November 2017 Meeting Announcement, Delaware Valley Mass Spectrometry Discussion Group
NOTE: We will be following the REGULAR SCHEDULE for the November meeting. Dr Vitek has graciously rearranged her schedule. The social hour will begin at 6:00 and the talk at 7:00
- Topic: "MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
- Speaker:Olga Vitek, Northeastern University
- Date: Monday, November 13, 2017. 6:00 PM
- Please RSVP to XQiu2@ITS.JNJ.com by Thursday November 9.
- Time: Social Hour: 6:00 PM.
Talk: 7:00 PM.
- Place: Department of Chemistry, Villanova University (Mendel Hall 154)
Parking for the monthly meetings of the DVMSDG will change on a monthly basis due to heavy construction on campus over the next 1-2 years. Please check monthly for parking updates. Access to the Mendel Lot (S-3) from the Main Campus Gate on Ithan Avenue is closed due to SEPTA construction. October, January, and March meetings will be during fall/winter/spring breaks and traffic on campus should be greatly reduced. Evening classes will be going on during the other months and parking in Mendel may be limited.
1. To access the Mendel Lot off of Spring Mill Road, ring the doorbell at the gate entrance and ask to raise the gate. All attempts will be made to have the gate raised in advance of the 3 meetings during campus breaks.
2. If you enter through the guard shack on Ithan Avenue, ask the guard for a parking pass for the inner campus M-2 parking garage. The main parking garage (I-1) is across Lancaster Avenue and they may direct you to park there.
Abstract: Statistical methodology is key for quantitative proteomics, as it requires to reduce bias and inefficiencies, distinguish the systematic variation from random artifacts, and maximize the reproducibility of the results. This talk will overview the statistical methodology implemented in MSstats, an open-source R package for statistical relative quantification of proteins and peptides. MSstats supports experiments with complex designs, such as comparisons of multiple groups or time course comparisons. It handles quantitative shotgun DDA (data-dependent acquisition) experiments, targeted SRM (selected reaction monitoring), and SWATH/DIA (data independent acquisition) experiments. It can be used in conjunction with label-free experimental workflows, or with workflows that utilize stable isotope reference proteins or peptides. MSstats contains functionalities for data processing and quality control, model-based statistical analysis (including testing proteins and peptides for differential abundance, or estimating protein abundance on a relative scale), and model-based calculation of a sample size for a future experiment. MSstats is available stand-alone, or via graphical user interface as an external tool in the software framework Skyline. The talk will discuss the general statistical approach underlying MSstats, motivate some of the data representation choices, and outline directions of future research.
Olga Vitek holds a BS degree from the University of Geneva, Switzerland, and a MS in Mathematical Statistics and a PhD in Statistics from Purdue University. She interned at Eli Lilly & Company in Indianapolis and held a position of post-doctoral associate in the Aebersold Lab at the Institute for Systems Biology in Seattle. Between 2006-2014 she was an assistant professor, and then an associate professor with tenure at Purdue University, with a joint appointment in the Department of Statistics and Department of Computer Science. In the summer of 2014 she joined Northeastern University, with a joint appointment in the College of Science and the College of Computer and Information Science.
Professor Vitek was named the Sy and Laurie Sternberg Interdisciplinary Associate Professor at Northeastern University, and University Faculty Scholar at Purdue University. While at Purdue, she was recognized with an Outstanding Assistant Professor Teaching Award, a Graduate Student Mentoring Award, and a Teaching for Tomorrow Award. She is a recipient of the National Science Foundation CAREER Award. She serves on the Board of Directors of the US Human Proteome Organization.
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