Handling peptide-spectrum matches

PSMatch is a simple package to load, process and analyse PSMs (Peptide-Spectrum Matches). The following references are a good way to get started with the package:

• The package manual package for a general overview of the main concepts tackled by the PSMatch package.
• The Working with PSM data vignette to learn about the PSM to read and filter peptide-spectrum matches.
• The Understanding protein groups with adjacency matrices vignette to learn about adjaceny matrices and connected components to explore and manage protein groups.
• The MS2 fragment ions vignette to calculate and visualise MS2 fragment ions.

Installation instructions

To install the package from Bioconductor, make sure you have the BiocManager package, available from CRAN, and then run

BiocManager::install("PSMatch")

Contributions

Contributions are welcome, and should ideally be provided through a Github pull request. Feel free to discuss any more non-trivial suggestions or changes first in an issue. See also the main R for Mass Spectrometry contribution guide and code of conduct

Credit

Code in this package is partly composed of functions ported from MSnbase with the goal to (1) make them more general and (2) integrate them with the R for Mass Spectrometry infrastructure.