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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 iProphetproteinProphet

Tools Used:
- ProteinProphet: (http://proteinprophet.sourceforge.net) used to identify high-confident protein hits
  - protXML output file that has list of validated protein hits.