Introduction | Calculating fragment ions | Visualising fragment ions | Session information
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:
PSMatch_1.17.0.tar.gz
PSMatch_1.17.0.zip(r-4.7)PSMatch_1.17.0.zip(r-4.6)PSMatch_1.17.0.zip(r-4.5)
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
Last updated from:3ec4d55b28. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 245 | ||
| linux-devel-x86_64 | NOTE | 475 | ||
| source / vignettes | OK | 557 | ||
| linux-release-x86_64 | NOTE | 482 | ||
| macos-release-arm64 | NOTE | 298 | ||
| macos-oldrel-arm64 | NOTE | 247 | ||
| windows-devel | NOTE | 331 | ||
| windows-release | NOTE | 402 | ||
| windows-oldrel | NOTE | 394 | ||
| wasm-release | OK | 215 |
Exports:adjacencyMatrixcalculateFragmentsccMatrixconnectedComponentsConnectedComponentsdefaultNeutralLossdescribePeptidesdescribeProteinsdimsfilterPsmDecoyfilterPsmFdrfilterPsmRankfilterPSMsfilterPsmSharedgetAminoAcidsgetAtomicMasslabelFragmentsmakeAdjacencyMatrixmakePeptideProteinVectorncolsnrowsplotAdjacencyMatrixplotSpectraPTMprioritiseConnectedComponentsprioritizeConnectedComponentsPSMpsmVariablesreadPSMsreducedreduced<-reducePSMs
Dependencies:abindAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelbslibcachemcliclueclustercodetoolscpp11crosstalkcurldata.tableDelayedArraydigestdplyrevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMultiAssayExperimentopensslotelpillarpkgconfigplotlyplyrpromisesProtGenericsPTModspurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2rlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySpectrastringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
MS2 fragment ions
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
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
Last update: 2026-04-03
Started: 2022-02-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert to/from an adjacency matrix. | adjacencyMatrix makeAdjacencyMatrix makePeptideProteinVector plotAdjacencyMatrix |
| Calculate ions produced by fragmentation with variable modifications | calculateFragments calculateFragments,character,missing-method defaultNeutralLoss modificationPositions |
| Connected components | adjacencyMatrix,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 compositions | describePeptides describeProteins |
| Filter out unreliable PSMs. | filterPsmDecoy filterPsmFdr filterPsmRank filterPSMs filterPsmShared |
| Amino acids | getAminoAcids |
| Atomic mass. | getAtomicMass |
| labels MS2 Fragments | labelFragments |
| Function to plot MS/MS spectra with PTMs | plotSpectraPTM |
| A class for peptide-spectrum matches | adjacencyMatrix,PSM-method PSM PSM,character PSM,data.frame PSM,PSM PSM-class psmVariables readPSMs reduced reduced<- reducePSMs |
| PSMatch: Handling and Managing Peptide Spectrum Matches | PSMatch-package PSMatch |
