mWISE: An Algorithm for Context-Based Annotation of Liquid Chromatography-Mass Spectrometry Features through Diffusion in Graphs
Por:
Barranco-Altirriba, M, Sola-Santos, P, Picart-Armada, S, Kanaan-Izquierdo, S, Fonollosa, J, Perera-Lluna, A
Publicada:
10 ago 2021
Ahead of Print:
1 jul 2021
Resumen:
Untargeted metabolomics using liquid chromatography coupled to mass spectrometry (LC-MS) allows the detection of thousands of metabolites in biological samples. However, LC-MS data annotation is still considered a major bottleneck in the metabolomics pipeline since only a small fraction of the metabolites present in the sample can be annotated with the required confidence level. Here, we introduce mWISE (metabolomics wise inference of speck entities), an R package for context-based annotation of LC-MS data. The algorithm consists of three main steps aimed at (i) matching mass-to-charge ratio values to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, (ii) clustering and filtering the potential KEGG candidates, and (iii) building a final prioritized list using diffusion in graphs. The algorithm performance is evaluated with three publicly available studies using both positive and negative ionization modes. We have also compared mWISE to other available annotation algorithms in terms of their performance and computation time. In particular, we explored four different configurations for mWISE, and all four of them outperform xMSannotator (a state-of-the-art annotator) in terms of both performance and computation time. Using a diffusion configuration that combines the biological network obtained from the FELLA R package and raw scores, mWISE shows a sensitivity mean (standard deviation) across data sets of 0.63 (0.07), while xMSannotator achieves a sensitivity of 0.55 (0.19). We have also shown that the chemical structures of the compounds proposed by mWISE are closer to the original compounds than those proposed by xMSannotator. Finally, we explore the diffusion prioritization separately, showing its key role in the annotation process. mWISE is freely available on GitHub (https://github.com/b2slab/mWISE) under a GPL license.
Filiaciones:
Barranco-Altirriba, M:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
Hosp Santa Creu & Sant Pau, Dept Endocrinol & Nutr, Barcelona 08041, Spain
Inst Invest Biomed St Pau IIB St Pau, Barcelona 08041, Spain
Sola-Santos, P:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
Picart-Armada, S:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
Kanaan-Izquierdo, S:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
Fonollosa, J:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
Perera-Lluna, A:
Univ Politecn Cataluna, Dept Engn Sistemes Automat & Informat Ind, B2SLab, Barcelona 08028, Spain
Networking Biomed Res Ctr Subject Area Bioengn Bi, Madrid 28029, Spain
Inst Recerca St Joan de Deu, Barcelona 08950, Spain
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