Course content
These materials were part of past live ‘Proteomics Bioinformatics’ courses. Please refer to the course page of the 2025 edition, 2024 edition, 2023 edition, 2022 edition and 2021 edition to check details about these live events and their original programmes.
The content table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it. You can access the most up-to-date materials in our FTP for the 2025 course, 2024 course and 2023 course.
Presentation slides – View or download the slides
Recorded lectures – Watch the lecture videos
Practicals – View or download the slides, exercises, datasets, analysis scripts and results
| Format | Subject | Trainers |
| Protein identification | ||
| LC & MS Technologies and Protein Identification | Lennart Martens |
| Proteogenomics | Jyoti Choudhary, Sreejan Bandyopadhyay, James Wright |
| DIA-Proteomics | Andy Jones, Kerry Ramsbottom, Jordan Tzvetkov, Megan Hasoon, Yasset Perez-Riverol |
| Protein quantification | ||
| Post-transcriptional buffering of gene copy-number changes | Pedro Beltrao |
| Protein quantification approaches and Experimental Design | Kathryn Lilley, Lisa Breckels, Christophe Vanderaa |
| Software for large-scale quantitative proteomics | Yasset Perez-Riverol |
| MaxQuant | Carlo de Nart, Jinqiu Xiao, Peli Kyriakidou, Helen Hohenthanner |
| Perseus | Carlo de Nart, Jinqiu Xiao, Peli Kyriakidou, Helen Hohenthanner |
| Downstream analysis for quantitative proteomics | Lieven Clement, Christophe Vanderaa, Kathryn Lilley, Lisa Breckels |
| Resources for protein identification and submission | ||
| PRIDE/ProteomeXchange and Data re-use | Juan A. Vizcaino, Deepti J. Kundu, Ananth Prakash, Shengbo Wang |
| Protein interaction and network analysis | ||
| Introduction to IntAct, IMEx and PSICQUIC | Kalpana Panneerselvam, Juan Jose Medina Reyes, Eliot Ragueneau |
| Introduction to Network Analysis using the IntAct Cytoscape App | Kalpana Panneerselvam, Juan Jose Medina Reyes, Eliot Ragueneau |
| Functional analysis: Reactome | Krishna Kumar Tiwari, Eliot Ragueneau, Chuqaio Gong |
| Final overview and Recap | Juan A. Vizcaíno, Lennart Martens |