| name | bioconductor-psmatch |
| description | 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 m |
| when_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
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