Andromeda statistics

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Citations per year

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Popular tool citations

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Associated diseases

Associated diseases


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Andromeda specifications


Unique identifier OMICS_19843
Name Andromeda
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline Matthias Mann <>
  • person_outline Juergen Cox <>

Additional information

Andromeda is available as a stand-alone, but also as a sub tool of MaxQuant.

Publication for Andromeda

Andromeda in pipelines

PMCID: 5772234
PMID: 29150517
DOI: 10.1128/AEM.02091-17

[…] of an unknown charge state were rejected for ms/ms. mass spectra were recorded with xcalibur software 2.2 sp1.48 (thermo scientific)., proteins under both culture conditions were identified with andromeda () and quantified with the lfq algorithm () embedded in maxquant version (). the fasta protein database for identification was taken from the output of the functional annotation […]

PMCID: 5778013
PMID: 29358734
DOI: 10.1038/s41467-017-02694-8

[…] were correlated with the s. cerevisiae protein database (uniprotkb canonical set including isoforms for strain ac204508/s288c, proteome id up000002311, release 01.10.2015, 6,740 entries) using andromeda. n-terminal and lysine dimethylation were set as light (+28.03 da) and heavy (+34.06 da) labels, respectively. trypsin/p was set as the enzyme in specific digestion mode allowing up to two […]

PMCID: 5788924
PMID: 29379051
DOI: 10.1038/s41598-018-20130-9

[…] and peptide areas were calculated using the precursor ions area detector node., identification and label-free quantification of ubiquitinated peptides in hela cells was performed using the andromeda and the maxlfq algorithm, respectively, implemented in the maxquant computational proteomics platform (v1.5.1.2). ms2 spectra were searched against the human uniprot complete proteome set […]

PMCID: 5836539
PMID: 29507054
DOI: 10.15252/msb.20177858

[…] loaded and washed with 0.6% acetic acid and eluted with 80% acn/0.6% acetic acid., label‐free quantification was performed by analyzing the raw data by maxquant (version; cox & mann, ). andromeda (cox et al, ) was used to search the ms/ms data against the uniprot homo sapiens database (containing canonical and isoforms_42144 entries downloaded on march 21, 2016) complemented […]

PMCID: 5325209
PMID: 28234898
DOI: 10.1371/journal.pone.0170762

[…] and quantitated peptides/proteins using the piqmie proteomics server []. about one-fourth of the human or mouse proteome (as defined by the uniprotkb database) was identified by the maxquant/andromeda analysis (, – tables), with mean coverage of 27.30% for human and of 25.35% for mouse cells. approximately half of the identified protein accessions belong to the high-quality and manually […]

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Andromeda in publications

PMCID: 5928194
PMID: 29712969
DOI: 10.1038/s41598-018-25137-w

[…] 20 s dynamic exclusion; top 10 precursor fragmentation in the ion trap with a collision energy of 35%., analysis of the raw data was performed using maxquant (version,) with the built-in andromeda search engine. the spectra were searched against the human swissprot database version 06/2015 (canonical and isoforms). the maxquant default settings (including mass tolerance) were used. […]

PMCID: 5946459
PMID: 29694890
DOI: 10.1016/j.celrep.2018.03.116

[…] in ms1, and all xic values were normalized over the full total ion current of the injection. for peptide annotation, raw data files were analyzed using the maxquant software, v. (), with the andromeda search engine (). the acquisitions were searched against a human database (uniprot databases containing 89,706 entries, including 42,034 swissprot entries, downloaded on january 13, 2015). […]

PMCID: 5910380
PMID: 29679077
DOI: 10.1038/s41467-018-04003-3

[…] peptide, protein, and site false discovery rate (fdr) was set to 1 %. modification by light and heavy iodoacetamide on cysteine residues (carbamidomethylation) was set as label type modification in andromeda configuration. compositions set in the software were: hnocx(2)hx(2) for heavy and h(3)noc(2) for light label. as such, cysteine-containing peptide pairs were treated in the same way […]

PMCID: 5897034
PMID: 29608573
DOI: 10.1371/journal.pntd.0006351

[…] fdr was calculated in the proteome discoverer software and kept below 1%., the raw files were also processed using the maxquant [] version and the ms/ms spectra were searched using the andromeda search engine [] against the uniprot t. cruzi protein database (release july 11, 2017; 51,738 entries). the initial maximal allowed mass tolerance was set to 20 ppm for precursor […]

PMCID: 5934616
PMID: 29618087
DOI: 10.1093/nar/gky224

[…] dimethylation and trimethylation, (iii) d3-acetylation/propionylation, lysine monomethylation with d3-acetylation/propionylation, trimethylation and lysine acetylation. peptides with andromeda score <60 (corresponding to a mascot score of 15 (), which has been previously used as a cut-off value ()) and localization probability score <0.75, were removed. identifications […]

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Andromeda institution(s)
Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
Andromeda funding source(s)
Supported by the European Union seventh Framework Program (HEALTH-F4-2008-201648/ PROSPECTS).

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