P35579 1211.57823 53.21980166666667 2 606.7963915 225858.3732724161 53.10722 53.35618 53.573535 606.7963037852395 2 2 MSMS 1 1 1 0 -0.144795668 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib KLEEEQIILEDQNCK KLEEEQIILEDQNC[Common Fixed:Carbamidomethyl on C]K P35579 1887.924793 68.32702666666667 3 630.3155408472123 208872.53124654636 68.28945666666667 68.28945666666667 68.45279666666667 630.3167655742124 3 2 MSMS 1 1 1 0 1.9461479682636622 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib HSQAVEELAEQLEQTK HSQAVEELAEQLEQTK P35579 1838.901021 86.09026666666666 3 613.9742833822124 166894.54266420094 86.01096166666667 86.15383666666666 86.38907333333333 613.9740422526637 3 2 MSMS 1 1 1 0 -0.393380958 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 90.11525666666667 3 783.6885426762124 138279.19638925703 90.02841333333333 90.16685166666667 90.26825833333334 784.0261652745988 3 2 MSMS 1 1 1 0 4.267032316150502 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 2 783.3410344 99267.25203033721 60.962671666666665 61.045605 61.10184 783.3418417994318 2 1 MBR 1.632030821768306 1 1 1 0 1.0320659751486791 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 73.35699333333334 2 827.3963322908791 87770.85344287424 73.23190833333334 73.36315333333333 73.62131166666667 827.3954599191136 2 1 MSMS 1 1 1 0 -1.055642932 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 2 617.2776972 40932.94366624206 45.68785166666667 45.80453333333333 45.87990833333333 617.2771872366573 2 1 MBR 2.8401243065738733 1 1 1 0 -0.827527502 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 49.97873 3 752.3042964215457 10952300.88 49.63998 49.81736666666667 51.689915 752.6381075363786 3 2 MSMS 2 1 1 49.61596333333333 -0.634908997 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.49504666666667 2 1247.090621700879 3148985.406 98.48087833333334 98.48087833333334 98.51524 1247.5911969142182 2 3 MSMS 2 1 1 0 -0.69394695 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 89.5037 2 1236.5904545248789 636161.207 89.45790500000001 89.56405333333333 90.007305 1237.0919099842033 2 2 MSMS 2 1 1 0 0.008372271 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 47.497405 2 1127.952806398879 511996.7617 47.28210833333333 47.52796166666666 47.88753333333333 752.6385159990706 3 2 MSMS 1 1 1 47.25998333333333 -0.091474087 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib RQLEEAEEEAQR RQLEEAEEEAQR P35579 1486.701199 50.25985333333333 2 744.3578758 498082.7291666667 50.20192333333333 50.24260833333333 50.39678 496.5741099380876 3 2 MSMS 1 1 1 0 -0.46971266 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib HSQAVEELAEQLEQTK HSQAVEELAEQLEQTK P35579 1838.901021 87.788365 3 613.9742833822124 305352.9739583333 87.73844666666666 87.91946166666666 88.16866666666667 613.9742719348463 3 2 MSMS 1 1 1 0 -0.018675338 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib KQELEEICHDLEAR KQELEEIC[Common Fixed:Carbamidomethyl on C]HDLEAR P35579 1768.841398 80.38430166666667 3 590.6210757562123 228448.83854166666 80.266275 80.51658833333333 80.72221 590.6216910359977 3 1 MSMS 1 1 1 0 1.0435301655489853 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib NSFREQLEEEEEAK NSFREQLEEEEEAK P35579 1736.785322 69.46551 3 579.9357172285456 213097.8789 69.17601166666667 69.6168 70.16763333333334 579.9359322702767 3 2 MSMS 2 1 1 0 0.37144786123481105 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib KLEEEQIILEDQNCK KLEEEQIILEDQNC[Common Fixed:Carbamidomethyl on C]K P35579 1887.924793 69.52021500000001 3 630.3155408472123 193543.3555 69.43117833333334 69.68283833333334 69.91933833333333 630.3157698226437 3 2 MSMS 1 1 1 0 0.36385257335909454 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib DLEAHIDSANK DLEAHIDSANK P35579 1211.57823 54.00954833333333 2 606.7963915 175890.4941 53.734991666666666 53.999085 54.361785 606.7963782355677 2 2 MSMS 1 1 1 0 -0.021897573 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 90.35007 3 783.6885426762124 163739.54752604166 90.262325 90.38699666666666 90.537515 784.0228694064318 3 2 MSMS 1 1 1 0 0.057833435 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 2 783.3410344 106228.93387955021 61.144255 61.20769 61.265883333333335 783.3408263767589 2 1 MBR 2.6474488281579367 1 1 1 0 -0.26587453 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 2 827.3963322908791 60768.932840920555 74.12348833333333 74.30683333333334 74.42354166666667 827.3958642 2 1 MBR 1.108583807 1 1 1 0 -0.566418146 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 45.83017 2 617.2776972 24634.006331501503 45.702378333333336 45.81216666666667 45.873005 617.2773197625814 2 1 MSMS 1 1 1 0 -0.612482418 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 49.615988333333334 2 1127.952806398879 12188759.039877081 49.53844333333333 49.66673333333333 51.96572333333334 752.6376533970578 3 2 MSMS 2 1 1 49.50959 -1.239113898 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.63595666666666 2 1247.090621700879 6919891.272707425 98.600025 98.62186833333334 98.62186833333334 1247.5905539807213 2 2 MSMS 2 1 1 0 -1.209702881 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 89.73690833333333 2 1236.5904545248789 561577.3483977612 89.68536666666667 89.81029833333332 90.11336833333334 1237.092520236172 2 2 MSMS 1 1 1 0 0.5020698363715178 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 90.54012 3 783.6885426762124 186152.49822675713 90.49435333333334 