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proteomics-identification

Identify peptides and proteins from MS/MS spectra using MaxQuant, MS-GF+, or Comet.

155|26|Updated Mar 14, 2026
Search Tags:#mass spectrometry#proteomics#FDR#Comet#peptide identification#MaxQuant#MS-GF+
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-identification
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: proteomics-identification
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/proteomics/proteomics-identification
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-identification

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

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.

Frequently Asked Questions about proteomics-identification

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I identify peptides from MS/MS spectra using search engines?▼

Peptide identification from MS/MS spectra is performed by searching experimental data against digested protein databases using integrated engines like MaxQuant, MS-GF+, and Comet to accurately map peptides.

How does FDR filtering work for peptide identification in mass spectrometry?▼

FDR filtering for peptide identification controls false discoveries by applying statistical validation through Percolator or Andromeda, ensuring only high-confidence peptide and protein matches are retained from the MS/MS search results.

Can I use MaxQuant, MS-GF+, and Comet interchangeably for proteomics identification?▼

Yes, the Skill standardizes execution across MaxQuant, MS-GF+, and Comet, allowing you to interchangeably use these leading search engines for flexible peptide identification from your mass spectrometry data.

What is the best way to process raw mass spectrometry data for protein mapping?▼

Processing raw mass spectrometry data involves searching MS/MS spectra against protein databases to identify peptides, applying FDR filtering for confidence, and generating structural mappings of peptides to proteins for downstream analysis.

Does peptide identification from MS/MS spectra support local processing and reporting?▼

Yes, peptide identification supports local processing of MS/MS spectra and generates comprehensive auditability reports, ensuring your mass spectrometry data analysis remains secure and fully traceable.

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