Gpm (proteomics)

In proteomics, GPM stands for "Global Proteome Machine". It is a web-based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis and first released in 2003.^[1] The interface creates a series of web browser page views of tandem mass spectrometry data that has been assigned to protein sequences. The underlying data documents are stored in BIOML^[2] format files.

Since its original creation, GPM has been under continuous development. Major developments include the following:

1. Creation of GPMDB: a large proteomics database generated using GPM; ^[3]
2. Inclusion in the Human proteome project as a data analysis and information resource; ^[4]
3. Development of a REST API for GPMDB.^[5]

References

1. Craig, Robertson; Cortens, John P.; Beavis, Ronald C. (2004). "Open Source System for Analyzing, Validating, and Storing Protein Identification Data". Journal of Proteome Research 3 (6): 1234–42. doi:10.1021/pr049882h. PMID 15595733.
2. Fenyo, D (1999). "The Biopolymer Markup Language". Bioinformatics 15 (4): 339–40. doi:10.1093/bioinformatics/15.4.339. PMID 10320402.
3. Craig, Robertson; Cortens, John P.; Beavis, Ronald C. (2004). "Open Source System for Analyzing, Validating, and Storing Protein Identification Data". Journal of Proteome Research 3 (6): 1234–1242. doi:10.1021/pr049882h. ISSN 1535-3893.
4. Omenn, Gilbert S.; Lane, Lydie; Lundberg, Emma K.; Beavis, Ronald C.; Nesvizhskii, Alexey I.; Deutsch, Eric W. (2015). "Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification". Journal of Proteome Research 14 (9): 3452–3460. doi:10.1021/acs.jproteome.5b00499. ISSN 1535-3893.
5. Fenyö, David; Beavis, Ronald C. (2015). "The GPMDB REST interface". Bioinformatics 31 (12): 2056–2058. doi:10.1093/bioinformatics/btv107. ISSN 1367-4803.

External links

• GPM project website