The Global Proteome Machine was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. This project is supported by the GPMO to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.

The GPM is currently configured to use proteomes from a variety of sources, mainly EBI's ENSEMBL and NCBI's RefSeq. The current sequence files associated with GPM can be obtained by FTP at ftp.thegpm.org/fasta. These file versions are updated when a significant number of new sequences are added (or removed) from a particular species' proteome.

All sequences obtained from Unigene are updated every Monday evening, at 22:00 CST.

Bacterial proteomes are updated from NCBI, when significant new species are added.

Viral proteomes are updated from NCBI, as necessary. Viral proteomes were first added to the GPM on August 5, 2009.

In addition to the proteomes listed, a small collection of common contaminant and "test" proteins is included. These proteins include bovine and porcine trypsin and bovine serum albumin. If you would like to see any other contaminants included in this collection, please click here.