0000-0002-5923-9863 (Mikan), 0000-0001-7746-7758 (Harvey)

Document Type


Publication Date




Publication Title

Journal of Proteome Research








In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for deriving "metapeptides" (short amino acid sequences that may be represented in multiple organisms) from shotgun metagenomic sequencing of microbiome samples. In two ocean microbiome samples, we constructed site-specific metapeptide databases to detect more than one and a half times as many peptides as by searching against predicted genes from an assembled metagenome and roughly three times as many peptides as by searching against the NCBI environmental proteome database. The increased peptide yield has the potential to enrich the taxonomic and functional characterization of sample metaproteomes.


This is the author's manuscript version of a work that was published in Journal of Proteome Research

The American Chemical Society allows authors to deposit a copy of the accepted manuscript to online repositories for non-commercial purposes for public availability no sooner than 12 months after publication on the ACS website.

Data Availability

Article states: "The software (including source code) and data described in this manuscript may be downloaded at http://noble.gs.washington.edu/proj/metapeptide."

Original Publication Citation

May, D. H., Timmins-Schiffman, E., Mikan, M. P., Haryey, H. R., Borenstein, E., Nunn, B. L., & Noble, W. S. (2016). An alignment-free "metapeptide" strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing. Journal of Proteome Research, 15(8), 2697-2705. doi:10.1021/acs.jproteome.6b00239