Shimadzu ASMS 2014 Tuesday Breakfast Seminar 

“Prepare Your Lab for the Future: Next Generation Immuno-MRM Analysis and Skyline Software for Peptide MRM Method Development”

Prof. Fred Regnier

Professor Emeritus & John H. Law Distinguished Professor of Chemistry Purdue University and Novilytic Laboratories, Indianapolis, IN, USA

Dr. Pawel Sadowski

Proteomics Research Officer, Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Australia

Abstract:

This seminar will introduce immuno-MRM measurements using ultra-fast & automated protein digestions, as well as “lab-on-a-card” plasma collection technology. Perfinity Workstation and integrated Digestion Platform (iDP) technologies enable automated, reproducible protein digests on a sub-minute timescale, greatly improving the applicability of peptide-based SRM assays. These technologies, used with ultra-fast mass spectrometry, save your laboratory time, money and resources and will greatly improve data reproducibility and quality. In addition, we will present new Noviplex Card technology (Novilytic Labs), which enables rapid plasma generation in just minutes without the need for venipuncture, centrifugations, etc. Lastly, stable isotope dilution multiple reaction monitoring mass spectrometry (SID/MRM-MS) using a triple quadrupole instrument is a widely employed analytical method for quantitative measurement of plasma protein biomarkers. The assay requires powerful software tools to handle multiplexed peptide MRM data as much as powerful instruments to generate reliable quantitative measurements. Here, we will present work that was done to ensure compatibility between Skyline, a vendor-neutral freeware software tool that provides a common framework that proteomics labs can adopt, and Shimadzu's most sensitive and ultra-fast platform, LCMS-8050. This compatibility greatly simplifies the development of an assay that aims to monitor biomarkers in a serum of large animal models, and shows how the employment of a SISCAPA approach pushes the limits of detection of proteins where abundant plasma protein depletion protocols are unavailable.