GitHub - rformassspectrometry/PSMatch: Peptide Spectrum Matching (original) (raw)

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 packagefor a general overview of the main concepts tackled by the PSMatchpackage.
• The Working with PSM datavignette to learn about the PSM to read and filter peptide-spectrum matches.
• The Understanding protein groups with adjacency matricesvignette to learn about adjaceny matrices and connected components to explore and manage protein groups.
• The MS2 fragment ionsvignette to calculate and visualise MS2 fragment ions.

Installation instructions

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

BiocManager::install("PSMatch")

Credit

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