PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data

Gloaguen, Y. , Morton, F., Daly, R. , Gurden, R., Rogers, S. , Wandy, J., Wilson, D., Barrett, M. and Burgess, K. (2017) PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics, 33(24), pp. 4007-4009. (doi:10.1093/bioinformatics/btx499) (PMID:28961954) (PMCID:PMC5860087)

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Abstract

Summary: The Polyomics integrated Metabolomics Pipeline (PiMP) fulfils an unmet need in metabolomics data analysis. PiMP offers automated and user-friendly analysis from mass spectrometry data acquisition to biological interpretation. Our key innovations are the Summary Page, which provides a simple overview of the experiment in the format of a scientific paper, containing the key findings of the experiment along with associated metadata; and the Metabolite Page, which provides a list of each metabolite accompanied by ‘evidence cards’, which provide a variety of criteria behind metabolite annotation including peak shapes, intensities in different sample groups and database information. Availability: PiMP is available at http://polyomics.mvls.gla.ac.uk, and access is freely available on request. 50 GB of space is allocated for data storage, with unrestricted number of samples and analyses per user. Source code is available at https://github.com/RonanDaly/pimp and licensed under the GPL.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gurden, Mr Ross and Rogers, Dr Simon and Wandy, Dr Joe and Gloaguen, Mr Yoann and Burgess, Dr Karl and Barrett, Professor Michael and Daly, Dr Ronan and Morton, Mr Fraser
Authors: Gloaguen, Y., Morton, F., Daly, R., Gurden, R., Rogers, S., Wandy, J., Wilson, D., Barrett, M., and Burgess, K.
College/School:College of Medical Veterinary and Life Sciences
College of Medical Veterinary and Life Sciences > Institute of Cancer Sciences
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:14 August 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Bioinformatics 33(24): 4007-4009
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
617301The iomarkers in Stroke Programme; Detecting, Understanding, and Predicting Outcome After Stroke (ISSF Catalyst Fund)Jesse DawsonWellcome Trust (WELLCOTR)097821/Z/11ZRI CARDIOVASCULAR & MEDICAL SCIENCES
632234Funding SchemesAnna DominiczakWellcome Trust (WELLCOTR)105614/Z/14/ZRI CARDIOVASCULAR & MEDICAL SCIENCES
5887510BBSRC Doctoral Training Partnership 2012George BaillieBiotechnology and Biological Sciences Research Council (BBSRC)BB/J013854/1MVLS COLLEGE SENIOR MANAGEMENT
690421Glasgow Molecular Pathology (GMP) NodeKarin OienMedical Research Council (MRC)MR/N005813/1ICS - EXPERIMENTAL THERAPEUTICS