Journal
BIOINFORMATICS
Volume 35, Issue 20, Pages 4089-4097Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz207
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Funding
- Generalitat de Catalunya [FI-DGR 2014]
- Ministry of Economy and Competitiveness of Spain [FIS2013-47532-C3-1-P, FIS2016-78904-C3-1-P, BFU201457466-P, BES-2012-052585 (SAF2011-30578)]
- Ministerio de Ciencia e Innovacion [SAF2011-28331]
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), an initiative of Instituto de Investigacion Carlos III (ISCIII)
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Motivation: The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample. Results: Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generative model; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools.
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