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

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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