90.62357166666666 90.74611166666666 784.0226913092001 3 2 MSMS 1 1 1 0 -0.169617006 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib KLEEEQIILEDQNCK KLEEEQIILEDQNC[Common Fixed:Carbamidomethyl on C]K P35579 1887.924793 3 630.3155408472123 167009.06802504198 69.687945 69.95631 70.23285333333334 630.3163658995207 3 1 MBR 0.3606017268662839 1 1 1 0 1.311046358599231 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 2 783.3410344 88010.53977071817 60.95787833333333 61.06701166666667 61.14930666666667 783.3420809020222 2 1 MBR 1.9418272429139862 1 1 1 0 1.3376933215090614 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 2 827.3963322908791 63638.38805828863 74.07379833333333 74.22011166666667 74.383065 827.3963709338321 2 1 MBR 0.8613650072892128 1 1 1 0 0.046761211095394384 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib ELEDATETADAMNR ELEDATETADAM[Common Variable:Oxidation on M]NR P35579 1580.66243 2 791.3384917 27633.44629098234 50.96749333333334 50.96749333333334 50.96749333333334 791.3408058927987 2 1 MBR 5.875219317 4 1 1 0 2.928143764445995 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 2 617.2776972 26268.358241793474 45.57045333333333 45.70037666666666 45.770075 617.2772088407572 2 1 MBR 2.927768661658136 1 1 1 0 -0.7924713 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.57078333333334 2 1247.090621700879 8622871.303291587 98.53562333333333 98.56078000000001 98.56078000000001 1247.5910587882445 2 2 MSMS 2 1 1 0 -0.804750463 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 46.497323333333334 3 752.3042964215457 1757394.3623839763 46.10923833333334 46.529015 46.91209666666667 752.6375811935187 3 2 MSMS 2 1 1 46.927640000000004 -1.33517634 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib GAGDGSDEEVDGKADGAEAK GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAK P35579 1956.758589 42.669095 2 979.386571 1008174.8848002183 42.60885 42.76900166666667 42.95082 653.2595503 3 2 MSMS 1 1 1 0 -0.903416696 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 90.0908 2 1236.5904545248789 765521.4028107105 89.98529666666667 90.11952333333333 90.41682166666666 825.0636326747539 3 2 MSMS 2 1 1 0 -0.071885593 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 47.194583333333334 2 1127.952806398879 366844.87351056444 46.94462166666667 47.157725 47.64134333333333 752.6378553341721 3 2 MSMS 1 1 1 46.927640000000004 -0.97044878 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IAQLEEQLDNETK IAQLEEQLDNETK P35579 1529.757317 69.04316666666666 2 765.8859347833791 225538.78392175032 68.773455 68.964555 69.14227833333334 765.8860014151303 2 1 MSMS 1 1 1 0 0.087114146 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib ELEDATETADAMNR ELEDATETADAM[Common Variable:Oxidation on M]NR P35579 1580.66243 50.756375 2 791.3384917 174536.78623839872 50.709790000000005 50.88298333333333 50.915011666666665 791.3398764303466 2 2 MSMS 1 1 1 0 1.752102081970097 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 90.83709166666667 3 783.6885426762124 162801.96893371333 90.77736166666666 90.89512333333333 90.99868000000001 784.0229296803524 3 2 MSMS 1 1 1 0 0.13481009390232318 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 2 783.3410344 104345.22716767705 60.81474833333333 60.883435 61.01361333333333 783.341029 2 1 MBR 4.324739373554447 1 1 1 0 -0.00684073 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 2 827.3963322908791 56477.48363561119 74.37745166666667 74.56285666666666 74.74984333333333 827.3959288483918 2 1 MBR 0.6851301741676963 1 1 1 0 -0.488199214 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 2 617.2776972 25458.88361559614 45.25213333333333 45.325705 45.44559666666667 617.2768519 2 1 MBR 1.966849569953239 1 1 1 0 -1.371699734 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 49.744123333333334 3 752.3042964215457 10497055.091427047 49.65333833333334 49.84179666666667 51.653241666666666 752.6379424232689 3 2 MSMS 1 1 1 49.62014666666667 -0.854582004 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib DFSALESQLQDTQELLQEENR DFSALESQLQDTQELLQEENR P35579 2492.16669 98.60420833333333 3 831.7295066228791 1696531.6941107486 98.57369666666666 98.61498333333334 98.61498333333334 832.0628158595173 3 2 MSMS 2 1 1 0 -1.184373585 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib GAGDGSDEEVDGKADGAEAK GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAK P35579 1956.758589 43.141225 2 979.386571 1129710.110808444 43.02979833333333 43.20666333333334 43.403598333333335 653.2603819212685 3 2 MSMS 1 1 1 0 0.3716463405335355 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IAQLEEELEEEQGNTELINDR IAQLEEELEEEQGNTELINDR P35579 2471.166356 90.291765 2 1236.5904545248789 673951.2295456128 90.250425 90.40211333333333 90.72089 1237.0917101385376 2 2 MSMS 2 1 1 0 -0.153304091 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib GAGDGSDEEVDGKADGAEAKPAE GAGDGS[UniProt:Phosphoserine on S]DEEVDGKADGAEAKPAE P35579 2253.89106 48.11857666666667 3 752.3042964215457 402658.7631 47.654545 47.872616666666666 48.36544666666667 752.6391562262496 3 2 MSMS 1 1 1 47.62211166666666 0.7603094562195052 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib RQLEEAEEEAQR RQLEEAEEEAQR P35579 1486.701199 51.229085 2 744.3578758 259156.43585394902 50.856143333333335 51.220486666666666 51.559115000000006 496.57378966833585 3 2 MSMS 2 1 1 0 -1.115981901 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IAQLEEQLDNETK