MSClust protocols

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MSClust specifications

Information


Unique identifier OMICS_01954
Name MSClust
Alternative name Multi-Seeds based Clustering algorithm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Multi-Seeds based Clustering algorithm

MSClust in pipelines

 (2)
2017
PMCID: 5337870
PMID: 28303155
DOI: 10.1155/2017/1919474

[…] the metalign software program, with a final alignment of 5592 mass signals. subsequently, the signals belonging to the same molecules, isotopes, fragments, and adducts, were regrouped using the msclust software, resulting in 67 reconstructed metabolites. the molecular formulas of the major compounds were determined by peaks obtained by the mass spectrometer, taking into account the elements […]

2014
PMCID: 4267269
PMID: 25566535
DOI: 10.3389/fbioe.2014.00072

[…] xcms with isa-tab (gonzález-beltrán et al., )., also, feature grouping can be performed by different algorithms, e.g., the correlation-based r package camera (kuhl et al., ) and the clustering-based msclust software (tikunov et al., )., the association of (groups of) experimental features to specific metabolites is commonly referred as “annotation” and it is, most likely, the biggest challenge […]


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MSClust in publications

 (21)
PMCID: 5653705
PMID: 29104520
DOI: 10.1007/s11306-017-1284-x

[…] than three rils or lower than 35 were discarded. remaining peaks below background were randomized from 50 to 100%. out of all the remaining mass signals (5601), centrotypes were formed using the msclust program (tikunov et al. ) with the following parameters: correlation threshold at 0.9 with 0.01 margin softness; pdf correlation of 0.8 with margin of 0.02; a peak width of 20 with a margin […]

PMCID: 5688192
PMID: 29046998
DOI: 10.1007/s11103-017-0665-x

[…] and further baseline correction, accurate mass calculation, data smoothing and noise reduction, followed by alignment between chromatograms were performed using the metalign software (lommen ). msclust was used to remove metabolite signal redundancy in aligned mass peaks tables and to retrieve mass spectral information of metabolites using mass peak clustering (tikunov et al. ). the mass […]

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] camera or by the allocatorsd algorithm, which is optimized for dealing with the particularities of 13c labeled data by grouping mirrored isotopes (lighter isotopologues from the feeding experiment). msclust [] has the same general features as the others, but it was developed in the c++ language and it is optimized to work with the output files of metalign. ramclustr [] was developed in matlab […]

PMCID: 5486769
PMID: 28508929
DOI: 10.1007/s00497-017-0301-6

[…] signal was subtracted to the estimated noise signal. compound mass spectra and quantitative ions were extracted from the modified metalign outputs using a method described in tikunov et al. () by msclust software (available from www.metalign.nl). msclust output was reduced by keeping compounds that were quantitatively present in all the replicates of one of the experimental treatments: heat […]

PMCID: 5421760
PMID: 28481937
DOI: 10.1371/journal.pone.0176978

[…] meja, and sa., the netcdf files were obtained from chromatof software 4.50.8.0 chromatography version (leco corporation, usa) gc-ms were further analysed using metalign 3.0 (www.metalign.nl) [] and msclust [] software with a signal to noise ratio of ≥ 2, for baseline correction, noise estimation, alignment and extraction of ionwise mass signal. the mass signals that were present in <3 […]


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MSClust institution(s)
College of Automation, Northwestern Polytechnical University, XI'an, China; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Keck Biotechnology Laboratory, Biostatistics Resource, Yale School of Medicine, New Haven, CT, USA
MSClust funding source(s)
This work was supported in part by NIH GM59507, UL1 RR024139, National Natural Science Foundation of China (No. 61170134), Aeronautical Science Foundation of China (No.20100853010) and Doctorate Foundation of Northwestern Polytechnical University (No. cx201017).

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