PRE-CONGRESS TRAINING COURSES

Proteomics 101

Characterization of complex proteomes is the key to reveal their composition and functions. This session will present an overview of the current methodology used to identify and quantify proteins. Three experts will cover the basic principles and practice of proteomics, analytical workflows and data interpretation of mass spectrometry based proteomics, global (isotopic labeling, label-free, DIA) and targeted quantitative proteomics methods [e.g., selected reaction monitoring (SRM) and parallel reaction monitoring (PRM)].

Chair: Marc Wilkins

Co-Chair: Maike Langini

Pre-Recorded Talks

• Introduction to Proteomics and Mass Spectrometry, Lindsay Pino
• From Mass Spectrum to Protein, David Tabb
• Quantitative and Targeted Proteomics, Michael MacCoss

Statistics and Experimental Design

Tutorials covering statistics essential for proteomics experiments, and considerations for proteomics experimental design will be presented in this session. Attendees will learn the basics of designing a proteomics experiment for biological research and biomarker discovery, as well as issues related to analysing (large) quantitative proteomic data sets generated by data-dependent acquisition (DDA; including label-free and label-based-methods), data-independent acquisition (DIA), and targeted proteomics. The session will also cover the statistical principles for peptide and protein identification and quantification, taking into account the specific challenges of large data sets and cohorts.

Chair: Tiannan Guo

Co-Chair: Mathieu Lavallée-Adam

Pre-Recorded Talks

• Statistical Considerations for Biomarker Discovery Experiments, Meena Choi
• Statistics for Peptide and Protein Identification and Quantification, Alexey I. Nesvizhskii
• Experimental Design and Data-Analysis in Label-Free Quantitative LC/MS Proteomics: A Tutorial with MSqRob - Lieven Clement

Interactomics Approaches

Proteins do not function in isolation, but rather, they associate with other proteins to form complexes and interaction networks with distinct structure and composition to execute their function. Moreover, disease-causing genetic mutations may lead to alterations in protein function by modulating the interactions of the mutated proteins. Thus, a fundamental part of understanding a protein’s function in health and disease is to systematically study the proteins and other molecules that it interacts with and their dynamic changes in a cellular or disease state. Proteomics is the premier method for mapping protein-protein and protein-ligand interactions. This session will highlight approaches for identification and characterization of protein-protein interactions and complexes.

Chair: Ileana Cristea

Co-Chair: Ruth Hüttenhain

Pre-Recorded Talks

• Thermal Protein Profiling, Mikhail M Savitski
• Complex Centric Proteome Profiling, Isabel Bludeau
• Protein-protein Interactions/Spatial Proteomics, Anne-Claude Gingras

Proteomics Informatics Workflows

Managing the informatics pipeline of a typical proteomics experiment is as important and challenging as managing the experimental and analytical workflows. This session will provide examples of large scale computational workflows for proteomics data management and analysis.

Chair: Eric Deutsch

Co-Chair: Cheng Chang

Pre-Recorded Talks

• MaxQuant and Perseus Workflows, Jürgen Cox
• DIA Workflows, Brian Searle
• ProteORE for Proteomics Data Interpretation in Galaxy, Yves Vandenbrouck

Biological Context and Interpretation

Large-scale proteomics experiments generate an immense amount of data that need to be comprehensively interpreted to extract biological meaning after computational/statistical analyses are completed. This crucial step is required in order to select targets for functional follow-up which could take months to years of work. More specialized mass spectrometry-based experiments (such as interactome identification) also bring specific challenges for biological interpretation. This session will focus on use of large-scale datasets for elucidation of biological function, highlighting tools and strategies that can aid in these steps.

Chair: Jennifer Geddes-McAlister

Co-Chair: Andreas Hober

Pre-Recorded Talks

• BioPlex 2.0 Project, Interactome, Ed Huttlin
• HPA for Proteomics Data Interpretation, Cecilia Lindskog Bergström
• Large-scale Phosphoproteomics, Judit Villen