IAQLEEQLDNETK P35579 1529.757317 69.59264666666667 2 765.8859347833791 208722.01640478775 69.37728833333333 69.51729833333333 69.74654333333334 765.8861690615697 2 1 MSMS 1 1 1 0 0.3062945843928997 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ELEDATETADAMNR ELEDATETADAM[Common Variable:Oxidation on M]NR P35579 1580.66243 51.33627166666667 2 791.3384917 185801.08485158838 51.264765000000004 51.440884999999994 51.50308 791.3389188 2 2 MSMS 1 1 1 0 0.5403682693509887 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib MQQNIQELEEQLEEEESAR M[Common Variable:Oxidation on M]QQNIQELEEQLEEEESAR P35579 2348.043799 91.10349833333333 3 783.6885426762124 171687.9630481927 90.98907666666668 91.18490666666666 91.30301833333334 784.0226451166334 3 2 MSMS 1 1 1 0 -0.228610173 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib QAQQERDELADEIANSSGK QAQQERDELADEIANSSGK P35579 2087.971954 69.12504166666666 3 696.9979277 142246.93291501343 68.96042333333332 69.20646833333333 69.49450833333334 697.3321522870123 3 1 MSMS 1 1 1 0 -0.062192371 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib QAQQERDELADEIANSSGK QAQQERDELADEIANSS[UniProt:Phosphoserine on S]GK P35579 2167.938285 64.98433 3 723.6533714135458 114751.3176953209 64.76555 64.94381333333332 65.086025 723.9878999658591 3 1 MSMS 1 1 1 0 0.35814684671371905 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ELEDATETADAMNR ELEDATETADAMNR P35579 1564.667516 61.472030000000004 2 783.3410344 85936.82893377185 61.36162333333333 61.44853166666667 61.550981666666665 783.3410793756756 2 2 MSMS 1 1 1 0 0.057515473520803564 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib NKHEAMITDLEER NKHEAMITDLEER P35579 1584.756606 73.23035166666668 3 529.2594783382124 70504.00270377457 73.02085333333333 73.54389833333333 74.218805 529.2593334274371 3 1 MSMS 1 1 1 0 -0.274321195 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IAEFTTNLTEEEEK IAEFTTNLTEEEEK P35579 1652.778112 2 827.3963322908791 51048.61704 75.017065 75.13984333333333 75.377595 827.3963712714221 2 1 MBR 1.1209021364299836 1 1 1 0 0.047169723 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib EQLEEEEEAK EQLEEEEEAK P35579 1232.540842 2 617.2776972 27851.420137778532 45.91882666666667 46.020873333333334 46.107115 617.2779893744223 2 1 MBR 1.8683349269844693 1 1 1 0 0.474072799 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSS[UniProt:Phosphoserine on S]PVYGSSAK P49023 2026.914971 52.95729833333333 3 676.6456 232427.84841880683 52.876884999999994 53.06270833333334 53.37154666666667 676.9798783785016 3 2 MSMS 1 1 1 0 -0.020458574 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 3 678.6054758 214529.65854255646 48.71275333333333 48.834223333333334 49.009881666666665 678.9397215 3 1 MBR 5.888874367 2 1 1 0 -0.010683091 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 2 922.8776622198791 76569.96190734288 50.20735 50.28671166666666 50.46589 922.8774106698306 2 1 MBR 8.022340757859478 3 1 1 0 -0.272869215 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 2 807.8454282 62551.21276844649 57.392084999999994 57.77388166666667 58.28333666666667 807.8451168719147 2 2 MBR 2.4345992792758935 1 1 1 0 -0.385892714 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSS[UniProt:Phosphoserine on S]PVYGSSAK P49023 2026.914971 53.066253333333336 3 676.6456 237707.46301364418 52.925493333333335 53.14550833333334 53.464176666666674 676.9795482647029 3 2 MSMS 1 1 1 0 -0.508812379 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 48.75612 3 678.6054758 207812.77889845654 48.70684166666667 48.80764166666667 48.94770166666667 678.9397906934917 3 2 MSMS 1 1 1 0 0.091346891 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 2 922.8776622198791 76269.35486 50.09159833333334 50.302225 50.37024 922.8778776655672 2 1 MBR 6.246245283675748 3 1 1 0 0.2337049671737249 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 2 807.8454282 65517.59024477765 57.54164333333333 57.754315000000005 58.311366666666665 538.8990007200488 3 2 MBR 1.6177050271680933 1 1 1 0 -0.700733157 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSSPVY[UniProt:Phosphotyrosine on Y]GSSAK P49023 2026.914971 50.718048333333336 3 676.6456 60686.84366435347 50.62163333333333 50.655276666666666 50.75024333333334 676.9802148058861 3 1 MSMS 1 1 1 0 0.4772352329669248 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 3 678.6054758 134625.5944847525 48.735825 48.864266666666666 49.08755166666667 678.9395517112016 3 1 MBR 5.865090678174673 2 1 1 0 -0.261169484 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 50.467290000000006 2 922.8776622198791 84767.65501126903 50.30600833333333 50.434225 50.576775 922.8783178549393 2 1 MSMS 1 1 1 0 0.7112009133065059 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 2 807.8454282 66729.39966597187 57.820541666666664 58.29811 58.553373333333326 807.8446854925025 2 2 MBR 1.5606532615602593 1 1 1 0 -0.920546921 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSSPVY[UniProt:Phosphotyrosine on Y]GSSAK P49023 2026.914971 51.013725 3 676.6456 52397.91992 50.91447 50.950936666666664 51.186481666666666 676.9794806621508 3 1 MSMS 1 1 1 0 -0.608820205 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 49.02993333333333 3 678.6054758 183192.57521398453 48.851193333333335 48.945475 49.04098166666667 678.9397052568798 3 1 MSMS 1 1 1 0 -0.034678367 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 50.314859999999996 