Tutorials & protocols from PAF
Tutorials
- Shotgun analysis (Scaffold)
- Interpretation of quantitative analysis
- Interpretation of quantitative analysis (commented version)
- Phosphoproteomic analysis
- Affinity Purification analysis
- Upload proteomic data into repositories (PRIDE submission)
Protocols
Others
- Simple Western characteristics
- PUMBA: OUR gel migration datatbase, useful for evaluating your Western Blot results
Links
Databases
- PhosphositePlus: most comprehensive PTM database
- Gingras lab protocols – useful for IPs
- ProteomicsDB – a large scale proteomics database covering several organisms
- ProteomeXchange – proteomics data repository
- Reprint (ex-CRAPOME) – database of unspecific proteins in interactomics
- Simple Western validated antibodies
- StringDB – protein/protein interactions of many types
- Uniprot – the reference protein knowledgebase
Softwares
- Compass – for Simple Western data analysis
- MaxQuant – (free) for proteomics quantification data
- Perseus – (free) for post-processing of proteomics data
- Proteome Discoverer – for DDA quantification data
- Scaffold – for post-processing of proteomics identification data
- Spectronaut – for DIA quantification data