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      Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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          Abstract

          A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. 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. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.

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          Author and article information

          Journal
          Journal of Proteome Research
          J. Proteome Res.
          American Chemical Society (ACS)
          1535-3893
          1535-3907
          April 2011
          April 2011
          : 10
          : 4
          : 1794-1805
          Article
          10.1021/pr101065j
          21254760
          © 2011

          http://pubs.acs.org/page/policy/authorchoice_termsofuse.html

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