Andromeda - Start


Cox Lab


November 15, 2023

Andromeda1 is a peptide search engine based on probabilistic scoring. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches.

It can handle data with arbitrarily high fragment mass accuracy, it is also able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. Andromeda can function independently or integrated into MaxQuant. This combination enables analysis of large datasets on a desktop computer. Identification of co-fragmented peptides improves the number of identified peptides.

To run Andromeda, you will need .NET framework 4.5.

1 Documentation outline

This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, please let us know. The wiki can be browsed by using the links below or by searching with the magnifying glass in the upper right corner.

You can find raw file format examples to test Andromeda here.

For additional training, consider attending the annual MaxQuant Summer School. Also watching some MaxQuant videos provides more insight.


Cox, J. et al. Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. Journal of Proteome Research 10, 1794–1805 (2011).