Package proteoqc. June 14, 2018

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1 Type Package Package proteoqc June 14, 2018 Title An R package for proteomics data quality control Version Author, Laurent Gatto <lg390@cam.ac.uk> Maintainer This package creates an HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data. Depends R (>= 3.0.0), XML, VennDiagram, MSnbase Imports rtandem, plyr, seqinr, Nozzle.R1, ggplot2, hape2, parallel, rpx, tidyr, dplyr, plotly, rmarkdown, License LGPL-2 Suggests RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics VignetteBuilder knitr URL biocviews Proteomics, MassSpectrometry, QualityControl, Visualization, ReportWriting RoxygenNote R topics documented: addsummarychart calcmsqcmetrics chargestat cntstat combinerun createtargetdecoydb getenzyme getmods labelratio loadmsqc msqcpipe plotbiorepvenn plotfractionidresult plotms1error

2 2 calcmsqcmetrics plotms2error plotms2error_obsolete plotsampleidresulterrorbar plotsamplevenn plottechrepvenn print.msqc proteingroup reporthtml runtandem showenzyme showmods Index 16 addsummarychart Add PRIDE summary charts Add PRIDE summary charts in the technical replicate level addsummarychart() An object returned by msqcpipe function calcmsqcmetrics Calculate the MS1 and MS2 level QC metrics Calculate the MS1 level QC metrics calcmsqcmetrics(spectralist = NULL, cpu = 2, outdir = "./") spectralist cpu outdir An experiment design input file The number of cpu used Output directory A data frame

3 chargestat 3 chargestat Charge distribution Read the charge information from mgf file chargestat(mgf = NULL) mgf A file of mgf. A data.frame object mgf.zip <- system.file("extdata/mgf.zip", package = "proteoqc") unzip(mgf.zip) charge <- chargestat("test.mgf") cntstat contaminants stat Common Contaminants in Proteomics Mass Spectrometry Experiments cntstat() An object of msqc A data.frame will be shown in HTML report

4 4 createtargetdecoydb combinerun Combine multiple ults Combine multiple ults combinerun(pepfiles, fasta, outpathfile, outdir, prefix) pepfiles fasta outpathfile outdir prefix peptidesummary files database file out file output directory output prefix A data.frame createtargetdecoydb Create target-decoy database Create target-decoy database createtargetdecoydb(fa, outdb) fa outdb target database output target-decoy database target-decoy database file name

5 getenzyme 5 getenzyme Get the enzymes list Get the enzymes list getenzyme() A data frame which contains all of the enzymes getmods Get the modification list Get the modification list getmods() A data frame which contains all of the modifications

6 6 loadmsqc labelratio Calculate the labeling efficiency of isobaric labeling data Calculate the labeling efficiency of isobaric labeling data labelratio(ms = NULL, reporter = 1, plot = TRUE) ms reporter plot MS/MS file. Isobaric tag class, 1=iTRAQ-4plex, 2=iTRAQ-8plex, 3=TMT-6plex. 4=TMT- 10plex. Logical value A vector object mgf.zip <- system.file("extdata/mgf.zip", package = "proteoqc") unzip(mgf.zip) a <- labelratio("test.mgf",reporter=2) loadmsqc Load the ult of msqcpipe Load the ult of msqcpipe loadmsqc(outdir) outdir The output directory of msqcpipe Laurent Gatto <lg390@cam.ac.uk>,

7 msqcpipe 7 zpqc <- system.file("extdata/qc.zip", package = "proteoqc") unzip(zpqc) qc <- loadmsqc("./qc") msqcpipe The main function of msqc pipeline This function is designed to automate generating of target-decoy database, database searcing, postprocessing and report generation. msqcpipe(spectralist = NULL, fasta = "", outdir = "./", mode = "", miss = 2, enzyme = 1, varmod = NULL, fixmod = NULL, tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", thhold = 0.01, cpu = 0, xmx = 2, refine = TRUE, ntt = 1,...) spectralist fasta outdir mode miss enzyme varmod fixmod tol tolu itol itolu thhold cpu xmx refine A file contains the experiment design or a single mgf file database file, must contain decoy sequences output directory identification or quantification max miss clevage enzyme Variable modifications are those which may or may not be pent. Fixed modifications are applied universally, to every instance of the specified idue(s) or terminus. The error window on experimental peptide mass values Units can be selected from: ppm, Daltons(also da or Da). Error window for MS/MS fragment ion mass values. Units can be selected from: Daltons(also da or Da) FDR value for PSM Max number of cpu used JAVA -Xmx Refine search for X!Tandem, default is TRUE. ntt Semi-tryptic, 1; fully-tryptic, Additional parameters passed to read.table used to read the experimental design. A list which contains all of the information for data quality report generating

