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Protocols

Andromeda specifications

Information


Unique identifier OMICS_19843
Name Andromeda
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 1.5.6.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • 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 citations

 (551)
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Trafficking, localization and degradation of the Na+,HCO3− co transporter NBCn1 in kidney and breast epithelial cells

2018
Sci Rep
PMCID: 5943355
PMID: 29743600
DOI: 10.1038/s41598-018-25059-7
call_split See protocol

[…] er). The raw data files were processed using MaxQuant (version 1.3.05). Data were blasted against Uniprot (http://www.uniprot.org/) human proteome dataset (release 2013_01, 87613 sequences) using the Andromeda search engine. […]

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Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

2018
Biotechnol Biofuels
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x
call_split See protocol

[…] HCD with NCE of 30, analysis in the Orbitrap at R = 15,000 with max inject time of 22 ms, and AGC target set to 2 × 105.Raw files were analyzed using MaxQuant 1.5.8.3. Spectra were searched using the Andromeda search engine against a target decoy database generated in house. As described previously [, ], label-free quantitation and match between runs were toggled on and the number of peptides meas […]

library_books

An effector from the Huanglongbing associated pathogen targets citrus proteases

2018
Nat Commun
PMCID: 5928222
PMID: 29712915
DOI: 10.1038/s41467-018-04140-9

[…] ll ratio was 1%.Peptide identification, analyses, and quantification: The raw data files were imported into MaxQuant v1.5.6.5 for label-free intensity-based quantification. The database search engine Andromeda was used to search MS/MS spectra against the C. clementina and C. sinensis databases downloaded from Phytozome with a tolerance level of 20 ppm for the first search and 6 ppm for the main se […]

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Nucleolar nucleoplasmic shuttling of TARG1 and its control by DNA damage induced poly ADP ribosylation and by nucleolar transcription

2018
Sci Rep
PMCID: 5928194
PMID: 29712969
DOI: 10.1038/s41598-018-25137-w
call_split See protocol

[…] mode; 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 1.5.1.2,) 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. Sp […]

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Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity

2018
PLoS Pathog
PMCID: 5927403
PMID: 29709033
DOI: 10.1371/journal.ppat.1006980
call_split See protocol

[…] Raw mass-spectrometry data were processed with MaxQuant software versions 1.4.1.8 and version 1.5.1.6 [] using the built-in Andromeda search engine to search against human and mouse proteomes (UniprotKB, release 2012_06) containing forward and reverse sequences, and the label-free quantitation algorithm as described previo […]

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Quantitative Tandem Affinity Purification, an Effective Tool to Investigate Protein Complex Composition in Plant Hormone Signaling: Strigolactones in the Spotlight

2018
Front Plant Sci
PMCID: 5932160
PMID: 29755490
DOI: 10.3389/fpls.2018.00528
call_split See protocol

[…] All raw files were processed with the MaxQuant software (version 1.4.1.2) (). The derived data were searched with the built-in Andromeda search engine against the Arabidopsis thaliana forward/reversed version of the TAIR10_pep_20101214 database containing also sequences of frequently observed contaminants, including human ker […]

Citations

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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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