Shaping the Future of DIA Proteomics with Spectronaut™

Using Spectronaut to Maximize Biologically Meaningful DIA Data and Shared Knowledge in an Academic Core Facility

Brett S. Phinney (UC Davis, Genome Center – Proteomics Core Facility)

Academic core facilities have several unique challenges. Foremost is how to maximize biologically meaningful data for a wide variety of collaborating biologists while minimizing cost and turnaround time.  Although these challenges are not necessarily unique to core facilities, often core facilities deal with a wide variety of organisms and questions that that need to be answered quickly. Here I will present several recent projects from a wide range of collaborators and how we used DIA and Spectronaut to streamline and acquire data as efficiently as we currently can. Several features, in particular, will be explored such as generating and using DIA and DDA libraries across multiple projects, maximizing data for fast LC runs for large numbers of samples, and using Spectronaut’s post-analysis visuals for diagnosing potential problems with your datasets.

Short-Bio Brett S. Phinney

Brett Phinney received his Ph D. from the University of Texas at Austin where he used mass spectrometry to study the protein conformation of the viral spike protein complexes of a virus similar to SARS-CoV-2 way back in the mass spectrometry dark ages circa 2000. After receiving his Ph D. he did a Postdoc with noted mass spectrometrist Jack Watson at Michigan State University. From there he became the assistant director of the newly formed Michigan Proteome Consortium and became the director of the new Michigan State proteomics core facility. In 2005 Brett accepted the position of the Director of the new UC Davis Genome Center Proteomics Core facility where he designed and established the new core on campus and has been there ever since. Brett has also taught proteomics at a number of institutions including Michigan State University, and Cold Spring Harbor, and UC Davis, where he teaches an intense summer short course every summer.
The UC Davis Genome Center Proteomics Core, has a staff of four dedicated scientists. The Proteomics Core provides state-of-the-art LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics, and Post Translational Modification analysis for clients on and off-campus. We provide services at a reasonable rate (we try and breakeven) and a reasonable turnaround time