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Andromeda 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 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. If you use Windows you should have Vista or newer. Like most Windows software, Andromeda can also be run on a Mac.
This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wiki, but to make changes you will have to register and login using the button in the upper right.
You can find raw file format examples to test Andromeda here.
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M., Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment, J. Proteome Res., 2011, 10, 1794–1805