Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry

Wandy, J., Zhu, Y., van der Hooft, J. J.J. , Daly, R. , Barrett, M. P. and Rogers, S. (2018) Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. Bioinformatics, 34(2), pp. 317-318. (doi:10.1093/bioinformatics/btx582) (PMID:28968802) (PMCID:PMC5860206)

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Abstract

Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Zhu, Mr Yunfeng and Van Der Hooft, Mr Justin and Rogers, Dr Simon and Barrett, Professor Michael and Daly, Dr Ronan and Wandy, Dr Joe
Authors: Wandy, J., Zhu, Y., van der Hooft, J. J.J., Daly, R., Barrett, M. P., and Rogers, S.
College/School:College of Medical Veterinary and Life Sciences
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Science and Engineering > School of Computing Science
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:14 September 2017
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Bioinformatics 34(2): 317-318
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
623593Institutional Strategic Support Fund (ISSF)Anna DominiczakWellcome Trust (WELLCOTR)105614/Z/14/ZRI CARDIOVASCULAR & MEDICAL SCIENCES
371799The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOTR)104111/Z/14/Z & AIII - PARASITOLOGY
680241Unifying metabolome and proteome informaticsSimon RogersBiotechnology and Biological Sciences Research Council (BBSRC)BB/L018616/1COM - COMPUTING SCIENCE
690421Glasgow Molecular Pathology (GMP) NodeKarin OienMedical Research Council (MRC)MR/N005813/1ICS - EXPERIMENTAL THERAPEUTICS