The San Francisco Bay Area Mass Spectrometry (BAMS) discussion group

  Tuesday, April 7, 2015 from 6:00 pm to 9:30 pm

Crowne Plaza Hotel
Foster City, CA

Dinner reservations required by Midnight Sunday April 5, 2015

Josh Elias, PhD.
Assistant Professor of Chemical and Systems Biology
Stanford University, CA


Fast, accurate, and unrestricted spectrum interpretation: having your cake and eating it too

Database-dependent search engines like SEQUEST, Mascot and others are the foundation of modern proteomics. However, applications aimed at discovering unanticipated sequence variants, post-translational modifications (PTMs), or even entire proteins are poorly served by these work-horses of the field. Several existing solutions improve sequencing depth in PTM or sequence space realms, but often at a great cost of memory utilization, search speed, or discriminatory power. In this talk, I will describe new software we have developed that efficiently searches extremely large sequence spaces to accurately identify peptides from tandem mass spectra. We demonstrate the effectiveness of this approach through the re-analysis of over 2,000 spectrum sets described in a recently published human proteome mega-dataset, finding dozens of highly represented, yet unanticipated PTMs. We further describe the analysis of a meta-proteomic specimen derived from the most complex ecosystem known, the human gut. Our approach led to the elucidation of peptides derived from human, microbial, and dietary sources without placing prior constraint on the underlying source organisms.

Josh Elias has been an assistant professor in the department of Chemical & Systems Biology at Stanford University since 2009. His lab develops and applies mass spectrometry techniques towards addressing biomedically important challenges ranging from cancer immunology to host-microbiome interactions. Dr. Elias received his B.A. From Cornell University in Biology, and his PhD from Harvard Medical School in Cell Biology. As a doctoral student in the lab of Stephen Gygi, he developed the target-decoy strategy for false discovery rate estimation among other techniques for large-scale proteome characterization. Subsequently, he was jointly advised by Peter Sicinski at Dana Farber Cancer Institute and Dr. Gygi for his postdoctoral studies. Dr. Elias received a Damon Runyon-Rachleff Innovation Award in 2011 and a Keck Medical Research Award in 2013.

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