MQSS 2019 | L2: Andromeda | Petra Gutenbrunner

A key ingredient of MaxQuant is the Andromeda search engine, which calculates a probability-based score for peptide spectrum matches comparable to the Mascot search engine. In this lecture, we will discuss the underlying search strategy as well as more advanced topics regarding the identification of peptides and protein assembly. We will illustrate how MaxQuant processes raw data and assigns identification scores for modified, unmodified and co-fragmented peptides. Furthermore, we will discuss the posterior error probability and how MaxQuant calculates peptide and protein false discovery rates ensuring high-confidence spectra interpretation. Additionally, we want to introduce Andromeda 2.0, which supports two new scoring methods. The symmetric binomial score, which uses intensities predicted by a conventional and deep learning model and the tag-based scoring.

[michaella]

Great video! I wish it wasn't as blurry. Still very helpful though