https://github.com/rformassspectrometry/psmatch

Peptide Spectrum Matching
https://github.com/rformassspectrometry/psmatch

mass-spectrometry peptide-spectrum-matches proteomics rstats

Last synced: about 1 month ago
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Peptide Spectrum Matching

• Host: GitHub
• URL: https://github.com/rformassspectrometry/psmatch
• Owner: rformassspectrometry
• Created: 2020-10-28T14:32:57.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-10-28T13:22:57.000Z (about 2 months ago)
• Last Synced: 2024-11-07T22:42:10.601Z (about 1 month ago)
• Topics: mass-spectrometry, peptide-spectrum-matches, proteomics, rstats
• Language: R
• Homepage: https://rformassspectrometry.github.io/PSMatch
• Size: 15.9 MB
• Stars: 3
• Watchers: 5
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

        
# 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.