PTXQC: Quality Report Generation for MaxQuant Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (see <>). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Install the latest version of this package by entering the following in R:
AuthorChris Bielow <>
Date of publication2017-04-03 16:41:26 UTC
MaintainerChris Bielow <>

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Man pages

addGGtitle: Add title and subtitle to a ggplot

alignmentCheck: Verify an alignment by checking the retention time...

appendEnv: Add the value of a variable to an environment (fast append)

assignBlocks: Assign set numbers to a vector of values.

boxplotCompare: Boxplots - one for each condition (=column) in a data frame.

brewer.pal.Safe: Return color brew palettes, but fail hard if number of...

byX: Calls FUN on a subset of data in blocks of size 'subset_size'...

byXflex: Same as 'byX', but with more flexible group size, to avoid...

computeMatchRTFractions: Combine several data structs into a final picture for...

correctSetSize: Re-estimate a new set size to split a number of items into...

createReport: Create a quality control report (in PDF format).

CV: Coefficient of variation (CV)

del0: Replace 0 with NA in a vector

delLCP: Removes the longest common prefix (LCP) from a vector of...

delLCS: Removes the longest common suffix (LCS) from a vector of...

findAlignReference: Return list of raw file names which were reported by MaxQuant...

fixCalibration: Detect (and fix) MaxQuant mass recalibration columns, since...

flattenList: Flatten lists of lists with irregular depths to just a list...

getAbundanceClass: Assign a relative abundance class to a set of (log10)...

getECDF: Estimate the empirical density and return it

getFragmentErrors: Extract fragment mass deviation errors from a data.frame from...

getMaxima: Find the local maxima in a vector of numbers.

getMetaData: Extract meta information (orderNr, metric name, category)...

getMQPARValue: Retrieve a parameter value from a mqpar.xml file

getPCA: Create a principal component analysis (PCA) plot for the...

getPeptideCounts: Extract the number of peptides observed per Raw file from an...

getProteinCounts: Extract the number of protein groups observed per Raw file...

getQCHeatMap: Generate a Heatmap from a list of QC measurements.

getReportFilenames: Assembles a list of output file names, which will be created...

ggAxisLabels: Function to thin out the number of labels shown on an axis in...

ggText: Plot a text as graphic using ggplot2.

grapes-plus-grapes: A string concatenation function, more readable than...

grepv: Grep with values returned instead of indices.

idTransferCheck: Check how close transferred ID's after alignment are to their...

inMatchWindow: For grouped peaks: separate them into in-width vs. out-width...

lcpCount: Count the number of chars of the longest common prefix

LCS: Compute longest common substring of two strings.

lcsCount: Count the number of chars of the longest common suffix

LCSn: Find longest common substring from 'n' strings.

longestCommonPrefix: Get the longest common prefix from a set of strings.

longestCommonSuffix: Like longestCommonPrefix(), but on the suffix.

mosaicize: Prepare a Mosaic plot of two columns in long format.

MQDataReader-cash-getInvalidLines: Detect broken lines (e.g. due to Excel import+export)

MQDataReader-cash-getShortNames: Shorten a set of Raw file names and return a data frame with...

MQDataReader-cash-new: Constructor for class 'MQDataReader'.

MQDataReader-cash-plotNameMapping: Plots the current mapping of Raw file names to their...

MQDataReader-cash-readMappingFile: Reads a mapping table of full Raw file names to shortened...

MQDataReader-cash-readMQ: Wrapper to read a MQ txt file (e.g. proteinGroups.txt).

MQDataReader-cash-substitute: Replaces values in the member with (binary) values.

MQDataReader-cash-writeMappingFile: Writes a mapping table of full Raw file names to shortened...

pasten: paste with newline as separator

pastet: paste with tab as separator

peakSegmentation: Determine fraction of evidence which causes segmentation,...

peakWidthOverTime: Discretize RT peak widths by averaging values per time bin.

plot_CalibratedMSErr: Plot bargraph of uncalibrated mass errors for each Raw file.

plot_Charge: Plot MaxQuant Match-between-runs id transfer performance.

plot_ContEVD: Plot contaminants from evidence.txt, broken down into...

plot_ContsPG: Plot contaminants from proteinGroups.txt

plot_ContUser: Plot user-defined contaminants from evidence.txt

plot_ContUserScore: Plot Andromeda score distribution of contaminant peptide vs....

plot_CountData: Plot Protein groups per Raw file

plot_IDRate: Plot percent of identified MS/MS for each Raw file.

plot_IDsOverRT: Plot IDs over time for each Raw file.

plot_IonInjectionTimeOverRT: Plot line graph of TopN over Retention time.

plot_MBRAlign: Plot MaxQuant Match-between-runs alignment performance.

plot_MBRgain: Plot MaxQuant Match-between-runs id transfer performance.

plot_MBRIDtransfer: Plot MaxQuant Match-between-runs id transfer performance.

plot_MissedCleavages: Plot bargraph of missed cleavages.

plot_MS2Decal: Plot bargraph of oversampled 3D-peaks.

