May 9 – May 20, 2022, online: May Institute on computation and statistics for mass spectrometry and proteomics
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vitek...@gmail.com
Mar 23, 2022, 8:59:28 PM3/23/22
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Dear Colleagues:
May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on May 9 – May 20, 2022 on the Boston campus of Northeastern University (online), is now accepting applications.
The program includes tutorials and practical hands-on sessions, presenting open-access data processing tools (Skyline, FragPipe), programming languages (R, Python), statistical analysis tools (MSstats), and data repositories (MassIVE, PRIDE and Panorama). Instructors are leading experts, who contributed numerous computational methods and software. The presentations are integrated to focus on analyses of several well-chosen datasets. Together we will take an in-depth look into case studies of design and analysis of mass spectrometry-based experiments.
Week 1:
* Intro and hands-on, Sue Abbatiello: targeted MS-based proteomics with Skyline
* Intro and hands-on, Lindsay Pino: targeted MS-based proteomics with Skyline
* Hands-on, Brendan MacLean: Part 1: Skyline processing of proteome-wide DIA of a controlled mixture
* Hands-on, Brendan MacLean: Part 2: Skyline-based comparison of refined versus proteome-wide queries of DIA experiments
* Keynote, Alexey Nesvizhskii: Quantification workflows in FragPipe computational pipeline
* Hands-on, Felipe Leprevost: Quantification workflows in FragPipe computational pipeline
* Hands-on, Ryan Benz: Part 1: Introduction to R for beginners
* Hands-on, Ryan Benz: Part 2: Introduction to R for beginners
Week 2:
* Tutorial, Kylie Bemis: Intermediate R crash course for MS practitioners
* TutTutorial, Olga Vitek: Introduction to statistical methods and MSstats for label-free proteomics
* Hands-on, Meena Choi and Brendan MacLean: Analysis of data in Skyline Part 1 and Part 2 in MSstats, and comparison of the results
* Tutorial, Olga Vitek: Introduction to statistical methods and MSstatsTMT for label-based proteomics.
* Hands-on, Ting Huang: Analysis of data in the FragPipe tutorial with MSstatsTMT.
* Tutorial, Nuno Bandeira: Reproducible quantitative MS-based proteomics with MassIVE
* Tutorial, Meena Choi: Reproducible quantitative MS-based proteomics with MassIVE.quant
* Tutorial, Yasset Perez-Riverol: Reproducible quantitative MS-based proteomics with PRIDE
* Tutorial, Vagisha Sharma: Reproducible quantitative MS-based proteomics with Panorama
* Hands-on, Charles Tapley Hoyt: Modern software development practice with Python
More information is at https://computationalproteomics.khoury.northeastern.edu/
Please share this widely.
---
Olga Vitek
Professor
Khoury College of Computer Sciences, Northeastern University
URL: olga-vitek-lab.ccis.northeastern.edu
Twitter: @olgavitek
May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on May 9 – May 20, 2022 on the Boston campus of Northeastern University (online), is now accepting applications.
The program includes tutorials and practical hands-on sessions, presenting open-access data processing tools (Skyline, FragPipe), programming languages (R, Python), statistical analysis tools (MSstats), and data repositories (MassIVE, PRIDE and Panorama). Instructors are leading experts, who contributed numerous computational methods and software. The presentations are integrated to focus on analyses of several well-chosen datasets. Together we will take an in-depth look into case studies of design and analysis of mass spectrometry-based experiments.
Week 1:
* Intro and hands-on, Sue Abbatiello: targeted MS-based proteomics with Skyline
* Intro and hands-on, Lindsay Pino: targeted MS-based proteomics with Skyline
* Hands-on, Brendan MacLean: Part 1: Skyline processing of proteome-wide DIA of a controlled mixture
* Hands-on, Brendan MacLean: Part 2: Skyline-based comparison of refined versus proteome-wide queries of DIA experiments
* Keynote, Alexey Nesvizhskii: Quantification workflows in FragPipe computational pipeline
* Hands-on, Felipe Leprevost: Quantification workflows in FragPipe computational pipeline
* Hands-on, Ryan Benz: Part 1: Introduction to R for beginners
* Hands-on, Ryan Benz: Part 2: Introduction to R for beginners
Week 2:
* Tutorial, Kylie Bemis: Intermediate R crash course for MS practitioners
* TutTutorial, Olga Vitek: Introduction to statistical methods and MSstats for label-free proteomics
* Hands-on, Meena Choi and Brendan MacLean: Analysis of data in Skyline Part 1 and Part 2 in MSstats, and comparison of the results
* Tutorial, Olga Vitek: Introduction to statistical methods and MSstatsTMT for label-based proteomics.
* Hands-on, Ting Huang: Analysis of data in the FragPipe tutorial with MSstatsTMT.
* Tutorial, Nuno Bandeira: Reproducible quantitative MS-based proteomics with MassIVE
* Tutorial, Meena Choi: Reproducible quantitative MS-based proteomics with MassIVE.quant
* Tutorial, Yasset Perez-Riverol: Reproducible quantitative MS-based proteomics with PRIDE
* Tutorial, Vagisha Sharma: Reproducible quantitative MS-based proteomics with Panorama
* Hands-on, Charles Tapley Hoyt: Modern software development practice with Python
More information is at https://computationalproteomics.khoury.northeastern.edu/
Please share this widely.
---
Olga Vitek
Professor
Khoury College of Computer Sciences, Northeastern University
URL: olga-vitek-lab.ccis.northeastern.edu
Twitter: @olgavitek
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