https://github.com/rformassspectrometry/psmatch
Peptide Spectrum Matching
https://github.com/rformassspectrometry/psmatch
mass-spectrometry peptide-spectrum-matches proteomics rstats
Last synced: 2 months 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 (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2025-08-01T08:55:32.000Z (2 months ago)
- Last Synced: 2025-08-01T10:46:14.469Z (2 months ago)
- Topics: mass-spectrometry, peptide-spectrum-matches, proteomics, rstats
- Language: R
- Homepage: https://rformassspectrometry.github.io/PSMatch
- Size: 18.9 MB
- Stars: 4
- Watchers: 3
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
Awesome Lists containing this project
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.