2 922.8776622198791 86162.00042200933 50.120403333333336 50.26945666666666 50.32055333333333 922.8763060119159 2 1 MSMS 1 1 1 0 -1.471148205 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 58.088044999999994 2 807.8454282 65262.22872 57.75537833333333 57.898606666666666 58.20663833333333 538.9000670712185 3 2 MSMS 1 1 1 0 1.2817298080097066 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSS[UniProt:Phosphoserine on S]PVYGSSAK P49023 2026.914971 52.99206166666667 3 676.6456 222345.7170194948 52.86877333333333 53.088415000000005 53.40512833333333 676.9798708727615 3 2 MSMS 1 1 1 0 -0.03156219 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 3 678.6054758 167616.2966660909 48.478881666666666 48.594845 48.71919666666667 678.9396644463608 3 1 MBR 4.610589040425788 2 1 1 0 -0.09487687 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 49.99642 2 922.8776622198791 97759.55099 49.764248333333335 49.91679 50.114315000000005 922.8770129367275 2 1 MSMS 1 1 1 0 -0.704310673 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 2 807.8454282 66208.16148140033 57.736001666666674 57.98743833333333 58.46666166666667 807.8456410521403 2 2 MBR 1.4706534281927772 1 1 1 0 0.2637793725340474 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib FIHQQPQSSSPVYGSSAK FIHQQPQSSS[UniProt:Phosphoserine on S]PVYGSSAK P49023 2026.914971 53.59611833333334 3 676.6456 237626.04102667686 53.40081833333333 53.67197333333333 54.0925 676.9789643912351 3 2 MSMS 1 1 1 0 -1.372565516 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib DGGRSSPGGQDEGGFMAQGK DGGRSS[UniProt:Phosphoserine on S]PGGQDEGGFM[Common Variable:Oxidation on M]AQGK P49023 2032.794598 3 678.6054758 200542.31210879268 49.033465 49.11294166666667 49.26135166666667 678.9400794242035 3 1 MBR 4.381823897 2 1 1 0 0.5172458291633993 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib TSSVSNPQDSVGSPCSR TSSVSNPQDSVGS[UniProt:Phosphoserine on S]PC[Common Fixed:Carbamidomethyl on C]SR P49023 1843.740772 2 922.8776622198791 97062.76814436313 50.20625666666667 50.481355 50.60599166666667 922.8773857827516 2 1 MBR 6.422546058822704 3 1 1 0 -0.299865503 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib VGEEEHVYSFPNK VGEEEHVY[UniProt:Phosphotyrosine on Y]SFPNK P49023 1613.676304 2 807.8454282 67079.14383 58.22854 58.55681833333333 58.944206666666666 807.8454260206292 2 2 MBR 1.8518489502015236 1 1 1 0 -0.00273196 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 2 947.9028213 299070.0096570242 51.44582 51.51287833333333 51.92900833333333 947.9030457212297 2 1 MBR 2.4557242200960516 1 1 1 0 0.23701225758229869 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 2 795.8580043 253274.47373873473 79.75918333333334 80.04003166666666 80.429745 795.8589449468328 2 1 MBR 4.236607228377767 2 1 1 0 1.1834447914183257 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 2 947.9028213 284356.9809652915 51.459425 51.62960666666667 52.042390000000005 947.9025831667393 2 1 MBR 1.9946439491856849 1 1 1 0 -0.251483536 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 79.84721166666667 2 795.8580043 240423.99221637164 79.72307166666667 80.062425 80.34033833333334 795.8583326365061 2 1 MSMS 1 1 1 0 0.41309847951622974 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 2 795.8580043 274672.6367 80.122855 80.32448833333333 80.72221 795.8589259703234 2 1 MBR 2.474378469119621 2 1 1 0 1.1595704855328934 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 2 947.9028213 213624.3594 51.61906166666667 51.73775833333333 52.21845166666667 947.9027074856466 2 1 MBR 4.011193380840787 1 1 1 0 -0.120192489 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 2 795.8580043 315649.36872523156 80.05492166666667 80.350725 80.63371666666666 795.8584418980817 2 1 MBR 5.033251348831904 2 1 1 0 0.5505602338973078 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 51.47492666666667 2 947.9028213 246028.9676757249 51.466575 51.55077166666667 51.932365000000004 947.90263 2 1 MSMS 1 1 1 0 -0.202006205 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 2 795.8580043 324025.4066618768 80.03334666666667 80.32323000000001 80.63744666666666 795.8587353520367 2 1 MBR 4.877594302 2 1 1 0 0.919754027 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 2 947.9028213 230464.17415369145 51.25590166666667 51.364855 51.78196166666666 947.9026596 2 1 MBR 2.968675172572692 1 1 1 0 -0.170741943 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib LPSSPVYEDAASFK LPSS[UniProt:Phosphoserine on S]PVYEDAASFK Q14247 1589.701456 80.69973 2 795.8580043 295098.18547402276 80.59814666666666 80.89105 81.15433666666667 795.8581849438428 2 1 MSMS 1 1 1 0 0.2272866558347681 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib TQTPPVSPAPQPTEER TQT[UniProt:Phosphothreonine on T]PPVS[UniProt:Phosphoserine on S]PAPQPTEER Q14247 1893.79109 2 947.9028213 241389.95230617875 51.670701666666666 51.730129999999996 52.25835 947.9026331062004 2 1 MBR 2.2547029642984158 1 1 1 0 -0.198743335 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR Q15149 1833.814588 65.748405 2 917.9145704 1313061.2544358457 65.01107333333333 65.56924000000001 66.33377666666667 917.9140132362868 2 1 MSMS 1 1 1 0 -0.607671676 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib SSSVGSSSSYPISPAVSR S[UniProt:Phosphoserine on S]SSVGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 2 957.8977359 677268.5565848133 68.71752333333333 69.20080333333333 