1. Introduction The GPM project (The Global Proteome Machine Organization) Salvador Martínez de Bartolomé smartinez@proteored.org Bioinformatics support – ProteoRed Proteomics Facility, National Center for Biotechnology, Madrid

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

3. The GPM Project The GPMDB The X! series project: –X! Tandem –X! P3 –X! Hunter

4. The GPM Proteomics Database 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 GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists. You can install your own GPMDB. It can be used as a template for constructing an in-house data storage system, or it can be used as an add-on to an existing LIMS system.

5. The 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. Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments.

6. The X! P3 (Proteotypic Peptide Profiler) Project In the first round, the spectrum data set is examined for the presence of proteotypic peptides. The full protein sequences of the proteins identified in the first round are then pulled from a sequence library. Using this small set of full sequences, multiple rounds of refinement are performed to extract all of the non-proteotypic peptides from the full spectrum data set.

7. The X! Hunter X! Hunter is a search engine that compares experimentally observed spectra directly with consensus mass spectra obtained from the GPMDB. It can identify proteins for human, budding yeast, mouse and thale cress samples. Because the sequence modifications and cleavage sites for the peptides in the sequence library are already known, it is not necessary to specify as many parameters for this type of search as in more conventional search engines.