Introduction

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.

Publications

  1. Andromeda: a peptide search engine integrated into the MaxQuant environment.
    Cite this
    Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M, 2011-04-01 - Journal of proteome research

Credits

  1. Jürgen Cox
    Developer

  2. Nadin Neuhauser
    Developer

  3. Annette Michalski
    Developer

  4. Richard A Scheltema
    Developer

  5. Jesper V Olsen
    Developer

  6. Matthias Mann
    Investigator

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Summary
AccessionBT002749
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMatthias Mann