69.646015 957.8987646234987 2 1 MBR 1.360830966126577 1 1 1 0 1.07505369 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 65.87715166666668 2 931.8832703 276587.7124553637 65.545505 65.96717833333334 66.10356666666667 931.8827198938536 2 1 MSMS 1 1 1 0 -0.591262455 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 2 1031.4906421848789 101524.52693641969 70.11943166666667 70.41006999999999 70.55119833333333 1031.992634750634 2 1 MBR 1.5331454341241515 1 1 1 0 0.5180281865222549 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR Q15149 1833.814588 2 917.9145704 1317512.9632080868 64.96657166666667 65.55018666666668 66.04940666666667 917.9177802743296 2 1 MBR 1.828459029426672 1 1 1 0 3.500745900602982 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib SSSVGSSSSYPISPAVSR S[UniProt:Phosphoserine on S]SSVGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 69.565515 2 957.8977359 729630.5652720869 68.891375 69.44024666666667 69.81291666666667 957.9006677620227 2 1 MSMS 1 1 1 0 3.063931837511401 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 65.91401666666667 2 931.8832703 240199.0843406262 65.67792166666666 65.93795 66.20769833333333 931.8862847959318 2 1 MSMS 1 1 1 0 3.2383583555817586 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 2 1031.4906421848789 94014.15302232033 69.96892666666668 70.254075 70.40558 1031.9956443578208 2 1 MBR 1.5361251370189843 1 1 1 0 3.4371857882749337 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR|SSSVGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1833.814588 65.36606 2 917.9145704 1216641 65.09386833333333 65.66093000000001 66.43780500000001 917.9142299779276 2 1 MSMS 2 1 2 0 -0.371288301 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 2 957.8977359 481791.8945 69.09183 69.59177166666667 69.948525 957.8983658902664 2 1 MBR 2.131509237431475 1 1 1 0 0.6583568486329135 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 66.00134666666666 2 931.8832703 220565.5 65.79727333333332 66.10325833333334 66.27568000000001 931.8827209048178 2 1 MSMS 1 1 1 0 -0.59017642 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 70.580725 2 1031.4906421848789 82138.16987186101 70.26165 70.587525 70.717545 1031.992086771442 2 1 MSMS 1 1 1 0 -0.013482248 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR Q15149 1833.814588 2 917.9145704 1212736.154 65.09684333333334 65.61554666666667 66.15864333333333 917.9145654232709 2 1 MBR 1.5398516526999677 1 1 1 0 -0.005443962 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 69.59206 2 957.8977359 521346.31267157366 69.01784333333333 69.46946166666667 69.82681333333333 957.8994385 2 1 MSMS 1 1 1 0 1.7792701098950285 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 65.91480166666668 2 931.8832703 220061.52695495597 65.68535333333334 65.99797666666667 66.15864333333333 931.8832355205323 2 1 MSMS 1 1 1 0 -0.037346915 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 2 1031.4906421848789 87910.05727469278 70.15792166666667 70.37948 70.57741166666666 1031.9930757746652 2 1 MBR 3.394179286976966 1 1 1 0 0.9457978499614443 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR Q15149 1833.814588 2 917.9145704 1099521.860497115 64.899045 65.32940833333333 65.98267166666666 917.9138670431744 2 1 MBR 1.306831156983644 1 1 1 0 -0.767113218 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 2 957.8977359 499136.3755 68.68767666666668 69.14227833333334 69.43728 957.8979354908157 2 1 MBR 1.817777593622271 1 1 1 0 0.20856717161914184 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 65.77510666666666 2 931.8832703 229233.76829856174 65.67289833333332 65.85002333333333 66.01199833333332 931.8826153 2 1 MSMS 1 1 1 0 -0.703601086 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 2 1031.4906421848789 109801.37652643895 69.93281833333333 70.10840833333334 70.39679 1031.9925144441488 2 1 MBR 2.234144568061855 1 1 1 0 0.4013373465966469 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGSSSSYPISPAVSR Q15149 1833.814588 2 917.9145704 1170193.3725362835 65.42933666666667 65.91005166666667 66.49063166666666 917.9151292177405 2 1 MBR 1.449942768635538 1 1 1 0 0.609443141 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib SSSVGSSSSYPISPAVSR SSS[UniProt:Phosphoserine on S]VGS[UniProt:Phosphoserine on S]SSSYPISPAVSR Q15149 1913.780919 2 957.8977359 468941.7421 69.19314666666666 69.58479666666666 69.97521333333333 957.8978309311035 2 1 MBR 1.5007827485089962 1 1 1 0 0.099296867 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib GYYSPYSVSGSGSTAGSR GYYSPYSVSGSGSTAGS[UniProt:Phosphoserine on S]R Q15149 1861.751988 2 931.8832703 272931.57542322105 66.13215333333333 66.29789666666667 66.448605 931.8833674388112 2 1 MBR 11.934279685238241 5 1 1 0 0.10436721176227166 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ELEEVSPETPVVPATTQR ELEEVS[UniProt:Phosphoserine on S]PETPVVPATTQR Q15149 2060.966731 2 1031.4906421848789 110764.45086624891 70.45356333333334 70.75153166666666 70.86007333333333 1031.9936511945878 2 1 MBR 1.9525923367107085 1 1 1 0 1.5039243219408294 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib VASEEEEVPLVVYLK VAS[UniProt:Phosphoserine on S]EEEEVPLVVYLK Q8N3V7;UNDEFINED 1782.869249 2 892.4419011 606594.3878491583 98.54785 98.56307833333334 98.56307833333334 892.4419814434491 2 1 MBR 8.352983554944952 2 1 1 0 0.090142415 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 85.21874333333334 3 628.9992031328791 