plot_MS2Oversampling: Plot bargraph of oversampled 3D-peaks.

plot_RatiosPG: Plot ratios of labeled data (e.g. SILAC) from...

plot_RTPeakWidth: Plot RT peak width over time

plot_ScanIDRate: Plot line graph of TopN over Retention time.

plotTable: Plot a table with row names and title

plotTableRaw: Colored table plot.

plot_TopN: Plot line graph of TopN over Retention time.

plot_TopNoverRT: Plot line graph of TopN over Retention time.

plot_UncalibratedMSErr: A boxplot of uncalibrated mass errors for each Raw file.

pointsPutX: Distribute a set of points with fixed y-values on a stretch...

print.PTXQC_table: helper S3 class, enabling print(some-plot_Table-object)

printWithFooter: Augment a ggplot with footer text

qcMetric-class: Class which can compute plots (usually for a single metric).

qcMetric_MSMSScans_TopNoverRT-class: Metric for msmsscans.txt, showing TopN over RT.

qualBestKS: From a list of vectors, compute all vs. all...

qualCentered: Quality metric for 'centeredness' of a distribution around...

qualCenteredRef: Quality metric for 'centeredness' of a distribution around...

qualGaussDev: Compute probability of Gaussian (mu=m, sd=s) at a position 0,...

qualHighest: Score an empirical density distribution of values, where the...

qualLinThresh: Quality metric with linear response to input, reaching the...

qualMedianDist: Quality metric which measures the absolute distance from...

qualUniform: Compute deviation from uniform distribution

read.MQ: Convenience wrapper for MQDataReader when only a single MQ...

renameFile: Given a vector of (short/long) filenames, translate to the...

repEach: Repeat each element x_i in X, n_i times.

RSD: Relative standard deviation (RSD)

RTalignmentTree: Return a tree plot with a possible alignment tree.

scale_x_discrete_reverse: Inverse the order of items on the x-axis (for discrete...

scale_y_discrete_reverse: Inverse the order of items on the y-axis (for discrete...

ScoreInAlignWindow: Compute the fraction of features per Raw file which have an...

shortenStrings: Shorten a string to a maximum length and indicate shorting by...

simplifyNames: Removes common substrings (infixes) in a set of strings.

supCount: Compute shortest prefix length which makes all strings in a...

theme_blank: A blank theme (similar to the deprecated theme_blank())

thinOut: Thin out a data.frame by removing rows with similar numerical...

thinOutBatch: Apply 'thinOut' on all subsets of a data.frame, split by a...

wait_for_writable: Check if a file is writable and blocks an interactive...

YAMLClass-class: Query a YAML object for a certain parameter.


\%+\% Man page
addGGtitle Man page
alignmentCheck Man page
appendEnv Man page
assignBlocks Man page
boxplotCompare Man page
brewer.pal.Safe Man page
byX Man page
byXflex Man page
computeMatchRTFractions Man page
correctSetSize Man page
createReport Man page
CV Man page
del0 Man page
delLCP Man page
delLCS Man page
findAlignReference Man page
fixCalibration Man page
flattenList Man page
getAbundanceClass Man page
getECDF Man page
getFragmentErrors Man page
getMaxima Man page
getMetaData Man page
getMQPARValue Man page
getPCA Man page
getPeptideCounts Man page
getProteinCounts Man page
getQCHeatMap Man page
getReportFilenames Man page
ggAxisLabels Man page
ggText Man page
grepv Man page
idTransferCheck Man page
inMatchWindow Man page
lcpCount Man page
LCS Man page
lcsCount Man page
LCSn Man page
longestCommonPrefix Man page
longestCommonSuffix Man page
mosaicize Man page
MQDataReader$getInvalidLines Man page
MQDataReader$getShortNames Man page
MQDataReader$new Man page
MQDataReader$plotNameMapping Man page
MQDataReader$readMappingFile Man page
MQDataReader$readMQ Man page
MQDataReader$substitute Man page
MQDataReader$writeMappingFile Man page
pasten Man page
pastet Man page
peakSegmentation Man page
peakWidthOverTime Man page
plot_CalibratedMSErr Man page
plot_Charge Man page
plot_ContEVD Man page
plot_ContsPG Man page
plot_ContUser Man page
plot_ContUserScore Man page
plot_CountData Man page
plot_IDRate Man page
plot_IDsOverRT Man page
plot_IonInjectionTimeOverRT Man page
plot_MBRAlign Man page
plot_MBRgain Man page
plot_MBRIDtransfer Man page
plot_MissedCleavages Man page
plot_MS2Decal Man page
plot_MS2Oversampling Man page
plot_RatiosPG Man page
plot_RTPeakWidth Man page
plot_ScanIDRate Man page
plotTable Man page
plotTableRaw Man page
plot_TopN Man page
plot_TopNoverRT Man page
plot_UncalibratedMSErr Man page
pointsPutX Man page
print.PTXQC_table Man page
printWithFooter Man page
qcMetric Man page
qcMetric-class Man page
qcMetric_MSMSScans_TopNoverRT Man page
qcMetric_MSMSScans_TopNoverRT-class Man page
qualBestKS Man page
qualCentered Man page
qualCenteredRef Man page
qualGaussDev Man page
qualHighest Man page
qualLinThresh Man page
qualMedianDist Man page
qualUniform Man page
read.MQ Man page
renameFile Man page
repEach Man page
RSD Man page
RTalignmentTree Man page
scale_x_discrete_reverse Man page
scale_y_discrete_reverse Man page
ScoreInAlignWindow Man page
shortenStrings Man page
simplifyNames Man page
supCount Man page
theme_blank Man page
thinOut Man page
thinOutBatch Man page
wait_for_writable Man page
YAMLClass Man page
YAMLClass-class Man page


