Bioinformatic solutions for designing quantitative targeted proteomics experiments

About this Class

Abstract: Targeted quantitative proteomics using multiple/parallel reaction monitoring (MRM, PRM) is already being applied by many researchers in biology, biochemistry, and clinical research laboratories. These methods allow rapid and precise quantitation of proteins in complex biological samples. Multiplexed MRM/PRM experiments are manageable manually for tens of target proteins in tens of samples, but scaling-up to hundreds of targets in thousands of samples is challenging. As a result, the planning, data analysis, and interpretation of the results from these experiments are all lengthy processes, usually requiring expertise in bioinformatics and proteomics. The talk will deal with few challenges in designing and running targeted experiments, and will focus on few own recent bioinformatic developments that helped accelerating the design and reducing human error by integrating information. A live demo of two of our tools will be part of the talk, this includes MRMAssayDB – an integrated resource for validated targeted proteomics assays, and the Mouse Quantitative Proteomics Knowledgebase – MouseQuaPro with reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays (PMID: 29762640, 33483739, and just accepted manuscript doi:10.1021/acs.jproteome.0c00961). Bio: Yassene is an assistant professor in bioinformatics at the Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands, and he is leading the bioinformatics core at the University of Victoria Proteomics Centre, Victoria, Canada. He received his PhD in Medical Informatics from the University of Göttingen, Germany. His research interests are targeted and quantitative proteomics, proteomics analysis of animal models, and data and information integration. Join ZoomGov Meeting https://nih.zoomgov.com/j/1612951422?pwd=bHRlYUVsaTFDWUF6Y2lpNzFDVTVBZz09 Meeting ID: 161 295 1422 Passcode: 498713 One tap mobile +16692545252,,1612951422#,,,,*498713# US (San Jose) +16468287666,,1612951422#,,,,*498713# US (New York) ----------------------------------------------- Aleksandra Nita-Lazar, Ph. D. Senior Investigator Chief, Functional Cellular Networks Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 4 Rm. 101 4 Memorial Dr Bethesda MD 20892-1892 Tel. 301-451-4394 website: www.niaid.nih.gov/lab-sections/3173 email: nitalazarau@niaid.nih.gov ORCID ID: 0000-0002-8523-605X