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Proteome & Proteomics

In support of proteomics research and activities at the University of Michigan, as well as providing basic information for the public.

Databases, Data Sets, Data Repositories

Chorus Project

JPOST (Japan Proteome Standard Repository Database)

NextProt 

ProteomeXchange (Consortium)

ProteomicsDB

RCSB Protein Data Bank (PDB)

UCSD: Center for Computational Mass Spectrometry: Proteomics: MassIVE (Mass Spectrometry Interactive Virtual Environment) 

UCSD: Center for Computational Mass Spectrometry: Proteomics: ProteoSAFe

UCSD: Center for Computational Mass Spectrometry: Proteomics: Submitted MassIVE Datasets

UM: HPSF (Human Proteome Structure and Function) database

Uniprot: Proteomes and Reference Proteomes

Other Resources

OmicsTools

PASSEL (PeptideAtlas SRM Experiment Library)

Pep2Pro (complete peptide dictionary)

PeptideAtlas

PRIDE PRoteomics IDEntifications (PRIDE)

Software

EXAMPLES

CRAPome (UofM)

DIA-Umpire (UofM)

MAP-DIA (UofM)

MaxQuant

MSFragger (UofM)

PEAKS Studio

ProteoWizard

REPRINT (Resource for Evaluation of Protein Interaction Networks)

TIQAM

Trans-Proteomic Pipeline (TPP) 

 

COLLECTIONS

Alexey Nesvizhskii Lab: Software (UofM)

Bioinformatics tools for proteomics

Minnesota Supercomputing Institute: Proteomics software available in the public domain

Wikipedia: List of mass-spectrometry software: Proteomics software

 

ABOUT

Välikangas T, Suomi T, Elo LL. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation. Briefings in Bioinformatics, bbx054, https://doi.org/10.1093/bib/bbx054