Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture

Authors

Chalkley RJ Robert J , Bandeira N Nuno , Chambers MC Matthew C , Clauser KR Karl R , Cottrell JS John S , Deutsch EW Eric W , Kapp EA Eugene A , Lam HH Henry H N , McDonald WH W Hayes , Neubert TA Thomas A , Sun RX Rui-Xiang .
Molecular & cellular proteomics : MCP. 2013 10 31; 13(1).
360-71

Abstract

The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community’s ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.