TY - JOUR

T1 - Andromeda - a peptide search engine integrated into the MaxQuant environment

AU - Cox, Jurgen

AU - Neuhauser, Nadin

AU - Michalski, Annette

AU - Scheltema, Richard A

AU - Olsen, Jesper Velgaard

AU - Mann, Matthias

PY - 2011/4/1

Y1 - 2011/4/1

N2 - 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 co-fragmented peptides, significantly improving the total number of identified peptides.

AB - 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 co-fragmented peptides, significantly improving the total number of identified peptides.

U2 - 10.1021/pr101065j

DO - 10.1021/pr101065j

M3 - Journal article

C2 - 21254760

VL - 10

SP - 1794

EP - 1805

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 4

ER -