Installation

pyXLMS is a python  package, naturally it requires a python installation . pyXLMS supports python version 3.7 and greater!

Installation via PyPI

pyXLMS is available on PyPI  and can easily be installed via pip:

pip install pyxlms

Installation via GitHub

Alternatively, you can install the latest stable version directly from GitHub :

pip install git+https://github.com/hgb-bin-proteomics/pyXLMS.git

or the latest development version:

pip install git+https://github.com/hgb-bin-proteomics/pyXLMS.git@develop

Quick Start

After installation you can use pyXLMS in python like this:

This example shows reading of MS Annika crosslink-spectrum-matches and exporting them to xiFDR format for external validation.

import pyXLMS
pr = pyXLMS.parser.read(
    "data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1_CSMs.xlsx",
    engine="MS Annika",
    crosslinker="DSS"
)

    Reading MS Annika CSMs...: 100%|████████████████████████████████████████████████████████████████████████████████| 826/826 [00:00<00:00, 20731.70it/s]

_ = pyXLMS.transform.summary(pr)

    Number of CSMs: 826.0
    Number of unique CSMs: 826.0
    Number of intra CSMs: 803.0
    Number of inter CSMs: 23.0
    Number of target-target CSMs: 786.0
    Number of target-decoy CSMs: 39.0
    Number of decoy-decoy CSMs: 1.0
    Minimum CSM score: 1.11
    Maximum CSM score: 452.99

_ = pyXLMS.exporter.to_xifdr(pr["crosslink-spectrum-matches"], filename="msannika_CSMs_for_xiFDR.csv")

pyXLMS Template

We offer a repository template for python projects using pyXLMS. The repository is available via github.com/hgb-bin-proteomics/pyXLMS-template  and uses uv  for project and dependency management (highly recommended). If used on GitHub it also directly integrates with GitHub Actions for automated linting, formatting, and testing.