Package: PSMatch 1.17.0

Laurent Gatto

PSMatch: Handling and Managing Peptide Spectrum Matches

The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

Authors:Laurent Gatto [aut, cre], Johannes Rainer [aut], Sebastian Gibb [aut], Samuel Wieczorek [ctb], Thomas Burger [ctb], Guillaume Deflandre [ctb]

PSMatch_1.17.0.tar.gz
PSMatch_1.17.0.zip(r-4.7-any)PSMatch_1.17.0.zip(r-4.6-any)PSMatch_1.17.0.zip(r-4.5-any)
PSMatch_1.17.0.tgz(r-4.6-any)PSMatch_1.17.0.tgz(r-4.5-any)
PSMatch_1.17.0.tar.gz(r-4.7-any)PSMatch_1.17.0.tar.gz(r-4.6-any)
PSMatch_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PSMatch/json (API)

# Install 'PSMatch' in R:
install.packages('PSMatch', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/psm/issues

On BioConductor:PSMatch-1.17.0(bioc 3.24)PSMatch-1.16.0(bioc 3.23)

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

9.78 score 6 stars 49 packages 54 scripts 4.2k downloads 31 exports 103 dependencies

Last updated from:3ec4d55b28. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE186
linux-develNOTE435
source / vignettesOK370
linux-releaseNOTE533
macos-releaseNOTE319
macos-oldrelNOTE297
windows-develNOTE455
windows-releaseNOTE325
windows-oldrelNOTE282
wasm-releaseOK192

Exports:adjacencyMatrixcalculateFragmentsccMatrixconnectedComponentsConnectedComponentsdefaultNeutralLossdescribePeptidesdescribeProteinsdimsfilterPsmDecoyfilterPsmFdrfilterPsmRankfilterPSMsfilterPsmSharedgetAminoAcidsgetAtomicMasslabelFragmentsmakeAdjacencyMatrixmakePeptideProteinVectorncolsnrowsplotAdjacencyMatrixplotSpectraPTMprioritiseConnectedComponentsprioritizeConnectedComponentsPSMpsmVariablesreadPSMsreducedreduced<-reducePSMs

Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericsPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

MS2 fragment ions
Introduction | Calculating fragment ions | Visualising fragment ions | Session information
Rendered fromFragments.Rmdusingknitr::rmarkdown

Last update: 2026-04-07
Started: 2022-02-14

Working with PSM data
Installation instructions | Introduction | Handling and processing identification data | Loading PSM data | Keeping all matches | Filtering data | Remove decoy hits | Keep first rank matches | Remove shared peptides | All filters in one function | The mzR and mzID parsers | Session information
Rendered fromPSM.Rmdusingknitr::rmarkdown

Last update: 2026-04-05
Started: 2020-10-28

Understanding protein groups with adjacency matrices
Introduction | Peptide-protein relation | Visualising adjacency matrices | Colouring the graph nodes | Colouring protein nodes | Colouring peptide nodes | Using quantitative data | Prioritising connected components | Session information
Rendered fromAdjacencyMatrix.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2022-02-09

Readme and manuals

Help Manual

Help pageTopics
Convert to/from an adjacency matrix.adjacencyMatrix makeAdjacencyMatrix makePeptideProteinVector plotAdjacencyMatrix
Calculate ions produced by fragmentation with variable modificationscalculateFragments calculateFragments,character,missing-method defaultNeutralLoss modificationPositions
Connected componentsadjacencyMatrix,ConnectedComponents adjacencyMatrix,ConnectedComponents-method ccMatrix ConnectedComponents connectedComponents ConnectedComponents-class dims,ConnectedComponents dims,ConnectedComponents-method length,ConnectedComponents length,ConnectedComponents-method ncols,ConnectedComponents ncols,ConnectedComponents-method nrows,ConnectedComponents nrows,ConnectedComponents-method prioritiseConnectedComponents prioritizeConnectedComponents show,ConnectedComponents [,ConnectedComponents,integer,ANY,ANY [,ConnectedComponents,integer,ANY,ANY-method [,ConnectedComponents,logical,ANY,ANY [,ConnectedComponents,logical,ANY,ANY-method [,ConnectedComponents,numeric,ANY,ANY [,ConnectedComponents,numeric,ANY,ANY-method
Describe protein and peptide compositionsdescribePeptides describeProteins
Filter out unreliable PSMs.filterPsmDecoy filterPsmFdr filterPsmRank filterPSMs filterPsmShared
Amino acidsgetAminoAcids
Atomic mass.getAtomicMass
labels MS2 FragmentslabelFragments
Function to plot MS/MS spectra with PTMsplotSpectraPTM
A class for peptide-spectrum matchesadjacencyMatrix,PSM-method PSM PSM,character PSM,data.frame PSM,PSM PSM-class psmVariables readPSMs reduced reduced<- reducePSMs
PSMatch: Handling and Managing Peptide Spectrum MatchesPSMatch-package PSMatch