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MS Amanda specifications


Unique identifier OMICS_06795
Name MS Amanda
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MS Amanda

MS Amanda in publications

PMCID: 5946477
PMID: 29747589
DOI: 10.1186/s12864-018-4730-x

[…] a. fumigatus af293 (; []) using mascot 2.4 (matrix science, uk), sequest ht and ms amanda including up to two missed tryptic cleavages, a precursor mass tolerance of 10 ppm, and a fragment mass tolerance of 0.02 da. dynamic modifications were oxidation of met and itraq labeling […]

PMCID: 5874770
PMID: 29439554
DOI: 10.3390/proteomes6010011

[…] all ms2 spectra were searched against a human reference proteome provided by uniprot knowledgebase (uniprotkb, retrieved 23 february 2017, 70,714 entries) in target/decoy mode. both sequest ht and ms amanda were used in parallel using the same parameters. precursor mass tolerance was set to 10 ppm, whereas the fragment mass tolerance was set to 0.05 da. two missed cleavages were allowed […]

PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] the sequence database search algorithm of choice. although the galaxy-deployed searchgui tool offers the use of multiple database search algorithms (e.g., ms-gf+, myrimatch, omssa, comet, myrimatch, ms-amanda and novor), x!tandem was determined to have a balance of speed and sensitivity that made it a good choice, especially for a training resource. the outputs from searchgui […]

PMCID: 5732977
PMID: 29312185
DOI: 10.3389/fmicb.2017.02475

[…] orbitrap at a resolution of 60,000 ms/ms spectra of the ten most intense precursors were detected in the ion trap., all database searches were performed using sequest algorithm (eng et al., ) and ms amanda (dorfer et al., ), both embedded in proteome discoverertm (rev. 1.4) with a database (uniprotkb december 16, 2008—v1) for the evolutionally closely related penicillium chrysogenum […]

PMCID: 5746369
PMID: 29299134
DOI: 10.18632/oncotarget.22654

[…] with activated dynamic exclusion (repeat count 1, duration 100 ms) was applied., for protein identification, proteome discoverer (version, thermo fisher scientific, bremen, germany) and the ms amanda search engine were considered. ms/ms-spectra were searched against the uniprotkb/swiss-prot database (human; including isoforms; date 04/12/2016). the following search parameters […]

MS Amanda institution(s)
Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria

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