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Description:
quantmsutils 0.0.11
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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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