602295.6008282208 84.96157333333333 85.43836333333333 85.79730500000001 629.3331751270787 3 2 MSMS 3 1 1 0 -0.529959856 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib DRASPAAAEEVVPEWASCLK DRAS[UniProt:Phosphoserine on S]PAAAEEVVPEWASC[Common Fixed:Carbamidomethyl on C]LK Q8N3V7;UNDEFINED 2265.013699 93.64985666666666 2 1133.5141259098789 533565.7411735932 93.30758166666666 93.79679666666667 94.13242166666667 756.3460718867537 3 2 MSMS 2 1 1 0 -0.076353199 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 84.965305 3 628.9992031328791 572816.1099789651 84.75308166666666 85.30821999999999 85.63641666666666 629.3332907805781 3 2 MSMS 3 1 1 0 -0.345893851 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib DRASPAAAEEVVPEWASCLK DRAS[UniProt:Phosphoserine on S]PAAAEEVVPEWASC[Common Fixed:Carbamidomethyl on C]LK Q8N3V7;UNDEFINED 2265.013699 93.67263166666666 2 1133.5141259098789 479437.47006854386 93.17495 93.65845666666667 93.97514333333334 756.3460149859881 3 2 MSMS 3 1 1 0 -0.151684641 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib VASEEEEVPLVVYLK VAS[UniProt:Phosphoserine on S]EEEEVPLVVYLK Q8N3V7;UNDEFINED 1782.869249 2 892.4419011 281405.47245525004 98.64503333333333 98.64503333333333 98.64503333333333 892.4426818118054 2 1 MBR 6.546245216779141 2 1 1 0 0.8758067106665175 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 85.49539666666666 3 628.9992031328791 815920.8333333334 85.37037833333333 85.85166 86.27682666666668 629.3332875132265 3 2 MSMS 4 1 1 0 -0.351093938 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib DRASPAAAEEVVPEWASCLK DRAS[UniProt:Phosphoserine on S]PAAAEEVVPEWASC[Common Fixed:Carbamidomethyl on C]LK Q8N3V7;UNDEFINED 2265.013699 93.78824333333334 2 1133.5141259098789 667729.6094 93.27654 93.86330333333333 94.123285 756.3459814516709 3 2 MSMS 3 1 1 0 -0.19608103 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib VASEEEEVPLVVYLK VAS[UniProt:Phosphoserine on S]EEEEVPLVVYLK Q8N3V7;UNDEFINED 1782.869249 2 892.4419011 410498.9355 98.48087833333334 98.48087833333334 98.48087833333334 892.4416484656966 2 1 MBR 9.229416506661499 2 1 1 0 -0.283387784 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 86.13772166666666 3 628.9992031328791 856970.5085697669 85.45314833333333 85.91885833333333 86.403095 629.3337866848522 3 2 MSMS 4 1 1 0 0.44335264126255247 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib DRASPAAAEEVVPEWASCLK DRAS[UniProt:Phosphoserine on S]PAAAEEVVPEWASC[Common Fixed:Carbamidomethyl on C]LK Q8N3V7;UNDEFINED 2265.013699 93.927385 2 1133.5141259098789 735476.3528038795 93.523485 94.08963166666666 94.40296 756.3456903968473 3 2 MSMS 3 1 1 0 -0.581411167 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib VASEEEEVPLVVYLK VAS[UniProt:Phosphoserine on S]EEEEVPLVVYLK Q8N3V7;UNDEFINED 1782.869249 2 892.4419011 494665.85058759694 98.600025 98.62186833333334 98.62186833333334 892.4412758756224 2 1 MBR 7.357359031148851 2 1 1 0 -0.70135458 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 86.33253333333333 3 628.9992031328791 776769.4606536403 85.67323833333333 86.281415 86.57245333333333 629.3335343386144 3 2 MSMS 2 1 1 0 0.041736053 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib DRASPAAAEEVVPEWASCLK DRAS[UniProt:Phosphoserine on S]PAAAEEVVPEWASC[Common Fixed:Carbamidomethyl on C]LK Q8N3V7;UNDEFINED 2265.013699 94.01728833333333 2 1133.5141259098789 685607.9547137084 93.57118666666668 94.152895 94.42126999999999 756.3456150716713 3 2 MSMS 3 1 1 0 -0.681134855 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib VASEEEEVPLVVYLK VAS[UniProt:Phosphoserine on S]EEEEVPLVVYLK Q8N3V7;UNDEFINED 1782.869249 98.58089666666666 2 892.4419011 545453.9824221317 98.53562333333333 98.56078000000001 98.56078000000001 892.4416895517686 2 1 MSMS 1 1 1 0 -0.237297952 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib AASPAKPSSLDLVPNLPK AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK Q8N3V7;UNDEFINED 1883.97578 86.70363 3 628.9992031328791 853108.7376359565 86.08751666666666 86.53297833333333 86.88808 629.3337182340307 3 2 MSMS 3 1 1 0 0.33441111061597806 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 2 1093.9768449483788 8450282.525193535 98.117795 98.22630500000001 98.32741166666666 1094.478068 2 2 MBR 7.716675041961788 3 1 1 0 -0.210242942 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib ATSNVFAMFDQSQIQEFK ATS[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK|AT[UniProt:Phosphothreonine on T]SNVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 98.65510166666667 2 1085.979387638379 7217299.168322638 98.640975 98.66034499999999 98.66034499999999 1086.4804010623327 2 2 MSMS 2 1 2 0 -0.404973689 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 3 930.0819820492125 292635.1743 98.22630500000001 98.25037666666667 98.27234666666666 930.4154773848722 3 1 MBR 11.843431471689632 4 1 1 0 -0.840113788 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 98.22923666666667 2 1093.9768449483788 7466835.731379788 98.16786666666667 98.25548666666667 98.37524833333333 1094.4786186243462 2 2 MSMS 1 1 1 0 0.2931020258733622 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ATSNVFAMFDQSQIQEFK ATS[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 98.72787333333333 2 1085.979387638379 6149619.870989608 98.69584166666667 98.71828333333333 98.71828333333333 1086.481731030771 2 2 MSMS 1 1 1 0 0.8202688981921974 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2249.910553 