8 8 plotbiorepvenn ## Not run: library("rpx") px <- PXDataset("PXD000864") mgfs <- grep("mgf", pxfiles(px), value = TRUE) mgfs <- grep("-0[5-6]-[1 2]", mgfs, value=true) mgffiles <- pxget(px, mgfs) library("r.utils") mgffiles <- sapply(mgffiles, gunzip) ## Generate the lightweight qc report, ## trim the mgf files to 1/10 of their size. trimmgf <- function(f, m = 1/10, overwrite = FALSE) { message("reading ", f) x <- readlines(f) beg <- grep("begin IONS", x) end <- grep("end IONS", x) n <- length(beg) message("sub-setting to ", m) i <- sort(sample(n, floor(n * m))) k <- unlist(mapply(seq, from = beg[i], to = end[i])) if (overwrite) { unlink(f) message("writing ", f) writelines(x[k], con = f) return(f) } else { g <- sub(".mgf", "_small.mgf", f) message("writing ", g) writelines(x[k], con = g) return(g) } } set.seed(1) mgffiles <- sapply(mgffiles, trimmgf, overwrite = TRUE) fas <- pxget(px, "TTE2010.zip") fas <- unzip(fas) design <- system.file("extdata/pxd design.txt", package = "proteoqc") read.table(design, header = TRUE) qc <- msqcpipe(spectralist = design, fasta = fas, outdir = "./qc", miss = 0, enzyme = 1, varmod = 2, fixmod = 1, tol = 10, itol = 0.6, cpu = 2, mode = "identification") ## End(Not run) plotbiorepvenn Venn plot in biological replicate level

9 plotfractionidresult 9 Venn plot in biological replicate level plotbiorepvenn() An object of msqc The name of the figure plotfractionidresult Barplot in different level for each fraction Barplot in different level for each fraction plotfractionidresult(, level = NA) level An object of msqc 1: total spectrum, 2: identified spectrum, 3: identified peptide, 4: identified protein. The name of the figure plotms1error plot MS1 mass error plot MS1 mass error plotms1error(, plot.class = "ppm")

10 10 plotms2error_obsolete plot.class An object of msqc ppm or da The name of the figure plotms2error plot MS2 mass error plot MS2 mass error plotms2error() An object of msqc The name of the figure plotms2error_obsolete plot MS2 mass error plot MS2 mass error plotms2error_obsolete() An object of msqc The name of the figure

11 plotsampleidresulterrorbar 11 plotsampleidresulterrorbar Error barplot in different level for each fraction Error Barplot in different level for each fraction plotsampleidresulterrorbar(, level = NA) level An object of parser ult 1: total spectrum, 2: identified spectrum, 3: identified peptide, 4: identified protein. The name of the figure plotsamplevenn Venn plot in sample level Venn plot in sample level plotsamplevenn() An object of msqc The name of the figure

12 12 print.msqc plottechrepvenn Venn plot in technical replicate level Venn plot in technical replicate level plottechrepvenn() An object of msqc The name of the figure print.msqc Print the information of msqc object Print the information of msqc object ## S3 method for class 'msqc' print(x,...) x A msqc object... Additional parameters Laurent Gatto <lg390@cam.ac.uk>, zpqc <- system.file("extdata/qc.zip", package = "proteoqc") unzip(zpqc) qc <- loadmsqc("./qc") print.msqc(qc)

13 proteingroup 13 proteingroup Protein inference Protein inference proteingroup(file = NULL, db = "", pepcolname = "peptide", procolname = "protein", spectrumcolname = "index", prosep = ";", outfile = NULL, xmx = 1) file db pepcolname A file containing the information of peptides to proteins. A protein database of fasta format. The column name of peptide sequence. procolname The column name of protein ID. spectrumcolname The column name of spectrum index. prosep The separator of protein ID, default is "". outfile xmx The output file name of protein group ult. JAVA -Xm pep.zip <- system.file("extdata/pep.zip", package = "proteoqc") unzip(pep.zip) proteingroup(file = "pep.txt", outfile = "pg.txt") reporthtml HTML format report generator HTML format report generator reporthtml() An object returned by msqcpipe function

14 14 runtandem null zpqc <- system.file("extdata/qc.zip", package = "proteoqc") unzip(zpqc) qc <- loadmsqc("./qc") html <- reporthtml(qc) runtandem Run X!Tandem Run X!Tandem run X!Tandem runtandem(spectra = "", fasta = "", outdir = "./", outprefix = "", cpu = 1, enzyme = 1, xmx = 2, varmod = NULL, fixmod = NULL, refine = TRUE, ntt = 1, tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", miss = 1) spectra fasta outdir outprefix cpu enzyme xmx varmod fixmod refine MS/MS peak list file database file output directory output file prefix ntt Default is 1 tol tolu itol itolu miss The number of CPU used for X!Tandem The ID of enzyme used for database searching. See showenzyme. Set for parameter of "Java -Xmx". Variable modifications used for database searching. See showmods. Fixed modifications used for database searching. See showmods. Refine search, default is TRUE The error window on experimental peptide mass values Units can be selected from: ppm, Daltons. Error window for MS/MS fragment ion mass values. Units can be selected from: Daltons Max miss clevage

15 showenzyme 15 a file path showenzyme Shown all enzymes Shown all enzymes showenzyme() A data frame which contains all of the enzymes showenzyme() showmods Shown all modifications Shown all modifications showmods() A data frame which contains all of the modifications showmods()

16 Index addsummarychart, 2 calcmsqcmetrics, 2 chargestat, 3 cntstat, 3 combinerun, 4 createtargetdecoydb, 4 getenzyme, 5 getmods, 5 labelratio, 6 loadmsqc, 6 msqcpipe, 6, 7, 13 plotbiorepvenn, 8 plotfractionidresult, 9 plotms1error, 9 plotms2error, 10 plotms2error_obsolete, 10 plotsampleidresulterrorbar, 11 plotsamplevenn, 11 plottechrepvenn, 12 print.msqc, 12 proteingroup, 13 read.table, 7 reporthtml, 13 runtandem, 14 showenzyme, 14, 15 showmods, 14, 15 16