Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update proteomics.md #49

Merged
merged 1 commit into from
Jul 25, 2023
Merged

Update proteomics.md #49

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 7 additions & 7 deletions pages/your_domain/proteomics.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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" %}
Expand Down