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small changes for review PR #48
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ypriverol authored and fabianegli committed Mar 17, 2023
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## Output structure

Output will be exported to the folder defined by parameter `--outdir`. Each step of the workflow export different files and reports with the specific data, peptide identifications, protein quantifications, etc. Most of the pipeline outputs are [HUPO-PSI](https://www.psidev.info/) standard file formats:
Output will be saved to the folder defined by parameter `--outdir`. Each step of the workflow export different files and reports with the specific data, peptide identifications, protein quantifications, etc. Most of the pipeline outputs are [HUPO-PSI](https://www.psidev.info/) standard file formats:

- [mzML](https://www.psidev.info/mzML): The mzML format is an open, XML-based format for mass spectrometer output files, developed with the full participation of vendors and researchers in order to create a single open format that would be supported by all software.
- [mzTab](https://www.psidev.info/mztab>): mzTab is intended as a lightweight supplement to the existing standard mzML to store and represent peptide and protein and identifications together with experimental metadata and basic quantitative information.
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