bioconductor-psmatch

name: bioconductor-psmatchdescription: 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 mwhen_to_use: "Use when: Fragment Ion Calculation: Calculating theoretical MS2 fragment ions (b and y ions) for a peptide sequence using calculateFragments.; Fragment Visualisation: Visualising matched b- and y-ion fragment sequences directly on an MS spectrum using plotSpectraPTM.; Peptide-Protein Modelling: Modelling the relation between peptides and proteins as an adjacency matrix using makeAdjacencyMatrix.; Protein Gr. Not for: For handling and processing raw mass spectrometry spectra, use Spectra because PSMatch relies on it for raw data representation and extraction.; For managing multi-level quantitative proteomics data, use QFeatures because PSMatch focuses on PSM-level"user-invocable: false

PSMatch

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.16.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: S4Vectors, PTMods
• Imports: igraph, Spectra, Matrix, BiocParallel, BiocGenerics, ProtGenerics, QFeatures, MsCoreUtils
• Install: BiocManager::install("PSMatch")

When to Use

• Fragment Ion Calculation: Calculating theoretical MS2 fragment ions (b and y ions) for a peptide sequence using calculateFragments.
• Fragment Visualisation: Visualising matched b- and y-ion fragment sequences directly on an MS spectrum using plotSpectraPTM.
• Peptide-Protein Modelling: Modelling the relation between peptides and proteins as an adjacency matrix using makeAdjacencyMatrix.
• Protein Group Resolution: Partitioning complex peptide-protein graphs into independent subgraphs using ConnectedComponents to explore shared and unique peptides.

When NOT to Use

• For handling and processing raw mass spectrometry spectra, use Spectra because PSMatch relies on it for raw data representation and extraction.
• For managing multi-level quantitative proteomics data, use QFeatures because PSMatch focuses on PSM-level filtering and structural relationships.
• For applying and managing peptide modifications, use PTMods because PSMatch delegates canonical modification handling to it.

Data Requirements

• Identification Data: Imported as a PSM object containing columns for peptide sequences (e.g., "sequence") and protein accessions (e.g., "DatabaseAccess").
• Raw MS Data: Loaded as a Spectra object for fragment ion visualisation.
• Quantitative Data: Can be imported as a SummarizedExperiment object with protein groups named by peptide sequences.

Key Parameters

• addCarbamidomethyl: Logical in calculateFragments and plotSpectraPTM to apply carbamidomethylation of cysteines by default.
• variableModifications: Named numeric vector in calculateFragments or plotSpectraPTM to apply variable mass modifications.
• binary: Logical in makeAdjacencyMatrix to create a binary matrix instead of counting occurrences.
• protColors: Numeric or character in plotAdjacencyMatrix to control protein node colours based on string distances.
• pepColors: Character vector in plotAdjacencyMatrix to colour peptide nodes (e.g., by search engine score).
• split: Character in makeAdjacencyMatrix (e.g., ";") to split protein groups into individual proteins.

Best Practices

• Filter out decoy hits and low-rank matches using filterPsmDecoy and filterPsmRank before constructing adjacency matrices.
• Merge raw Spectra data with PSM identification data using joinSpectraData to enable fragment visualisation.
• Use prioritiseConnectedComponents to rank and identify the most interesting connected components (e.g., those with multiple shared peptides).
• Extract specific subgraphs using connectedComponents to manually inspect complex protein groups with plotAdjacencyMatrix.

Common Pitfalls

• Overlapping fragment ions in visualisations: Restricted plot windows can cause text to overlap. Fix: Run plotSpectraPTM locally or adjust the xlim parameter in plotSpectra.
• Duplicate keys when merging: Merging spectra and PSMs can result in duplicates. Fix: Be aware that joinSpectraData will only keep the last instance if duplicates are found in the key.
• Missing modifications: Fragments might not match the spectrum if fixed modifications are ignored. Fix: Ensure addCarbamidomethyl = TRUE or explicitly pass modifications via fixedModifications.

Alternatives

• Spectra: For core MS data infrastructure and raw spectra manipulation.
• QFeatures: For downstream quantitative protein-level aggregation and statistical analysis.
• PTMods: For defining and retrieving canonical peptide modifications.

Citations

• Gatto L, Rainer J, Gibb S, Wieczorek S, Burger T, Deflandre G (2026). PSMatch: Handling and Managing Peptide Spectrum Matches. R package.

References

• Homepage: https://bioconductor.org/packages/PSMatch
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/PSMatch/inst/doc/PSMatch.html

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