METLIN: A Technology Platform for Identifying Knowns and Unknowns

By Carlos Guijas, J. R. Montenegro-Burke, Xavier Domingo-Almenara, Amelia Palermo, B. Warth, G. Hermann, G. Koellensperger, T. Huan, Winnie Uritboonthai, A. Aisporna and 4 more. Analytical Chemistry, 2018

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METLIN originated as a database to characterize known metabolites and has since expanded into a technology platform for the identification of known and unknown metabolites and other chemical entities. Through this effort it has become a comprehensive resource containing over 1 million molecules including lipids, amino acids, carbohydrates, toxins, small peptides, and natural products, among other classes. METLIN’s high-resolution tandem mass spectrometry (MS/MS) database, which plays a key role in the identification process, has data generated from both reference standards and their labeled stable isotope analogues, facilitated by METLIN-guided analysis of isotope-labeled microorganisms. The MS/MS data, coupled with the fragment similarity search function, expand the tool’s capabilities into the identification of unknowns. Fragment similarity search is performed independent of the precursor mass, relying solely on the fragment ions to identify similar structures within the database. Stable isotope data also facilitate characterization by coupling the similarity search output with the isotopic m/z shifts. Examples of both are demonstrated here with the characterization of four previously unknown metabolites. METLIN also now features in silico MS/MS data, which has been made possible through the creation of algorithms trained on METLIN’s MS/MS data from both standards and their isotope analogues. With these informatic and experimental data features, METLIN is being designed to address the characterization of known and unknown molecules.

Subfields: Ecology, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/4fb41059a32dada3130aae1566c01404c2a434df

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Citations in the corpus

Review on natural products databases: where to find data in 2020 (2020, background): “It is a comprehensive resource containing over 1 million molecules including primary metabolites, toxins, small peptides, and NPs. METLIN’s high-resolution tandem mass spectrometry (MS/MS) database, which plays a key role in the identification process, has data generated from both reference standard”
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics (2018, methodology): “NIST EI-MS, CID-MS/MS Curated DB, graphical interface WILEY EI-MS, CID-MS/MS Largest collection of EI-MS data METLIN [51] CID-MS/MS Developed for QTOF instruments MoNA EI, MS/MS, MSn Autocurated collection of spectra MassBank [52] EI, MS/MS, MSn Longest standing community database mzCloud [53] MSn M”
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, methodology): “MetaboAnalyst compares favorably with XCMS Online in several aspects including optimized raw data processing and downstream statistical and functional analysis, while XCMS Online excels in compound annotations based on the METLIN database (61).”
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics (2020, methodology): “…work will also implement workflows in Skyline to support fragmentation libraries of small molecules, such as Metlin (http://metlin.scripps.edu/) 47, 48 , MassBank 49 , the Human Metabolome Database (HMDB, http://www.hmdb.ca/) 50, 51 and the National Institute of Standards and Technology…”