|Brett Phinney, Ph.D., has been the manager of the Proteomics Core at UC Davis Genome Center, University of California since 2005 where he both uses Skyline in his research and has taught courses to help others learn more about using Skyline for targeted proteomics. His prior work experience includes: Research Assistant Professor, Michigan Proteome Consortium, Michigan State University, 2004 - 2005. Director, Michigan State University Proteomics Facility, Michigan State University, 2002 - 2005. Research Associate, Michigan Proteome Consortium, Michigan State University, 2001 - 2002. Postdoctoral Fellow, Michigan State University, 2000 - 2001.
Using Skyline to analyze the SPRG2013-2014 Targeted Proteomics StandardProteomics technologies are an integral part of biological and clinical research. Significant contributions by the proteomics field are driven by the diverse and advanced analytical approaches employed to comprehensively characterize proteomes, including quantitative analysis of proteome variations, modifications, and interactions. The ABRF Proteomics Standards Research Group (sPRG) functions to design and develop performance standards and resources for mass spectrometry-based proteomics applications. The sPRG is currently conducting a study focused on generation of a standard for interassay, interspecies, and interlaboratory normalization in label-free as well as in quantitative stable-isotope label-based analyses. The standard has been formulated as two mixtures: 1000 stable isotope 13C/15N-labeled synthetic tryptic peptides alone, and peptides mixed with a tryptic digest from HEK 293 cell lysate. This presentation will detail how the sPRG used skyline to analyze this standard and will present several of the challenges we encountered when analyzing isotope labeled peptide standards in complex matrices.