98.99745333333333 2 1125.962553138379 1349315.832170048 98.9765 98.9765 98.9765 1126.4652471883546 2 2 MSMS 1 1 1 0 1.1043300202808164 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 3 930.0819820492125 304952.50969453057 98.28851833333333 98.31230666666667 98.32795833333334 930.4167389538375 3 1 MBR 14.142388674852835 4 1 1 0 0.5172746061767568 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 98.57350166666667 2 1085.979387638379 10091151.66 98.5787 98.5787 98.59860166666667 1086.4801595896622 2 2 MSMS 1 1 1 0 -0.627432051 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 2 1093.9768449483788 8293451.906 98.05721 98.149675 98.24801666666666 1094.477371430563 2 2 MBR 10.800329566441984 3 1 1 0 -0.847480357 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2249.910553 98.84008333333334 2 1125.962553138379 2636907.922 98.83052833333333 98.83052833333333 98.86621166666667 1126.4632045485364 2 2 MSMS 2 1 1 0 -0.710612987 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 98.15930333333333 3 930.0819820492125 1372296.797 98.149675 98.149675 98.20298333333334 930.4156655769749 3 2 MSMS 1 1 1 0 -0.637628008 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib ATSNVFAMFDQSQIQEFK ATS[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 2 1085.979387638379 10423211.541008178 98.69208 98.71224833333333 98.73802166666667 1086.4797289407359 2 1 MBR 7.744366813064936 2 1 1 0 -1.024170341 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 98.253715 2 1093.9768449483788 9304612.821 98.21967166666667 98.27878666666668 98.38734333333333 1094.4769375575318 2 2 MSMS 2 1 1 0 -1.244265477 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 98.28840833333334 3 930.0819820492125 824513.8955644894 98.27878666666668 98.31014333333333 98.32924833333333 930.4153147496904 3 1 MSMS 1 1 1 0 -1.015101533 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 98.15598666666666 2 1093.9768449483788 6031603.330252521 98.11607166666667 98.22092666666667 98.32372666666667 1094.477351620684 2 2 MSMS 2 1 1 0 -0.865596867 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib ATSNVFAMFDQSQIQEFK ATS[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 2 1085.979387638379 3922318.3518067077 98.62746333333332 98.62746333333332 98.66462666666668 1086.4801578194267 2 1 MBR 9.488390282736194 2 1 1 0 -0.629062892 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 98.23215166666667 3 930.0819820492125 1109901.740932942 98.20534 98.22092666666667 98.265615 930.4157097717207 3 2 MSMS 1 1 1 0 -0.590076557 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]SNVFAM[Common Variable:Oxidation on M]FDQSQIQEFK O14950|P19105|P24844 2185.939137 2 1093.9768449483788 6818784.5567252245 98.18809499999999 98.26274833333333 98.34593333333333 1094.476177626233 2 2 MBR 10.230676164329754 3 1 1 0 -1.939237071 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ATSNVFAMFDQSQIQEFK ATS[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2169.944222 98.7038 2 1085.979387638379 6743580.3948958805 98.67718166666667 98.67718166666667 98.69229 1086.4791873006877 2 2 MSMS 1 1 1 0 -1.523159968 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib ATSNVFAMFDQSQIQEFK AT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2249.910553 98.967605 2 1125.962553138379 4234173.877 98.95812 98.95812 98.97774333333334 1126.4619375211494 2 2 MSMS 1 1 1 0 -1.836402505 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib RPQRATSNVFAMFDQSQIQEFK RPQRAT[UniProt:Phosphothreonine on T]S[UniProt:Phosphoserine on S]NVFAMFDQSQIQEFK O14950|P19105|P24844 2787.224117 98.27257666666667 3 930.0819820492125 856053.6046976105 98.26274833333333 98.26274833333333 98.29564666666667 930.4147666532365 3 1 MSMS 1 1 1 0 -1.604827331 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 2 633.2943116 126966.3548870874 61.89585166666667 61.97462666666667 62.04364833333333 633.2941542185788 2 1 MBR 7.497200684316957 3 1 1 0 -0.248929349 +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 104972.20855253664 64.62071166666666 64.78036 64.91077166666666 673.2768873275197 2 1 MBR 3.1784319330715274 2 1 1 0 -0.877304778 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 94329.26563 64.86583666666667 65.01069833333332 65.150865 673.2770621131566 2 1 MBR 2.448763188162019 2 1 1 0 -0.617311644 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 2 633.2943116 113925.70756380947 61.61488166666666 61.71356166666667 61.85085 633.2947817397329 2 1 MBR 6.278979072005675 3 1 1 0 0.743533123 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 94796.04291654254 64.69847666666668 64.88964166666666 65.01013833333333 673.2771379755701 2 1 MBR 2.6186521631903776 2 1 1 0 -0.504466521 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 61.50265666666667 2 633.2943116 133865.9758500041 61.426230000000004 61.50793 61.607135 633.2942515188375 2 1 MSMS 1 1 1 0 -0.095043134 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 64.64144166666667 2 673.2774771133791 130513.20674378073 64.42739833333333 64.60346166666668 64.75379833333332 673.2768593517005 2 1 MSMS 1 1 1 0 -0.918918729 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGTY[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1264.57407 2 633.2943116 143669.64531045672 61.92338 62.068884999999995 62.1854 633.2943373625029 2 1 MBR 7.936988119061599 3 1 1 0 0.040723789135849814 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib IGEGTYGVVYK IGEGT[UniProt:Phosphothreonine on T]Y[UniProt:Phosphotyrosine on Y]GVVYK P06493|P24941;UNDEFINED 1344.540401 2 673.2774771133791 119183.79826575483 64.96146999999999 65.14224 65.257965 673.2777346890584 2 1 MBR 2.7541674040199124 1 1 1 0 0.3831430861023523 \ No newline at end of file diff --git a/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv b/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv new file mode 100644 index 0000000..531a211 --- /dev/null +++ b/inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv @@ -0,0 +1,7 @@ +Run Condition BioReplicate +180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib control 1 +180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib control 2 +180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib 1_min 3 +180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib 1_min 4 +180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib 10_min 5 +180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib 10_min 6 \ No newline at end of file diff --git a/inst/tinytest/test_converters.R b/inst/tinytest/test_converters.R index 87f85f6..6b4b92b 100644 --- a/inst/tinytest/test_converters.R +++ b/inst/tinytest/test_converters.R @@ -172,3 +172,21 @@ expect_error(PDtoMSstatsPTMFormat(pd_psm_input, system.file("extdata", "pd_fasta.fasta", package="MSstatsPTM"), which_proteinid = "Master.Protein.Accessions")) + + +## Metamorpheus +input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", + package = "MSstatsPTM") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +metamorpheus_imported = MetamorpheusToMSstatsPTMFormat( + input, + annot, + fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", package="MSstatsPTM"), + use_unmod_peptides=TRUE, + mod_id = "\\[Common Fixed:Carbamidomethyl on C\\]" +) +expect_true(nrow(metamorpheus_imported$PTM) > 0) +expect_true(nrow(metamorpheus_imported$PROTEIN) > 0) diff --git a/man/MSstatsPTM.Rd b/man/MSstatsPTM.Rd index 0b01c82..7d35d0a 100644 --- a/man/MSstatsPTM.Rd +++ b/man/MSstatsPTM.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/MSstatsPTM.R \docType{package} \name{MSstatsPTM} +\alias{MSstatsPTM-package} \alias{MSstatsPTM} \title{MSstatsPTM: A package for detecting differentially abundant post-translational modifications (PTM) in mass spectrometry-based @@ -52,3 +53,23 @@ analysis and summarization } } +\seealso{ +Useful links: +\itemize{ + \item Report bugs at \url{https://github.com/Vitek-Lab/MSstatsPTM/issues} +} + +} +\author{ +\strong{Maintainer}: Devon Kohler \email{kohler.d@northeastern.edu} + +Authors: +\itemize{ + \item Tsung-Heng Tsai \email{tsai.tsungheng@gmail.com} + \item Ting Huang \email{thuang0703@gmail.com} + \item Mateusz Staniak \email{mtst@mstaniak.pl} + \item Meena Choi \email{mnchoi67@gmail.com} + \item Olga Vitek \email{o.vitek@northeastern.edu} +} + +} diff --git a/man/MetamorpheusToMSstatsPTMFormat.Rd b/man/MetamorpheusToMSstatsPTMFormat.Rd new file mode 100644 index 0000000..fbfce59 --- /dev/null +++ b/man/MetamorpheusToMSstatsPTMFormat.Rd @@ -0,0 +1,94 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/converters.R +\name{MetamorpheusToMSstatsPTMFormat} +\alias{MetamorpheusToMSstatsPTMFormat} +\title{Import Metamorpheus files into PTM format} +\usage{ +MetamorpheusToMSstatsPTMFormat( + input, + annotation, + fasta_path, + use_unmod_peptides = FALSE, + mod_id = "\\\\[Common Biological:Phosphorylation on S\\\\]", + useUniquePeptide = TRUE, + removeFewMeasurements = TRUE, + removeProtein_with1Feature = FALSE, + summaryforMultipleRows = max, + use_log_file = TRUE, + append = FALSE, + verbose = TRUE, + log_file_path = NULL +) +} +\arguments{ +\item{input}{name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output.} + +\item{annotation}{name of 'annotation.txt' data which includes Condition, BioReplicate.} + +\item{fasta_path}{string containing path to the corresponding fasta file for +the modified peptide dataset.} + +\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_id}{Character that indicates the modification of interest. Default +is \verb{Common Biological:Phosphorylation on S}. +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}{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 '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{ +Import Metamorpheus files into PTM format +} +\examples{ +input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", + package = "MSstatsPTM") +input = data.table::fread(input) +annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", + package="MSstatsPTM") +metamorpheus_imported = MetamorpheusToMSstatsPTMFormat( + input, + annot, + fasta_path=fasta_path, + use_unmod_peptides=TRUE, + mod_id = "\\\\[Common Fixed:Carbamidomethyl on C\\\\]" +) +head(metamorpheus_imported$PTM) +head(metamorpheus_imported$PROTEIN) +} +\author{ +Anthony Wu +} From 24a95d6a9c2aadf04b813ffd7b2d8c4dbc4bf5f3 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Fri, 23 Feb 2024 12:52:13 -0500 Subject: [PATCH 2/2] fix: For ptm_input, filter out rows without targeted ptm --- R/converters.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/converters.R b/R/converters.R index 49bb7de..1c4b1c2 100644 --- a/R/converters.R +++ b/R/converters.R @@ -1530,6 +1530,8 @@ MetamorpheusToMSstatsPTMFormat = function(input, verbose, log_file_path) + ptm_input = ptm_input[grepl(mod_id, ptm_input$PeptideSequence),] + msstats_format = list(PTM = ptm_input, PROTEIN = protein_input) }