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)].

Chairs: Marc Wilkins & Maike Langini

Pre-Recorded Talks (available as of October 25 in the Virtual Platform in the 'Education Session' area - pre-recordings must be watched in advance of the Live Days, as recordings will not be played during Live Session)

• 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.

Chairs: Tiannan Guo & Mathieu Lavallée-Adam

Pre-Recorded Talks (available as of October 25 in the Virtual Platform in the 'Education Session' area - pre-recordings must be watched in advance of the Live Days, as recordings will not be played during Live Session)

• 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.

Chairs: Ileana Cristea & Ruth Hüttenhain

Pre-Recorded Talks (available as of October 25 in the Virtual Platform in the 'Education Session' area - pre-recordings must be watched in advance of the Live Days, as recordings will not be played during Live Session)

• Thermal Protein Profiling
  Mikhail M Savitski
• Complex Centric Proteome Profiling
  Isabel Bludau
• 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.

Chairs: Eric Deutsch & Cheng Chang

Pre-Recorded Talks (available as of October 25 in the Virtual Platform in the 'Education Session' area - pre-recordings must be watched in advance of the Live Days, as recordings will not be played during Live Session)

• 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 & Andreas Hober

Pre-Recorded Talks (available as of October 25 in the Virtual Platform in the 'Education Session' area - pre-recordings must be watched in advance of the Live Days, as recordings will not be played during Live Session)

• Exploring the ‘Social Network’ within a Human Cell
  Ed Huttlin
• HPA for Proteomics Data Interpretation
  Cecilia Lindskog Bergström
• (Large-scale) Multi-omics Data Analysis
  Johannes Griss