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Welcome to the GPMDB wiki site. GPMDB contents (2016.1.2)

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.

The GPM is a user interface that allows scientists to run protein identifications searches and interpret the results of the searches. It currently supports three different search engines:

  1. X! Tandem - a conventional protein identification search engine;
  2. X! P3 - a search engine that uses proteotypic peptides; and
  3. X! Hunter - an annotated spectrum library search engine.

This wiki has been set up to allow the users of the GPM to annotate results sets stored in the GPMDB system. In order to add information, please create a user account by following the link in the top right corner.

models = 351,196
proteins = 370,863,788
distinct proteins = 2,704,633
protein redundancy = 137.1 ×
peptides = 3,257,113,337
distinct peptides = 12,283,123
peptide redundancy = 265.2 ×
AA residues = 45,599,586,718

Some of the most popular topics on this site are as follows:

  1. GPMDB Data Sources: where we get data from and a list of papers associated with that data;
  2. GPMDB REST: annotation and instructions on how to use the GPMDB REST API;
  3. G2PDB REST: annotation and instructions on how to use the g2pDB REST API;
  4. PTM annotation: a comprehensive reference to how we annotate PTMs;
  5. Amino acid symbols: a list of amino acids found in proteins; and
  6. GPMDB evidence codes: an explanation of the GPMDB evidence code system.
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