Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

TLDR

Peptide identification from fragmentation spectra is a key step in MS‑based proteomics. We present Andromeda, a novel peptide search engine that employs a probabilistic scoring model. Andromeda supports high‑accuracy fragment data, complex post‑translational modification patterns, and large databases, and can run independently, as part of MaxQuant, or via a web server, all freely available at www.maxquant.org. Andromeda matches Mascot’s sensitivity and specificity on proteome data and, by detecting co‑fragmented peptides, increases the total number of identified peptides.

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