# 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](https://rformassspectrometry.github.io/PSMatch/reference/PSMatch.html) for a general overview of the main concepts tackled by the `PSMatch` package. - The [Working with PSM data](https://rformassspectrometry.github.io/PSMatch/articles/PSM.html) vignette to learn about the `PSM` to read and filter peptide-spectrum matches. - The [Understanding protein groups with adjacency matrices](https://rformassspectrometry.github.io/PSMatch/articles/AdjacencyMatrix.html) vignette to learn about adjaceny matrices and connected components to explore and manage protein groups. - The [MS2 fragment ions](https://rformassspectrometry.github.io/PSMatch/articles/Fragments.html) 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 ```r BiocManager::install("PSMatch") ``` ## Credit Code in this package is partly composed of functions ported from [`MSnbase`](http://lgatto.github.io/MSnbase/) with the goal to (1) make them more general and (2) integrate them with the [*R for Mass Spectrometry*](https://github.com/rformassspectrometry) infrastructure.