A collection of useful websites related to proteomics.
General Guidelines for Handling Protein Gels - minimizing keratin contamination, mostly
Gel Staining Protocols - Don't. Use a kit instead. But if you must...
Short-Run SDS-PAGE Protocol - get all your protein into a wee bit of gel
Educational Resources for Proteomics
Bioinformatics for Proteomics tutorial in four parts - also from CompOmics
The Broad Institute 2012 Proteomics Workshop on iTunes (10 lectures)
IonSource - numerous tutorials, reference tables and tools
News in Proteomics Research - regularly updated blog covering... news in proteomics research
Proteomics Repositories and Resources
These sites are good resources for finding publicly-available raw and/or processed shotgun proteomics data. Most publications now reference a repository where the underlying data is stored. Search the article for "pride" or "proteomeexchange" to find the link or accession number. Sometimes buried in the supplemental data.
Proteome Exchange - provides "a globally coordinated submission of mass spectrometry proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination."
EBI PRIDE Archive - "a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence."
MassIVE - "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements."
- MassIVE Kownledge Base - curated, human spectral libraries
GPMdb - "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into the GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by users of the machine." -- Invaluable for quick research into whether your protein of interest is observable by mass spectrometry-based proteomics.
PNNL Biodiversity Library - "proteomics data from 112 microbial organisms representing 15 phyla" ... "the library contains >70 million spectra identified at q< 0.0001, with 3 million peptides from 230,000 proteins."
Human Protein Atlas - "a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology."
Allen Integrated Cell - "The Allen Integrated Cell is a predictive, 3D model of human induced pluripotent stem cell (hiPSC) organization. It provides a realistic, data-driven 3D visualization of a living hiPSC in its pluri-potent state. The visualization shows the many molecular machines and structures (organelles) inside the cell, simultaneously."
Proteomics Libraries and Databases
UniProt - protein sequence libraries, entries, annotations
NCBI Protein - "a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."
HOMD - human oral microbiome database, providing "the scientific community with comprehensive curated information on the bacterial species present in the human aerodigestive tract (ADT)."
Unimod - list of known protein modifications, masses and modification sites
ExPASy - large selection of proteomics tools
PeptideCutter - in silico protein cleavage by enzyme or chemical treatment
Translate - DNA sequence to protein sequence
T-Coffee - "a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment."
Comet - "an open source tandem mass spectrometry (MS/MS) sequence database search tool."
X!Tandem - "X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification."
BiblioSpec - "a suite of software tools for creating and searching MS/MS peptide spectrum libraries." In reality, the de facto standard for handling and interchange of tandem mass spectrometry protein sequence library search results.
Unipept - "blazingly fast biodiversity analysis of large and complex metaproteome samples."
Peptide Uniqueness Checker - from NextProt
PIR Peptide Match - pull proteins and organisms from petpide sequences, links to repository archives containing the queried peptide