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This page contains the announcement and results of all GPM Requests For Comment (RFCs). These RFCs are posted when significant changes are made to the GPM system that merit discussion and recommendations from the proteomics community at large.

   Requests for Comment

Request For Comment 2012.09.01: Nomenclature for the use of gene symbols

This RFC is associated with the development of a notation for the use of gene symbols in GPMDB. A wiki page has been established for the interface design proposal. This RFC will be open until September 14, 2012. Please send all comments and suggestions to Ron Beavis (rbeavis@thegpm.org).

This RFC began on September 1, 2012 and was completed on September 14, 2012. This RFC has been adopted.

Request For Comment 2012.06.11: REST interface for GPMDB

This RFC is associated with the development of a REST-style API for the data in GPMDB. A wiki page has been established for the interface design proposal. This RFC will be open until September 10, 2012. Please send all comments and suggestions to Ron Beavis (rbeavis@thegpm.org).

This RFC began on June 11, 2012 and was completed on September 10, 2012. This RFC has been adopted.

Request For Comment 2012.02.23: FTP site layout for the cHPP

This RFC describes a basic layout for the construction of FTP sites for the storage of data files, annotation and documentation associated with cHPP groups. A wiki page has been established for the site layout proposal. This RFC will be open until March 24, 2012. Please send all comments and suggestions to Ron Beavis (rbeavis@thegpm.org).

This RFC was adopted on March 25, 2012.

Request For Comment 2011.12.14: Adoption of a "Nomenclature for the description of protein sequence modifications"

GPM needs an established notation for accurately describing the types of protein residue modifications (e.g., post-translational modifications or experiment artifacts) commonly observed in proteomics experiments. A wiki page has been established with a proposed notation, which follows the example of the Human Genome Variation Society's notation for amino acid polymorphisms. The RFC process will be open until January 14, 2012. Please send all comments and suggestions to Ron Beavis (rbeavis@thegpm.org).

This RFC was adopted on January 15, 2012.

Request For Comment 2010.08.30: changes to cRAP

The common Repository of Adventitious Proteins project (cRAP) would like to request user comments on a proposed revision of the protein sequences currently included in its list of proteins. If you would like to comment, please email your suggestions to rfc@thegpm.org. This RFC will remain active until October 1, 2010, at which time the resulting changes will be posted on this page.

The proposed changes are as follows:

  1. The removal of the "category 4" proteins from the list (see the cRAP page for a complete list of these proteins). The affected sequences (the Sigma/Aldrich Universal Protein Standard) were originally place in cRAP in anticipation of broad use of this mixture resulting in significant levels of contamination of non-human samples. Our analysis of the data shows that this has not happened. The continued presence of these alternate protein sequences in cRAP has given rise to added complexity in human data samples, which we feel it would be best to eliminate.
  2. The addition of two new viral protein sequences. These sequences, the heavy and light chain of the human adenovirus C E1B control protein, are observed in proteomics data obtained from HEK293 cells. These proteins are not the result of an infection: they are caused by the DNA insertion that immortalized this cell line. These proteins have no significant homology to any non-viral proteins and their inclusion should not increase the complexity of analyzed results.
  3. The addition of one new bacterial protein, the DNA K chaperonin from common cell culture infectious agent Mycoplasma hominis. This bacteria can be present at some level in cell culture and this protein is meant serve as an indicator of the potential infection of any sample derived from these cells. M. hominis ATP synthase subunit beta is another potential candidate, however its sequence has sufficient homology to mammalian ATP synthase that the danger of false positive assignments makes it a less attractive candidate marker.

Final outcome: these changes were rejected because of problems associated with many existing implementations of the previous cRAP list of proteins.

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