Personal Proteomics poster accepted for Exploring Human Host-Microbiome Interactions conference

First steps on a road: Our poster got accepted for the Exploring Human Host-Microbiome Interactions in Health and Disease Conference, 8-10 May 2012 taking place at Wellcome Trust Conference Centre in the Genome Campus, roughly 2 min walk from my workplace at the EBI. Draft schedule is here. An earlier version of the abstract I dug up:

Analyzing the personal oral microbioproteome and human saliva proteome via mass spectrometry proteomics

Attila Csordas1, Johannes Griss1, Henning Hermjakob1, Brian Balgley2

1 European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; 2Bioproximity, LLC, Springfield, Virginia, USA

Collecting and interpreting the human saliva microbioproteome of diseased and healthy human individuals over different time points via high-throughput methods might be a routine practice in the near future. Here we present a pipeline specifically designed for personal proteomics. Human saliva samples from a 36 year old individual were analyzed using shotgun tandem mass spectrometry (MS) over 3 time points in 2011. MS data was searched against an oral microbiome, a human proteome and a contamination library on Proteome Cluster (https://www.proteomecluster.com) running on the Amazon Cloud. The complete MS data as well as the search engine results can be viewed and downloaded from Proteome Cluster. In order to make the data more transparent all the spectra information alongside with peptide assignments and protein identifications made by the X!Tandem search engine were submitted and made publicly available via the PRoteomics IDEntifications (PRIDE) public repository (http://www.ebi.ac.uk/pride/). Stringent score thresholds were applied. At a 0.001 peptide expectation score cutoff and requiring at least 2 peptides per protein the global false discovery rate was less than 1 percent, yielding ~4000 protein accessions per MS/MS run. Human proteins accounted for ~40% while oral microbiome proteins covered ~60% of the protein accessions. Concerning the oral microbiome all 6 major Bacteria phyla containing ~96% of the oral taxa were represented.

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