Quantitative Proteomics: Case Studies

Issued by: American Society for Mass Spectrometry (ASMS)
Instructors: Brendan MacLean (University of Washington), Devon Kohler (Northeastern University), Deanne Plubell (University of Washington), Olga Vitek (Northeastern University)
Completed on: June 2nd, 2024

Course Overview:
This case-study-driven course provides hands-on training in the analysis of quantitative proteomics data. It is designed for researchers who want to gain practical experience with state-of-the-art workflows for both Selected Reaction Monitoring (SRM) and Data-Independent Acquisition (DIA) mass spectrometry. The curriculum moves from experimental design and data acquisition considerations to in-depth statistical analysis and interpretation, using real-world datasets from clinical and pre-clinical studies.

Key Topics & Skills Acquired:

• SRM Data Analysis: Analyzing a case-control SRM dataset, with a focus on study design (normalization, randomization), chromatogram visualization, and statistical analysis using MSstats.
• DIA Data Analysis: Processing and analyzing a modern Orbitrap DIA dataset from a neurodegenerative disease cohort, exploring how data collection and processing choices (e.g., batching, filtering, missing values) impact statistical outcomes.
• Statistical Interpretation: Gaining proficiency in setting up, conducting, and interpreting statistical results for complex quantitative proteomics experiments.
• Hands-On Software Experience: Gaining practical skills with the Skyline and MSstats software ecosystems for robust analysis of both SRM and DIA data.
• Experimental Design Principles: Understanding the importance of proper experimental design, including the roles of biological and technical replicates, randomization, and normalization in generating reliable results.

Curriculum: The course was structured around two in-depth case studies over two days:

• Day 1: Introduction & SRM Case Study: Focused on the fundamentals of quantitative analysis and a deep dive into an SRM dataset from a heart failure study.
• Day 2: Advanced Topics & DIA Case Study: Covered the analysis of a complex DIA dataset from a Parkinson’s and Alzheimer’s cohort, emphasizing advanced data processing and statistical considerations.

This course provided practical, case-driven training in designing, executing, and interpreting quantitative proteomics experiments using state-of-the-art software tools.

You can view the certificate here.