Andromeda protocols

Andromeda computational protocol

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 (82) and quantified with the lfq algorithm (25) embedded in maxquant version (81). the fasta protein database for identification was taken from the output of the functional […]

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 andromeda55. 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 […]

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 andromeda56 and the maxlfq algorithm57, respectively, implemented in the maxquant computational proteomics platform (v1.5.1.2)58. ms2 spectra were searched against the human uniprot complete proteome […]

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

[…] 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, 2008). andromeda (cox et al, 2011) 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 [30]. about one-fourth of the human or mouse proteome (as defined by the uniprotkb database) was identified by the maxquant/andromeda analysis (table 1, s1–s3 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 […]

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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