Quantitative proteomics: strategies and tools to probe biology

Short Course, EMBL Heidelberg, 2023


The Bioinformatics course introduced statistical analysis approaches for detecting differentially abundant proteins. The approaches were implemented in the open-source software MSstats. We discussed issues such as preparation of tables of feature intensities (filtering, normalization); sample annotation and statistical modeling for realistic proteomic experiments (multi-group experiments, combination of biological and technical replicates, repeated measures); treatment of missing values; and visual exploration of the results. The discussion was illustrated in case studies of experimental datasets, using a graphical user interface MSstatsShiny. We explored the impact of different data processing options on the downstream results, highlighting significant choices in the workflow.