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.

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