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PUTMEDID-LCMS specifications


Unique identifier OMICS_06043
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


No version available

Publication for PUTMEDID-LCMS



Identification of the functional pathways altered by placental cell exposure to high glucose: lessons from the transcript and metabolite interactome

Sci Rep
PMCID: 5869594
PMID: 29588451
DOI: 10.1038/s41598-018-22535-y

[…] relative quantification; chromatographic peaks were used to define the individual metabolic features and these features were matched according to accurate mass of metabolites by applying the software PUTMEDID_LCMS. Putative (MSI level 2) and definitive identifications (MSI level 1) are reported.Full details of the Gas Chromatography-Mass Spectrometry (GC-MS) analysis process are given in supplemen […]


Exercise and high fat feeding remodel transcript metabolite interactive networks in mouse skeletal muscle

Sci Rep
PMCID: 5647435
PMID: 29044196
DOI: 10.1038/s41598-017-14081-w

[…] of 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 Wilcoxon–Mann […]


Adipose tissue and metabolic and inflammatory responses to stroke are altered in obese mice

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

[…] metabolite 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 […]


Navigating freely available software tools for metabolomics analysis

PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] ng online metabolite databases (HMDB (Wishart et al. ), METLIN (Smith et al. ), KEGG (Kanehisa et al. , etc.) or automatically using dedicated software tools including: MI-PACK (Weber and Viant ) and PUTMEDID-LCMS (Brown et al. ). Transformation mapping is used by metabolite identification package (MI-PACK) (Weber and Viant ) to putatively annotate metabolites by their interconnectivity in the KEG […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

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

[…] e 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 that is then ma […]


Stimulatory Effects of Acibenzolar S Methyl on Chlorogenic Acids Biosynthesis in Centella asiatica Cells

Front Plant Sci
PMCID: 5040108
PMID: 27733862
DOI: 10.3389/fpls.2016.01469

[…] nting 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 (; ). […]


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


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