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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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Cox, Jürgen, Neuhauser, Nadin, Michalski, Annette, Scheltema, Richard A., Olsen, Jesper V., Mann, Matthias·2011·Journal of Proteome Research

DOI 10.1021/pr101065j

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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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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
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Amyloid aggregates accumulate in melanoma metastasis modulating YAP activity
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Glycolysis in hepatic stellate cells coordinates fibrogenic extracellular vesicle release spatially to amplify liver fibrosis
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CD74-dependent deregulation of the tumor suppressor Scribble in human epithelial and breast cancer cells
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NetrinG1(+) cancer-associated fibroblasts generate unique extracellular vesicles that support the survival of pancreatic cancer cells under nutritional stress
Raghavan, K. S., Francescone, R., Franco-Barraza, J., Gardiner, J. C., Vendramini-Costa, D. B., Luong, T., Pourmandi, N., Andren, A., Kurimchak, A., Ogier, C., et al. (2022) · Cancer Research Communications · doi:10.1158/2767-9764.crc-21-0147 · Cited by 40
Lipid remodeling and an altered membrane-associated proteome may drive the differential effects of EPA and DHA treatment on skeletal muscle glucose uptake and protein accretion
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Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life
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High speed capillary zone electrophoresis–mass spectrometry via an electrokinetically pumped sheath flow interface for rapid analysis of amino acids and a protein digest
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CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae
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Proteolysis in Irish farmhouse Camembert cheese during ripening
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Interaction of suppressor of cytokine signalling 3 with cavin-1 links SOCS3 function and cavin-1 stability
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Substrate specificity of the TRAMP nuclear surveillance complexes
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THEM6‐mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer
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Capillary zone electrophoresis tandem mass spectrometry detects low concentration host cell impurities in monoclonal antibodies
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Untitled work
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Authors: Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M.
Venue: Journal of Proteome Research
Publisher: American Chemical Society (ACS)
Published: 2011-04
Volume: 10
Issue: 4
Pages: 1794-1805
ISSN: 1535-3893 (ISSN-L)
1535-3907
DOI: 10.1021/pr101065j
OpenAlex: W2036321220
Cited by: 5,500
References: 7
FWCI: 81.12
Type: journal article
Language: en
Open access: hybrid
Licence: pubs.acs.org/page/policy/authorchoice_termsofuse.html (vor)

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Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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