tests/testthat/test_computeQC.R tests/testthat/test_qualities.R tests/testthat/test_misc.R tests/testthat/test_qcMetric.R
R/MQDataReader.R R/fcn_misc.R R/fcn_MQalign.R R/qcMetric_PAR.R R/fcn_qualities.R R/fcn_PCA.R R/fcn_YAML.R R/qcMetric_PG.R R/qcMetric_MSMS.R R/fcn_computeQC.R R/fcn_miscGGplot.R R/fcn_MQ.R R/pkg_internal.R R/fcn_plots.R R/qcMetric_EVD.R R/qcMetric_MSMSScans.R R/qcMetric.R R/fcn_mqpar.R R/qcMetric_SM.R R/fcn_QCHeat.R
man/grepv.Rd man/longestCommonSuffix.Rd man/wait_for_writable.Rd man/RSD.Rd man/MQDataReader-cash-new.Rd man/plotTable.Rd man/MQDataReader-cash-substitute.Rd man/getProteinCounts.Rd man/peakWidthOverTime.Rd man/getPeptideCounts.Rd man/plot_IonInjectionTimeOverRT.Rd man/mosaicize.Rd man/qualBestKS.Rd man/plot_MS2Decal.Rd man/findAlignReference.Rd man/qualCentered.Rd man/plot_MBRgain.Rd man/printWithFooter.Rd man/plot_RTPeakWidth.Rd man/pasten.Rd man/getMQPARValue.Rd man/MQDataReader-cash-plotNameMapping.Rd man/plot_ContUserScore.Rd man/MQDataReader-cash-getShortNames.Rd man/thinOut.Rd man/lcsCount.Rd man/CV.Rd man/longestCommonPrefix.Rd man/plot_IDRate.Rd man/plot_RatiosPG.Rd man/ggText.Rd man/assignBlocks.Rd man/plot_ContEVD.Rd man/plot_TopNoverRT.Rd man/getMetaData.Rd man/plot_UncalibratedMSErr.Rd man/getPCA.Rd man/ggAxisLabels.Rd man/plot_CountData.Rd man/inMatchWindow.Rd man/plot_Charge.Rd man/plot_MBRIDtransfer.Rd man/pastet.Rd man/delLCP.Rd man/peakSegmentation.Rd man/computeMatchRTFractions.Rd man/MQDataReader-cash-readMQ.Rd man/qcMetric-class.Rd man/plot_CalibratedMSErr.Rd man/byX.Rd man/plot_ContsPG.Rd man/fixCalibration.Rd man/scale_y_discrete_reverse.Rd man/createReport.Rd man/getFragmentErrors.Rd man/print.PTXQC_table.Rd man/qualLinThresh.Rd man/getQCHeatMap.Rd man/plot_IDsOverRT.Rd man/plot_TopN.Rd man/MQDataReader-cash-getInvalidLines.Rd man/scale_x_discrete_reverse.Rd man/plot_MBRAlign.Rd man/plot_ScanIDRate.Rd man/simplifyNames.Rd man/boxplotCompare.Rd man/plot_ContUser.Rd man/del0.Rd man/LCSn.Rd man/theme_blank.Rd man/grapes-plus-grapes.Rd man/getECDF.Rd man/flattenList.Rd man/MQDataReader-cash-readMappingFile.Rd man/getMaxima.Rd man/shortenStrings.Rd man/getReportFilenames.Rd man/idTransferCheck.Rd man/supCount.Rd man/qualHighest.Rd man/qualUniform.Rd man/LCS.Rd man/thinOutBatch.Rd man/alignmentCheck.Rd man/byXflex.Rd man/addGGtitle.Rd man/YAMLClass-class.Rd man/qualMedianDist.Rd man/getAbundanceClass.Rd man/qcMetric_MSMSScans_TopNoverRT-class.Rd man/plot_MS2Oversampling.Rd man/ScoreInAlignWindow.Rd man/MQDataReader-cash-writeMappingFile.Rd man/plot_MissedCleavages.Rd man/repEach.Rd man/read.MQ.Rd man/plotTableRaw.Rd man/appendEnv.Rd man/RTalignmentTree.Rd man/renameFile.Rd man/qualCenteredRef.Rd man/delLCS.Rd man/brewer.pal.Safe.Rd man/correctSetSize.Rd man/qualGaussDev.Rd man/lcpCount.Rd man/pointsPutX.Rd

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