Evaluation of proteomic differential expression analysis/modeling on the peptide rather than protein(group) level

Bioinformatics & Data Science
R programming
Difficulty: Advanced
Master of Science

Johannes Graumann


January 18, 2023

The project aims at exploring the differences and advantages of proteomic differential expression analysis on quantified peptide input data rather than pre-aggregated protein(group) information in the context of the autonomics analysis framework and following the work of Lieven Clement (Sticker et al. 2020; Goeminne et al. 2020).


Goeminne, Ludger J. E., Adriaan Sticker, Lennart Martens, Kris Gevaert, and Lieven Clement. 2020. MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics.” Analytical Chemistry 92 (9): 6278–87. https://doi.org/10.1021/acs.analchem.9b04375.
Sticker, Adriaan, Ludger Goeminne, Lennart Martens, and Lieven Clement. 2020. “Robust Summarization and Inference in Proteome-Wide Label-Free Quantification.” Molecular & Cellular Proteomics 19 (7): 1209–19. https://doi.org/10.1074/mcp.RA119.001624.