Susan E. Abbatiello Susan E. Abbatiello, Ph.D., is a Research Scientist at the Proteomics Platform at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, where her work focuses on method development and optimization of targeted quantitative assays using SRM-MS. She is currently co-chair of the Verification Working Group, part of the National Cancer Institute’s Clinical Proteomics Technologies Assessment for Cancer (CPTAC) initiative. The efforts of this group concentrate on establishing rigorous protocols, reagents, methodologies and software for reproducible quantification of cancer-relevant protein targets in plasma using stable isotope dilution selected reaction monitoring mass spectrometry (SID-SRM-MS). She received her B.A. in Chemistry from the College of the Holy Cross in Worcester, Massachusetts, then spent five years working at Genetics Institute in Andover, MA, developing LC-based assays for protein pharmaceuticals. She earned her Ph.D. in Analytical Chemistry at the University of Florida in the lab of Dr. John Eyler, specializing in mass spectrometric characterization and quantification of a suspected leukemia biomarker. Her postdoctoral training was in the lab of Dr. Thomas P. Conrads at the University of Pittsburgh, where her work continued in peptide quantification using SID-MRM-MS in different areas of cancer research.

Effectively Dealing with Transition Selection and Data Analysis for Multiplexed Quantitative SRM-MS Assays across Multiple Vendor Instruments

Skyline has played a pivotal role in the success of the NCI’s Clinical Proteomics Technologies Assessment for Cancer consortium and our efforts in evaluating highly multiplexed quantitative assays for the verification of biomarker candidates in plasma. Capabilities such as automated transition selection from instrument-specific spectral libraries and document sharing has allowed for uncomplicated method design and implementation at various laboratories. Key features such as Peak Area View and Retention Time View were implemented to help track system performance before and during quantitative assays, and have been additionally helpful in the inspection of large sets of data. Custom data reports have made data processing straightforward, further facilitated by the ability of Skyline to process data from the four main MS vendors. This presentation will focus on the use of Skyline in the context of CPTAC Verification studies as well as its routine and specialized use in the Proteomics Platform at the Broad Institute.

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