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Clinical Metaproteomics 3: Verification

This workflow uses the PepQuery tool to verify peptides discovered with the clinical metaproteomics discovery workflow. The PepQuery tool outputs verified peptides that can be used to generate a verified protein database that can be used for the clinical metaproteomics quantitation workflow.

More background on this workflow can be found in the Clinical Metaproteomics 3: Verification tutorial

Inputs datasets

Tabular Input Files

  • SGPS peptide report
  • MaxQuant Peptide report
  • Distinct Peptides for PepQuery

Search Databases (FASTA)

  • Uniprot HUMAN database
  • cRAP

MSMS files

The tandem MS/MS files can be downloaded via Zenodo. These MS/MS input files are pilot datasets from Papanicolaou test samples from healthy, benign and ovarian cancer patients.

Input Values

For PepQuery:

  • Search Tolerances
  • Digestion Enzyme
  • Peptide Length
  • Modifications

Processing

Extract protein sequences for the verified peptides.

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