Proteomics Analysis

Comprehensive analysis of mass spectrometry-based proteomics data from protein identification through quantification, differential expression, post-translational modifications, and systems-level interpretation.

When to Use This Skill

Triggers: User has proteomics MS output files, asks about protein abundance/expression, differential protein expression, PTM analysis, protein-RNA correlation, multi-omics integration involving proteomics, protein complex/interaction analysis, or proteomics biomarker discovery.

Core Capabilities

Capability	Description
Data Import	MaxQuant, Spectronaut, DIA-NN, Proteome Discoverer, FragPipe outputs
Quality Control	Missing value analysis, intensity distributions, sample clustering
Normalization	Median, quantile, TMM, VSN normalization methods
Imputation	MinProb, KNN, QRILC for missing values
Differential Expression	Limma, DEP, MSstats for statistical testing
PTM Analysis	Phospho-site localization, PTM enrichment, kinase prediction
Protein-RNA Integration	Correlation analysis, translation efficiency
Pathway Enrichment	Over-representation and GSEA for protein sets
PPI Analysis	Protein complex detection, interaction networks via STRING/IntAct
Reporting	Comprehensive reports with volcano plots, heatmaps, pathway diagrams

Workflow Overview

Input: MS Proteomics Data
    |
Phase 1: Data Import & QC
Phase 2: Preprocessing (filter, impute, normalize)
Phase 3: Differential Expression Analysis
Phase 4: PTM Analysis (if applicable)
Phase 5: Functional Enrichment (GO, KEGG, Reactome)
Phase 6: Protein-Protein Interactions (STRING networks)
Phase 7: Multi-Omics Integration (optional, protein-RNA correlation)
Phase 8: Generate Report

See PHASE_DETAILS.md for detailed procedures per phase.

Integration with ToolUniverse

Skill	Used For	Phase
tooluniverse-gene-enrichment	Pathway enrichment	Phase 5
tooluniverse-protein-interactions	PPI networks	Phase 6
tooluniverse-rnaseq-deseq2	RNA-seq for integration	Phase 7
tooluniverse-multi-omics-integration	Cross-omics analysis	Phase 7
tooluniverse-target-research	Protein annotation	Phase 8

Quantified Minimums

Component	Requirement
Proteins quantified	At least 500 proteins
Replicates	At least 3 per condition
Filtering	2+ unique peptides per protein
Statistical test	limma or t-test with multiple testing correction
Pathway enrichment	At least one method (GO, KEGG, or Reactome)
Report	Summary, QC, DE results, pathways, visualizations

Limitations

• Platform-specific: Optimized for MS-based proteomics (not Western blot quantification)
• Missing values: High missing rate (>50% per protein) limits statistical power
• PTM analysis: Requires enrichment protocols for comprehensive PTM profiling
• Absolute quantification: Relative abundance only (unless TMT/SILAC used)
• Protein isoforms: Typically collapsed to gene level
• Dynamic range: MS has limited dynamic range vs mRNA sequencing

References

Methods: MaxQuant (doi:10.1038/nbt.1511), Limma for proteomics (doi:10.1093/nar/gkv007), DEP workflow (doi:10.1038/nprot.2018.107)

Databases: STRING, PhosphoSitePlus, CORUM

Reference Files

• PHASE_DETAILS.md - Detailed procedures for each analysis phase, including report template