Andromeda: a peptide search engine integrated into the MaxQuant environment.
By Jüergen Cox, N. Neuhauser, Annette Michalski, R. Scheltema, Jesper V. Olsen, Matthias Mann. Journal of Proteome Research, 2011
5,450 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/d038d7acea15ed1a4454ed47f53da7135415b8a4
How researchers see this paper
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In Molecular Biology
- Matthias Mann
- Jüergen Cox
- Stefka Tyanova
- Chunaram Choudhary
- Angus I. Lamond
- Christoph Schaab
- M. Larance
- T. Geiger
In Spectroscopy
- Matthias Mann
- Jüergen Cox
- Stefka Tyanova
- Chunaram Choudhary
- Angus I. Lamond
- Christoph Schaab
- M. Larance
- T. Geiger
Citations in the corpus
- Universal database search tool for proteomics (2014, neutral): “This simple ‘dot-product’ scoring model contrasts with many other database search 2,4,27,28 and re-scoring 9,10 tools, using sophisticated scoring functions that often make it difficult to satisfy the third condition.”
- 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data (2012, methodology): “While all examples show proteomics data obtained with the MaxQuant software [16,17] in combination with the Andromeda search engine [18], this is not a prerequisite for the application of the 2D annotation enrichment method.”
- Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation (2014, methodology): “MS and MS/MS spectra were analyzed using MaxQuant (version 1.4.0.5), utilizing its integrated ANDROMEDA search algorithms (Cox et al , 2011).”
- Plasma Proteome Profiling to Assess Human Health and Disease. (2016, methodology): “by the Andromeda search engine (Cox et al., 2011) with cysteine carbamido-”
- Global Subcellular Characterization of Protein Degradation Using Quantitative Proteomics (2012, positive): “5 as described previously (24, 25), using the default settings and employing the Human Uniprot database (06/07/11) containing 109,824 entries.”
- Transferrin Receptor Is a Specific Ferroptosis Marker (2020, neutral): “MS data analysis— Raw mass spectrometric data were analyzed using MaxQuant v.1.6.1.0 (Cox and Mann, 2008) (MaxQuant, RRID:SCR_014485) and employed Andromeda for database search (Cox et al., 2011) at default settings with a few modifications.”
- Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins (2012, methodology): “MS/MS spectra were searched by the Andromeda search engine (23) against the decoy IPI-human database version 3.”
- Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database (2012, methodology): “Analysis of the results was performed in MaxQuant (23) using the Andromeda search engine (24).”