proteomics-identification

What problem does it solve?

This Skill transforms raw MS/MS spectral data into meaningful peptide and protein identifications, bridging the gap between raw experimental output and biological insights.

Core Features & Use Cases

• Peptide Identification: Accurately identifies peptides by searching experimental MS/MS spectra against in silico digested protein databases.
• Multiple Engine Support: Integrates with leading search engines like MaxQuant, MS-GF+, and Comet for flexibility.
• FDR Filtering: Applies False Discovery Rate (FDR) control using Percolator or Andromeda to ensure high confidence identifications.
• Use Case: Analyze raw mass spectrometry data from a proteomics experiment to identify all peptides present, enabling downstream protein quantification and biomarker discovery.

Quick Start

Run peptide identification on the provided mzML file using the MaxQuant engine.