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HUPO Connect 2020 Pre-Congress Training Courses
Mass spectrometry has established itself as the basis of the majority of modern proteomics experiments. When coupled with the appropriate analytical and bioinformatics approaches, it enables the identification and quantification of peptides and proteins, as well as the characterization of their post-translational modifications. While proteomics pipelines enable fascinating discoveries, they harbour many steps, each with their own intricacies. In this series of lectures, we discuss such steps and provide tools and tips to bring a biological sample to a set of high-quality results.
In the first set of talks entitled “Introduction to Proteomics and Mass Spectrometry”, Lindsay Pino will present an overview on how a biological sample is processed using mass spectrometry approaches. Biochemical separations and enrichments, as well as mass spectrometry techniques will be explained and discussed. The following set of presentations by David Tabb, “From Mass Spectrum to Protein” will cover the computational methods required to convert the data obtained from mass spectrometry instruments into intelligible and interpretable results. Specifically, topics such as peptide identification using database search, statistical assessment, and protein inference will be discussed in this section. Finally, Michael MacCoss will present a set of lectures on “Quantitative proteomics”. These talks will discuss what quantification really implies in mass spectrometry-based proteomics, contrast peptide versus protein quantification, and present the basics of quantitative proteomics experimental design.- Total Presentations: 45
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PCT1 - Proteomics 101
- Type: Pre-Congress Training
- Presentations: 10
- Chair(s): Mathieu Lavallée-Adam
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PCT1.01.01 - Introduction to Proteomics and Mass Spectrometry - Segment 1: Biochemical Separations and Enrichments (View Presentation)
Lindsay Pino
- Presentation
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PCT1.01.02 - Introduction to Proteomics and Mass Spectrometry - Segment 2: Introduction to Mass Spectrometry (View Presentation)
Lindsay Pino
- Presentation
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PCT1.01.03 - Introduction to Proteomics and Mass Spectrometry - Segment 3: From Peptides to Fragments (View Presentation)
Lindsay Pino
- Presentation
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PCT1.02.01 - From Mass Spectrum to Protein - Segment 1. Database Searching (View Presentation)
David Tabb
- Presentation
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PCT1.02.02 - From Mass Spectrum to Protein - Segment 2. False Discovery Rate Control (View Presentation)
David Tabb
- Presentation
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PCT1.02.03 - From Mass Spectrum to Protein - Segment 3. Protein Inference (View Presentation)
David Tabb
- Presentation
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PCT1.03.01 - Quantitative Proteomics - Segment 1: What is Mass Spectrometry-Based Quantification? (View Presentation)
Mike MacCoss
- Presentation
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PCT1.03.02 - Quantitative Proteomics - Segment 2: Peptide Quantification vs Protein Quantification (View Presentation)
Mike MacCoss
- Presentation
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PCT1.03.03 - Quantitative Proteomics - Segment 3: Basics of Quantitative Proteomics Experimental Design (View Presentation)
Mike MacCoss
- Presentation
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- Presentation
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PCT2 - Proteogenomics
- Type: Pre-Congress Training
- Presentations: 10
- Chair(s): Harry Whitwell
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PCT2.01.01 - From Transcriptome to Proteome - Segment 1: Transcriptomics and Proteomics. What can we learn from RNA-seq and mass spectrometry techniques? (View Presentation)
Marc Wilkins
- Presentation
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PCT2.01.02 - From Transcriptome to Proteome - Segment 2: Alternate splicing - how can it be detected, in transcripts and in the proteome? (View Presentation)
Marc Wilkins
- Presentation
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PCT2.01.03 - From Transcriptome to Proteome - Segment 3: Alternate splicing - what are its biological effects in the proteome function, modifications and interactions? (View Presentation)
Marc Wilkins
- Presentation
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PCT2.02.01 - Protein to Genes – Analysing the Histone-code - Segment 1: Capturing a PTM dance on a protein dancefloor: what makes histone analysis so different from conventional proteomics. (View Presentation)
Maarten Dhaenens
- Presentation
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PCT2.02.02 - Protein to Genes – Analysing the Histone-code - Segment 2: Sample preparation and Data acquisition (View Presentation)
Maarten Dhaenens
- Presentation
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PCT2.02.03 - Protein to Genes – Analysing the Histone-code - Segment 3: Data Analysis: Identification and Quantification (View Presentation)
Maarten Dhaenens
- Presentation
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PCT2.03.01 - Navigating from Genome to Proteome - Segment 1: Visualization and Exploration of Protein-Centric Functional networks (View Presentation)
Vidya Venkatraman
- Presentation
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PCT2.03.02 - Navigating from Genome to Proteome - Segment 2: Exploring Proteogenomic relationships in the Context of PPIs, Signaling and PTM Crosstalk (View Presentation)
Vidya Venkatraman
- Presentation
