Protein Identification and Validation

Protein Identification and Validation

       Identify peptides/proteins given raw mass-spec data, 6 hour minimum ($282 internal, $360 external) per project.

1. Protein identification using Trans-Proteome Pipeline

Identify list of proteins in the sample using multiple search algorithms in Trans-Proteome Pipeline (TPP)

• Deliverables:

  • List of all peptide-spectral matches (no Post Translational Modifications identification). For PTM Identification, see Post-translational modification (PTM) identification

• Tools Used:

  • Trans-Proteome Pipeline: (http://www.proteomecenter.org/software.php) 

    • XML output of all peptide and protein hits.

2. Peptide hits validation

Validate the peptide hits returned by the mass-spectrometry peptide identification algorithms

• Deliverables:

  • reports generated by peptideProphet

• Tools Used:

  • peptideProphet: (http://peptideprophet.sourceforge.net) used to validate peptide hits

    • pepXML output file that has list of validated peptide hits.
      
      

3. Protein hits validation

Validate the protein hits using the pepXML peptideProphet output

• Deliverables:

  • reports generated by proteinProphet

• Tools Used:

  • ProteinProphet: (http://proteinprophet.sourceforge.net) used to identify high-confident protein hits

    • protXML output file that has list of validated protein hits.