quantms-utils

Python package with scripts and functions for the quantms workflow for the analysis of quantitative proteomics data.

The package is available on PyPI: quantms-utils

pip install quantms-utils

Available Scripts

The following functionalities are available in the package:

Diann scripts

• dianncfg - Create a configuration file for Diann including enzymes, modifications, and other parameters.
• diann2mztab - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab. The output formats are used for quality control and downstream analysis in quantms.

SDRF scripts

• openms2sample - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available here.
• checksamplesheet - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file.

ms2rescore scripts

• ms2rescore - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.

Features to percolator scripts

• sage2feature - The add_sage_feature function enhances an idXML file by appending additional features from a Sage feature table, excluding those generated by 'psm_file'.
• spectrum2feature - Add the signal-to-noise ratio (SNR) to the feature table for percolator.

Other scripts

• psmconvert - The convert_psm function converts peptide spectrum matches (PSMs) from an idXML file to a CSV file, optionally filtering out decoy matches. It extracts and processes data from both the idXML and an associated spectra file, handling multiple search engines and scoring systems.
• mzmlstats - The mzmlstats processes mass spectrometry data files in either .mzML or Bruker .d formats to extract and compile statistics about the spectra. It supports generating detailed or ID-only CSV files based on the spectra data.

Contributions and issues

Contributions and issues are welcome. Please, open an issue in the GitHub repository or PR in the GitHub repository.