PUTMEDID-LCMS protocols

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PUTMEDID-LCMS specifications

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Unique identifier OMICS_06043
Name PUTMEDID-LCMS
Software type Framework/Library
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 PUTMEDID-LCMS

PUTMEDID-LCMS in pipeline

2017
PMCID: 5665457
PMID: 28798136
DOI: 10.1242/dmm.030411

[…] features with an rsd >20% or with greater than 30% missing values for qc samples being removed from the dataset prior to data analysis. metabolite annotation was performed by applying the putmedid_lcms workflow as previously described (). all metabolite annotations are reported at level 2 according to msi reporting standards (). the processed data was analysed in r with the univariate […]


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PUTMEDID-LCMS in publications

 (7)
PMCID: 5647435
PMID: 29044196
DOI: 10.1038/s41598-017-14081-w

[…] samples were removed prior to univariate and multivariate data analysis as described previously. all metabolite features were annotated according to level 2 of the msi reporting standards applying putmedid_lcms, as previously described. the processed data were analysed in r applying the unsupervised multivariate principal components analysis (pca) and the univariate non-parametric […]

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

[…] output of camera as input and searches against 4 major metabolite databases, the human metabolome database (hmdb), madison metabolomics consortium database (mmcd), metlin, and lipidmaps. similarly, putmedid-lcms [], developed in the taverna workflow management system, also integrates a step of compound mass spectra extraction to define a molecular formula from high-resolution m/z […]

PMCID: 5040108
PMID: 27733862
DOI: 10.3389/fpls.2016.01469

[…] any possible metabolite were computed and searched on online databases such as chemspider, dictionary of natural products, knapsack as well as the taverna work-bench. the latter is based on the putmedid_lcms metabolite identification workflows that entail correlation analysis, metabolic feature annotation and metabolite annotation (; )., in this study, a semi-targeted (with the focus […]

PMCID: 4644200
PMID: 26594136
DOI: 10.1007/s11306-015-0878-4

[…] that crossed the 20 % rsd threshold within qc samples across the analytical run. data was normalised on the basis of fresh weight biomass. identification of lipid features was performed applying the putmedid-lcms set of workflows as previously described (brown et al. ). neutral lipids were also measured by nile red fluorescence staining as described previously (chen et al. ; dean et al. ). day […]

PMCID: 3909234
PMID: 24498209
DOI: 10.1371/journal.pone.0087846

[…] joseph, mi, usa) was used for automated data analysis from preprocessing to the compound identification step., selected mass ions from s- and vip plots were annotated using the taverna workbench for putmedid_lcms metabolite id workflows (www.taverna.org.uk). the taverna workflows allow for integrated, automated and high-throughput annotation and putative metabolite identification from esi-lc-ms […]


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PUTMEDID-LCMS institution(s)
School of Biomedicine, The University of Manchester, Manchester, UK

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