BinBase protocols

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BinBase specifications

Information


Unique identifier OMICS_02534
Name BinBase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BinBase

BinBase in pipeline

2012
PMCID: 3380062
PMID: 22745711
DOI: 10.1371/journal.pone.0039158

[…] set which cannot subsequently be revised when “correct” features are scanned later , . many alignment tools, both commercial ones and freeware, belong to this type e.g. metalign , msfacts , openms . binbase , mathdamp , chroma , lc-mssim , xcms , specalign , met-idea ., in order to increase alignment accuracy we recently developed pad (peak alignment via density maximisation), which adopted […]


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BinBase in publications

 (59)
PMCID: 5938422
PMID: 29654173
DOI: 10.1042/BSR20180223

[…] v; temperature, 350°c. metabolite-specific parameters are detailed in supplementary table s1. untargeted metabolomics analysis was performed by gas chromatography–mass spectrometry as described []. binbase numbers [] are given for those metabolites that could not be positively identified. raw data are available at metabolomicsworkbench.org (study id: st000900). metabolomics datasets […]

PMCID: 5914012
PMID: 29685148
DOI: 10.1186/s12931-018-0776-1

[…] just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. apex masses were reported for use in the binbase algorithm. result *.txt files were exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics binbase […]

PMCID: 5911922
PMID: 29419735
DOI: 10.3390/molecules23020355

[…] were set at 230 °c and 250 °c, respectively. the primary metabolites were identified and quantified using the quantifier ions shown in . the raw mass spectra for the metabolites were processed by binbase (bb) software (fiehnlab; davis, ca, usa). the relative quantification was carried out using the peak height of each quantifier ion. the peak heights were normalized by dividing […]

PMCID: 5764261
PMID: 29324762
DOI: 10.1371/journal.pone.0190632

[…] spanning diverse chemical classes. overall, we annotated or identified [] 447 distinct metabolites, in addition to detecting many unknown metabolic signals. gc-tofms data was processed using binbase [] and lc-qtofms data using ms-dial software []. data were normalized to the sum of all identified metabolites, log transformed, pareto scaled and subjected to multivariate and univariate […]

PMCID: 5713278
PMID: 29099052
DOI: 10.3390/ijms18112309

[…] of the mass spectra, gc/tof−ms data were pre-processed by the leco chroma tof software c version (leco, st. joseph, mi, usa). the pre-processed data were further processed using an in-house library, binbase, for identification of metabolites. binbase identified metabolites by comparing mass spectra and retention indices of peaks with the reference mass spectral and retention index libraries […]


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BinBase institution(s)
Genome Center, University of California, Davis, CA, USA

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