Proteomics Analysis
Proteomics
For DIA (data-independent acquisition) and DDA (data-dependent acquisition) mass spectrometry data, providing a complete workflow from protein identification and quantification to differential expression and post-translational modification (PTM) analysis, supporting biomarker discovery and drug target research.
Applicable Scenarios
- Disease biomarker discovery
- Drug mechanism of action research
- Signaling pathway perturbation analysis
- Post-translational modification regulation research
Data Inputs
- DIA/DDA mass spec raw data (raw / mzML)
- Experimental design grouping information
- FASTA database (target species)
Deliverables
- Protein identification and quantification matrix
- Differential expression protein volcano plot and heatmap
- GO/KEGG functional enrichment
- Protein-protein interaction (PPI) network
- PTM site identification and differential analysis
Analysis Pipeline
01
Database Search
MaxQuant / DIA-NN / Proteome Discoverer database search
02
Quantification
LFQ / TMT / DIA-NN quantification
03
QC
PCA, correlation heatmap, missing value assessment
04
DE Analysis
limma / Perseus / DEP differential analysis
05
Functional
GO/KEGG, GSEA, PPI (STRING/Cytoscape)
06
PTM
Phosphorylation / acetylation / ubiquitination site identification and differential analysis