quantmsio 0.0.3

Convert multiple files into quantms.io format

quantms.io

quantms is a nf-core pipeline for the analysis of quantitative proteomics data. The pipeline is based on the OpenMS framework and DIA-NN; and it is designed to analyze large scale experiments. the main outputs of quantms tools are the following:

• mzTab files with the identification and quantification information.
• MSstats input file with the peptide quantification values needed for the MSstats analysis.
• MSstats output file with the differential expression values for each protein.
• The input SDRF of the pipeline if available.

Here, we aim to formalize and develop a more standardized format that enables better representation of the identification and quantification results but also enables new and novel use cases for proteomics data analysis:

• Fast and easy visualization of the identification and quantification results.
• Easy integration with other omics data.
• Easy integration with sample metadata.
• AI/ML model development based on identification and quantification results.

Note: We are not trying to replace the mzTab format, but to provide a new format that enables AI-related use cases. Most of the features of the mzTab format will be included in the new format.

Data model

The GitHub repository aims to provide multiple formats for serialization of the data model, including:

• Tab-delimited format similar to mzTab.
• JSON format to enable integration with other bioinformatics resources.
• Parquet format to enable integration with big data frameworks and large-scale data integration.

How to contribute

External contributors, researchers and the proteomics community are more than welcome to contribute to this project.

Contribute with the specification: you can contribute to the specification with ideas or refinements by adding an issue into the issue tracker or performing a PR.

Core contributors and collaborators

The project is run by different groups:

• Yasset Perez-Riverol (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)

IMPORTANT: If you contribute with the following specification, please make sure to add your name to the list of contributors.

Code of Conduct

As part of our efforts toward delivering open and inclusive science, we follow the Contributor Covenant Code of Conduct for Open Source Projects.

How to cite

Copyright notice

This information is free; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This information is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this work; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.