From f96ab5450fef6431fc82dfea52c0fc5f677b1167 Mon Sep 17 00:00:00 2001 From: wittigue Date: Tue, 25 Jul 2023 10:07:14 +0200 Subject: [PATCH] Update proteomics.md small changes and links added --- pages/your_domain/proteomics.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pages/your_domain/proteomics.md b/pages/your_domain/proteomics.md index c155eb1ff..6cf897210 100644 --- a/pages/your_domain/proteomics.md +++ b/pages/your_domain/proteomics.md @@ -36,11 +36,11 @@ For different proteomics experiments and different steps of the respective data ### Solutions The Human Proteome Organisation (HUPO) Proteomics Standards Initiative ({% tool "proteomics-standards-initiative" %}), a proteomics community-driven organization, provides several different controlled vocabularies, standard data formats, converter and validator software tools. The most important include: - Controlled vocabularies: PSI-MS, PSI-MI, XLMOD and sepCV, which are provided as OBO files. -- The Minimum Information About a Proteomics Experiment (MIAPE) guidelines document. -- mzML - a standard format for encoding raw mass spectrometer output. -- mzIdentML - a standard exchange format for peptides and proteins identified from mass spectra. -- mzQuantML - a standard format that is intended to store the systematic description of workflows quantifying molecules (principally peptides and proteins) by mass spectrometry. -- mzTab - a tab delimited text file format to report proteomics and metabolomics results. +- The Minimum Information About a Proteomics Experiment ([MIAPE](https://psidev.info/miape)) guidelines document. +- [mzML](https://www.psidev.info/mzML) - a standard format for encoding raw mass spectrometer output. +- [mzIdentML](https://www.psidev.info/mzidentml) - a standard exchange format for peptides and proteins identified from mass spectra. +- [mzQuantML](https://psidev.info/mzquantml) - a standard format that is intended to store the systematic description of workflows quantifying molecules (principally peptides and proteins) by mass spectrometry. +- [mzTab](https://www.psidev.info/mztab) - a tab delimited text file format to report proteomics and metabolomics results. ## Processing and analysis of proteomics data @@ -52,12 +52,12 @@ For all steps within a FAIR proteomics data analysis pipeline software is needed - Can your proteomics raw data recorded by a mass spectrometer be stored as an mzML file? - Is it possible to convert your raw data to mzML? - Does your search engine support mzML and/or mzIdentML? -- Does your quantification software support mzQuantML or mzTAB? +- Does your quantification software support mzQuantML or mzTab? ### Solutions - Within the proteomics community various converter software tools such as {% tool "msconvert" %} were implemented, which support the conversion of mass spectrometer output formats to the mzML standard data format as well as other conversions to standard data formats. -- Information on software tools that support HUPO-PSI data formats can be found on the standard format-specific web pages of the HUPO-PSI (e.g., [mzML](https://www.psidev.info/mzML) , [mzIdentML](https://www.psidev.info/mzidentml) and [MZTAB](https://www.psidev.info/mztab) ). The following list shows just a few tools using standard data formats as input and/or output: +- Information on software tools that support HUPO-PSI data formats can be found on the standard format-specific web pages of the HUPO-PSI (e.g., [mzML](https://www.psidev.info/mzML) , [mzIdentML](https://www.psidev.info/mzidentml) and [mzTab](https://www.psidev.info/mztab) ). The following list shows just a few tools using standard data formats as input and/or output: * {% tool "comet" %} * {% tool "mascot" %} * {% tool "openms" %}