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: (Deutsch E. W. et. al. )
- XML output of all peptide and protein hits.
- Trans-Proteome Pipeline: (Deutsch E. W. et. al. )
2. Peptide hits validation
Validate the peptide hits returned by the mass-spectrometry peptide identification algorithms
- Deliverables:
- reports generated by peptideProphet
- Tools Used:
- peptideProphet: (Nesvhizskii et. al. ) used to validate peptide hits:
- pepXML output file that has list of validated peptide hits.
- pepXML output file that has list of validated peptide hits.
- peptideProphet: (Nesvhizskii et. al. ) used to validate peptide hits:
3. Protein hits validation
Validate the protein hits using the pepXML peptideProphet output
- Deliverables:
- reports generated by iProphet
- Tools Used:
- iProphet: (Nesvhizskii et. al. ) used to identify high-confident protein hits
- protXML output file that has list of validated protein hits.
- iProphet: (Nesvhizskii et. al. ) used to identify high-confident protein hits