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! align="center" | Welcome to the GPMDB wiki site.
! align="center" | Welcome to the GPMDB wiki site.
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! align="center" | GPMDB contents (2018.09.05)
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! align="center" | GPMDB contents (2024.01.02)
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| align="left" width="450px" |
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The [http://gpmdb.thegpm.org 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.   
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The [http://gpmdb.thegpm.org Generalized Proteoform Meta-analysis 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 [http://www.thegpm.org 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:  
The [http://www.thegpm.org 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:  
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# X! Hunter - an annotated spectrum library search engine.
# X! Hunter - an annotated spectrum library search engine.
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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.
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{| style="background:#FFFFAA"  width="280px"
{| style="background:#FFFFAA"  width="280px"
|-  
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| align="right" | models =  
| align="right" | models =  
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|  462,526
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|  598,204
|-  
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| align="right" | proteins =  
| align="right" | proteins =  
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|  771,469,877
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|  1,562,401,329
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| align="right" | distinct proteins =  
| align="right" | distinct proteins =  
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|  3,196,418
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|  3,724,740
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| align="right" | protein redundancy =  
| align="right" | protein redundancy =  
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|  241.4 ×
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|  419.5 ×
|-  
|-  
| align="right" | peptides =  
| align="right" | peptides =  
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| 7,851,008,060
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| 14.973 gigaTabbs
|-  
|-  
| align="right" | distinct peptides =  
| align="right" | distinct peptides =  
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| 17,931,287
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| 22,938,033
|-  
|-  
| align="right" | peptide redundancy =  
| align="right" | peptide redundancy =  
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| 437.8 ×
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| 652.7 ×
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| align="right" | AA residues =  
| align="right" | AA residues =  
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| 109,914,112,840
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| 209,615,634,424
|-  
|-  
| align="right" | Build # =  
| align="right" | Build # =  
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| 5,327
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| 7272
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|}
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#[[G2PDB REST|g2pDB REST API]]: annotation and instructions on how to use the g2pDB REST API;
#[[G2PDB REST|g2pDB REST API]]: annotation and instructions on how to use the g2pDB REST API;
#[[Nomenclature for the description of protein sequence modifications|PTM annotation]]: a comprehensive reference to how we annotate PTMs;
#[[Nomenclature for the description of protein sequence modifications|PTM annotation]]: a comprehensive reference to how we annotate PTMs;
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#[[Amino acid symbols|Amino acids]]: a list of amino acids found in proteins; and
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#[[Amino acid symbols|Amino acids]]: a list of amino acids found in proteins;
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#[[GPMDB evidence codes]]: an explanation of the GPMDB evidence code system.
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#[[GPMDB evidence codes]]: an explanation of the GPMDB evidence code system; and
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#[[Jsms|JSMS]]: JSMS JSON Lines MS/MS file format.

Latest revision as of 19:34, 2 January 2024

Welcome to the GPMDB wiki site. GPMDB contents (2024.01.02)

The Generalized Proteoform Meta-analysis 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.


models = 598,204
proteins = 1,562,401,329
distinct proteins = 3,724,740
protein redundancy = 419.5 ×
peptides = 14.973 gigaTabbs
distinct peptides = 22,938,033
peptide redundancy = 652.7 ×
AA residues = 209,615,634,424
Build # = 7272

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 API: annotation and instructions on how to use the GPMDB REST API;
  3. g2pDB REST API: annotation and instructions on how to use the g2pDB REST API;
  4. PTM annotation: a comprehensive reference to how we annotate PTMs;
  5. Amino acids: a list of amino acids found in proteins;
  6. GPMDB evidence codes: an explanation of the GPMDB evidence code system; and
  7. JSMS: JSMS JSON Lines MS/MS file format.
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