MetAlign protocols

View MetAlign computational protocol

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MetAlign specifications

Information


Unique identifier OMICS_02383
Name MetAlign
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Arjen Lommen <>

Publications for MetAlign

MetAlign in pipelines

 (4)
2017
PMCID: 5337870
PMID: 28303155
DOI: 10.1155/2017/1919474

[…] and the same concentration of 1 mg/ml. ms spectra were acquired in positive mode and for the metabolomic analysis; the mass signals obtained from raw data files were extracted and aligned within 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 […]

2014
PMCID: 4180160
PMID: 25279237
DOI: 10.5213/inj.2014.18.3.106

[…] samples taken from the ic patients and normal (control) subjects., several statistical tools are currently used to analyze nmr and ms-based metabolomics datasets, which include xcms, mzmine, metalign, mathdamp, and lcmstats. for nmr data analysis, the significantly altered nmr peaks can be identified by using a probabilistic approach called bayesian quantification (bquant) [], […]

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

[…] provided by all the instrument manufacturers, and it is also possible to rely on cross-platform solutions like the open-source mzmine (pluskal et al., ) and openms (sturm et al., ) or the freeware metalign (lommen, )., some of these approaches have a graphical user interface; others can be implemented in graphical software suites or web-based interfaces to make them easily accessible […]

2012
PMCID: 3901240
PMID: 24957762
DOI: 10.3390/metabo2040775

[…] value (or area under the peak), which indicates its relative abundance in the sample. overall, this complexity imposes the implementation of metabolomic softwares such as xcms [], mzmine [] or metalign [] that can provide automatic methods for peak picking, retention time alignment to correct experimental drifts in instrumentation, and relative quantification. as a result, […]


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MetAlign in publications

 (101)
PMCID: 5946010
PMID: 29780370
DOI: 10.3389/fmicb.2018.00857

[…] 76°c and finally 6°c/min to 350°c, held for 1 min. the transfer line to the mass spectrometer was set to 250°c. gas chromatography-mass spectrometry data were subjected to baseline correction using metalign (); chromatographic deconvolution and quantification of compounds was done using tagfinder (). using this latter program, a retention time index (ri) was calculated from the added n-alkanes. […]

PMCID: 5893800
PMID: 29670599
DOI: 10.3389/fmicb.2018.00628

[…] fisher scientific inc., san josé, ca), respectively. the obtained (*.cdf) data files were subjected to data pre-processing for retention time, normalized peak intensities, and accurate masses using metalign software package (http://www.metalign.nl), and the alignment data were exported to excel format. the multivariate statistical analysis for aligned metabolic profiling data was carried […]

PMCID: 5825098
PMID: 29474408
DOI: 10.1371/journal.pone.0193335

[…] co, usa) and openchrom community edition synge (version 0.6.0) (peter wenig; http://www.openchrom.net). gc–ms data integration, normalization (total signal) and alignment were performed using the metalign software (pri-rikilt, wageningen, the netherlands). statistical analysis was performed using a one-way anova across all time points and p conditions. metabolite differences were finally […]

PMCID: 5811519
PMID: 29479360
DOI: 10.3389/fpls.2018.00112

[…] that require both storage and data processing tools (reduction of data complexity) (; ; ). this can be achieved by using free statistical tools such as marvis1, mzine, xcms, maven, metaboanalyst, metalign () as well as commercial software such as markerlynx (waters), profiling solutions (shimadzu), mass profiler pro (agilent) and metabolic profiler (bruker). such tools focus on homogenous […]

PMCID: 5695601
PMID: 29117187
DOI: 10.1371/journal.pone.0187154

[…] converted into netcdf format (*.cdf) using masslynx databridge (version 4.1; waters corp.). after conversion, the peak detection, retention time correction, and alignment were processed using the metalign software package (http://www.metalign.nl). the resulting data were exported to an excel file. multivariate statistical analysis was conducted using simca-p+ (version 12.0, umetrics; umea, […]


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MetAlign institution(s)
RIKILT-Institute of Food Safety, Wageningen, Netherlands
MetAlign funding source(s)
Supported by the Dutch Ministry of Agriculture, Nature and Food Quality, Strategic Research Funds RIKILT-WUR (project 1217269301) and The Netherlands Toxicogenomics Centre (NTC) (project 05060510)—Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research (NWO).

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