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PCT2.03.03 - Navigating from Genome to Proteome - Segment 3: Proteogenomic Convergence for understanding pathways and networks (View Presentation)
Vidya Venkatraman
- Presentation
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Proteogenomics Q&A (View Presentation)
Marc Wilkins
Maarten Dhaenens
Vidya Venkatraman- Presentation
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PCT3 - Post-Translational Modification Analysis
- Type: Pre-Congress Training
- Presentations: 10
- Chair(s): Giuseppe Palmisano
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PCT3.01.01 - PTM Overview and Acetylation/Succinylation - Segment 1. Introduction to PTM, acetylation and succinylation (View Presentation)
Birgit Schilling
- Presentation
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PCT3.01.02 - PTM Overview and Acetylation/Succinylation - Segment 2. Proteomic methods to study protein acetylation and succinylation (View Presentation)
Birgit Schilling
- Presentation
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PCT3.01.03 - PTM Overview and Acetylation/Succinylation - Segment 3. Data analysis and biological validation for acetylation and succinylation studies (View Presentation)
Birgit Schilling
- Presentation
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PCT3.02.01 - Phosphoproteomics - Segment 1. Protein phosphorylation: structural and functional features (View Presentation)
Martin Larsen
- Presentation
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PCT3.02.02 - Phosphoproteomics - Segment 2. Proteomic methods to study protein phosphorylation (View Presentation)
Martin Larsen
- Presentation
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PCT3.02.03 - Phosphoproteomics - Segment 3. Data analysis and biological validation (View Presentation)
Martin Larsen
- Presentation
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PCT3.03.01 - Glycoproteomics - Segment 1. Introduction to protein glycosylation (View Presentation)
Kay-Hooi Khoo
- Presentation
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PCT3.03.02 - Glycoproteomics - Segment 2. From sample prep to MS data acquisition for glycoproteomics (View Presentation)
Kay-Hooi Khoo
- Presentation
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PCT3.03.03 - Glycoproteomics - Segment 3. Glycoproteomics data analysis (View Presentation)
Kay-Hooi Khoo
- Presentation
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Post-Translational Modification Analysis Q&A (View Presentation)
Birgit Schilling
Martin Larsen
Kay-Hooi Khoo- Presentation
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PCT4 - Computational Tools for Functional Analysis of Proteins
- Type: Pre-Congress Training
- Presentations: 10
- Chair(s): Lydie Lane
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PCT4.01.01 - Introduction to Protein Databases and Functional Annotation - Segment 1: Introduction to protein knowledgebases and query facilities (View Presentation)
Lydie Lane
- Presentation
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PCT4.01.02 - Introduction to Protein Databases and Functional Annotation - Segment 2: Functional annotation using the Gene Ontology (View Presentation)
Lydie Lane
- Presentation
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PCT4.02.01 - GO Term Enrichment Analysis - Segment 1: Principles of enrichment analysis (View Presentation)
Tania Wyss
- Presentation
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PCT4.02.02 - GO Term Enrichment Analysis - Segment 2. Tools for enrichment analysis I (View Presentation)
Tania Wyss
- Presentation
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PCT4.02.03 - GO Term Enrichment Analysis - Segment 3. Tools for enrichment analysis II (View Presentation)
Tania Wyss
- Presentation
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PCT4.02.04 - GO Term Enrichment Analysis - Segment 4. Visualization of enrichment results (View Presentation)
Tania Wyss
- Presentation
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PCT4.03.01 - Multi-omics Pathway Analysis with Reactome - Segment 1. Reactome introduction (View Presentation)
Henning Hermjakob
- Presentation
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PCT4.03.02 - Multi-omics Pathway Analysis with Reactome - Segment 2. Expert and community curation (View Presentation)
Henning Hermjakob
- Presentation
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PCT4.03.03 - Multi-omics Pathway Analysis with Reactome - Segment 3. Multi-omics analysis (View Presentation)
Johannes Griss
- Presentation
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Computational Tools for Functional Analysis of Proteins Q&A (View Presentation)
Lydie Lane
Tania Wyss
Henning Hermjakob
Johannes Griss- Presentation
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PCT5 - New Technologies and New Approaches
- Type: Pre-Congress Training
- Presentations: 5
- Chair(s): Justyna Fert-Bober
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PCT5.01 - Cell sorting meets mass spectrometry - A workflow for analysis of (bacterial) subpopulations
Uwe Volker
- Presentation
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PCT5.02 - Development of ultraviolet photodissociation for characterization of proteins
Jennifer Brodbelt
- Presentation
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PCT5.03 - Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Bernd Wollscheid
- Presentation
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PCT5.04 - Coupling mass spectrometry imaging with microscale separations to expand the neuropeptidome
Lingjun Li
- Presentation
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PCT5.05 - High-throughput proteomics: How fast can we go?
Christoph Messner
- Presentation
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