# quantms.io
[](https://github.com/bigbio/quantms.io/actions/workflows/python-app.yml)
[quantms](https://docs.quantms.org) is a nf-core pipeline for the analysis of quantitative proteomics data. The pipeline is based on the [OpenMS](https://www.openms.de/) framework and [DIA-NN](https://github.com/vdemichev/DiaNN); and it is designed to analyze large scale experiments. the main outputs of quantms tools are the following:
- [mzTab](https://github.com/HUPO-PSI/mzTab) files with the identification and quantification information.
- [MSstats](https://msstats.org/wp-content/uploads/2017/01/MSstats_v3.7.3_manual.pdf) input file with the peptide quantification values needed for the MSstats analysis.
- [MSstats](https://msstats.org/wp-content/uploads/2017/01/MSstats_v3.7.3_manual.pdf) output file with the differential expression values for each protein.
- The input [SDRF](https://github.com/bigbio/proteomics-sample-metadata) 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](https://github.com/bigbio/proteomics-quant-formats/issues) 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](https://www.contributor-covenant.org/version/2/0/code_of_conduct/).
## 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.
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"description": "# quantms.io\n[](https://github.com/bigbio/quantms.io/actions/workflows/python-app.yml)\n\n[quantms](https://docs.quantms.org) is a nf-core pipeline for the analysis of quantitative proteomics data. The pipeline is based on the [OpenMS](https://www.openms.de/) framework and [DIA-NN](https://github.com/vdemichev/DiaNN); and it is designed to analyze large scale experiments. the main outputs of quantms tools are the following: \n\n- [mzTab](https://github.com/HUPO-PSI/mzTab) files with the identification and quantification information.\n- [MSstats](https://msstats.org/wp-content/uploads/2017/01/MSstats_v3.7.3_manual.pdf) input file with the peptide quantification values needed for the MSstats analysis.\n- [MSstats](https://msstats.org/wp-content/uploads/2017/01/MSstats_v3.7.3_manual.pdf) output file with the differential expression values for each protein. \n- The input [SDRF](https://github.com/bigbio/proteomics-sample-metadata) of the pipeline if available. \n\nHere, 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: \n\n- Fast and easy visualization of the identification and quantification results.\n- Easy integration with other omics data.\n- Easy integration with sample metadata.\n- AI/ML model development based on identification and quantification results.\n\n**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. \n\n## Data model\n\nThe GitHub repository aims to provide multiple formats for serialization of the data model, including:\n\n- `Tab-delimited` format similar to mzTab. \n- `JSON` format to enable integration with other bioinformatics resources. \n- `Parquet` format to enable integration with big data frameworks and large-scale data integration. \n\n## How to contribute\n\nExternal contributors, researchers and the proteomics community are more than welcome to contribute to this project.\n\nContribute with the specification: you can contribute to the specification with ideas or refinements by adding an issue into the [issue tracker](https://github.com/bigbio/proteomics-quant-formats/issues) or performing a PR.\n\n## Core contributors and collaborators\n\nThe project is run by different groups:\n\n- Yasset Perez-Riverol (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)\n\nIMPORTANT: If you contribute with the following specification, please make sure to add your name to the list of contributors.\n\n## Code of Conduct\n\nAs part of our efforts toward delivering open and inclusive science, we follow the [Contributor Covenant Code of Conduct for Open Source Projects](https://www.contributor-covenant.org/version/2/0/code_of_conduct/).\n\n## How to cite\n\n## Copyright notice\n\n\n This information is free; you can redistribute it and/or modify it\n under the terms of the GNU General Public License as published by\n the Free Software Foundation; either version 2 of the License, or\n (at your option) any later version.\n\n This information is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU General Public License for more details.\n\n You should have received a copy of the GNU General Public License\n along with this work; if not, write to the Free Software\n Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.\n\n",
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