The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis Giselle M. Knudsen, Robert J. Chalkley* Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America > A recent study by Bromenshenk et al., published in PLoS One (2010), used proteomic analysis to identify peptides purportedly of Iridovirus and Nosema origin; however the validity of this finding is controversial. We show here through reanalysis of a subset of this data that many of the spectra identified by Bromenshenk et al. as deriving from Iridovirus and Nosema proteins are actually products from Apis mellifera honey bee proteins. We find no reliable evidence that proteins from Iridovirus and Nosema are present in the samples that were re-analyzed. This article is also intended as a learning exercise for illustrating some of the potential pitfalls of analysis of mass spectrometry proteomic data and to encourage authors to observe MS/MS data reporting guidelines that would facilitate recognition of analysis problems during the review process. *********************************************** The BEE-L mailing list is powered by L-Soft's renowned LISTSERV(R) list management software. For more information, go to: http://www.lsoft.com/LISTSERV-powered.html Guidelines for posting to BEE-L can be found at: http://honeybeeworld.com/bee-l/guidelines.htm