Proteomics (e)

datE: 12-03-2024 Status: Under DEVELOPMENT

 

Proteomics concerns experiments on all protein molecules in a sample, including information about so-called post-translational modifications. This may involve experiments that attempt to determine which proteins are found (identification) and in what concentration proteins are found (quantification). In addition, position-specific imaging techniques are also possible.

Experiments

• Labeled proteomics 

  • Identification 

  • Quantification 

• Unlabeled proteomics 

  • Identification 

  • Quantification 

• 2D MALDI 

File formats

• gelML (HUPO PSI, 2010) - gel electrophoresis

• TraML (HUPO PSI, 2013) - transition lists

• mzML (HUPO PSI, 2017) ; Raw spectrometer output

• mzIdentML (HUPO PSI, 2017) ; Protein identification data

• mzQuantML (HUPO PSI, 2017) ; Protein quantisation data

• mzTab (HUPO PSI, 2014) ; Reporting

Metadataschemes

• MIAPE 

• ISA-TAB with conversion to PRIDE format 

• SDRF: “Sample and Data Relationship Format for Proteomics”  https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics Koppel je Github-account