METLIN

Last updated
METLIN Database
Content
Descriptionrepository of chemical entity information as well as tandem mass spectrometry data
Contact
Research center The Scripps Research Institute
LaboratorySiuzdak laboratory at The Scripps Research Institute
Release date2005
Access
Website metlin.scripps.edu

The METLIN Metabolite and Chemical Entity Database [1] [2] [3] is the largest repository of experimental tandem mass spectrometry [4] and neutral loss [5] data acquired from standards. The tandem mass spectrometry data on over 930,000 molecular standards (as of December, 2023) [6] [7] [8] [9] [10] is provided to facilitate the identification of chemical entities from tandem mass spectrometry experiments. In addition to the identification of known molecules, it is also useful for identifying unknowns [3] using its similarity searching technology. [11] All tandem mass spectrometry data comes from the experimental analysis of standards at multiple collision energies and in both positive and negative ionization modes.

Contents

METLIN [12] serves as a data management system to assist in metabolite and chemical entity identification by providing public access to its repository of comprehensive MS/MS and neutral loss data. [7] [3] [5] METLIN's annotated list of molecular standards include metabolites and other chemical entities, searching METLIN can be done based on a molecule's tandem mass spectrometry data, neutral loss masses, precursor mass, chemical formula, and structure within the METLIN website. Each molecule is linked to outside resources such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) for further reference and inquiry. The METLIN database was developed and is maintained solely by the Siuzdak laboratory at The Scripps Research Institute.

Constantly evolving

Since its initial implementation in the early 2000s, [2] the freely available METLIN website has collected comments and suggestions for improvements from users in the biotechnology, pharmaceutical and academic communities ultimately resulting in functionally useful technology for metabolomics as well as hundreds of thousands of other molecular entities. [7] The METLIN interface allows researchers to readily search the database and characterize metabolites and other compounds through features such as accurate mass, single and multiple fragment searching, neutral loss and full spectrum search capabilities. The similarity searching feature introduced in 2008 [11] was designed to expedite the identification process of unknown molecules.

Also, METLIN has been used to create a novel multiple reaction monitoring (MRM) library of precursor to fragment ion transitions. [13] The METLIN-MRM transition repository for small-molecule quantitative tandem mass spectrometry was designed to facilitate data sharing across different instruments and laboratories. [13]

The METLIN database is implemented in the cloud to enable users throughout the world. [7] [12] In addition to expanding the tandem mass spectrometry database, METLIN is designed to search tandem mass spectrometry data, precursor mass, chemical formulas, compound names among other search capabilities. METLIN has also been implemented with cognitive computing applications. [14] The tandem MS high-resolution ESI-QTOF MS/MS data on now over 930,000 distinct chemical entities, includes mass spectral collision-induced dissociation data at four different collision energies, in both positive and negative ionization modes. [7] [9] [15]

References

  1. Xue, Jingchuan; Guijas, Carlos; Benton, H. Paul; Warth, Benedikt; Siuzdak, Gary (October 2020). "METLIN MS 2 molecular standards database: a broad chemical and biological resource". Nature Methods. 17 (10): 953–954. doi:10.1038/s41592-020-0942-5. ISSN   1548-7105. PMC   8802982 . PMID   32839599.
  2. 1 2 Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, et al. (December 2005). "METLIN: a metabolite mass spectral database". Therapeutic Drug Monitoring. 27 (6): 747–51. doi:10.1097/01.ftd.0000179845.53213.39. PMID   16404815. S2CID   14774455.
  3. 1 2 3 Guijas C, Montenegro-Burke JR, Domingo-Almenara X, Palermo A, Warth B, Hermann G, et al. (March 2018). "METLIN: A Technology Platform for Identifying Knowns and Unknowns". Analytical Chemistry. 90 (5): 3156–3164. doi:10.1021/acs.analchem.7b04424. PMC   5933435 . PMID   29381867.
  4. Hoang, Corey; Uritboonthai, Winnie; Hoang, Linh; Billings, Elizabeth M.; Aisporna, Aries; Nia, Farshad A.; Derks, Rico J. E.; Williamson, James R.; Giera, Martin; Siuzdak, Gary (2024-03-26). "Tandem Mass Spectrometry across Platforms". Analytical Chemistry. doi: 10.1021/acs.analchem.3c05576 . ISSN   0003-2700. PMC   11007677 .
  5. 1 2 Aisporna, Aries; Benton, H. Paul; Chen, Andy; Derks, Rico J. E.; Galano, Jean Marie; Giera, Martin; Siuzdak, Gary (2022-03-02). "Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN". Journal of the American Society for Mass Spectrometry. 33 (3): 530–534. doi:10.1021/jasms.1c00343. ISSN   1044-0305. PMC   10131246 . PMID   35174708. S2CID   246902725.
  6. Giera, Martin; Yanes, Oscar; Siuzdak, Gary (2022-01-04). "Metabolite discovery: Biochemistry's scientific driver". Cell Metabolism. 34 (1): 21–34. doi: 10.1016/j.cmet.2021.11.005 . hdl: 1887/3250578 . ISSN   1550-4131. PMC   10131248 . PMID   34986335. S2CID   245729571.
  7. 1 2 3 4 5 Xue J, Guijas C, Benton HP, Warth B, Siuzdak G (August 2020). "2 molecular standards database: a broad chemical and biological resource". Nature Methods. 17 (10): 953–954. doi:10.1038/s41592-020-0942-5. PMC   8802982 . PMID   32839599.
  8. Guijas, Carlos; To, Andrew; Montenegro-Burke, J. Rafael; Domingo-Almenara, Xavier; Alipio-Gloria, Zaida; Kok, Bernard P.; Saez, Enrique; Alvarez, Nicole H.; Johnson, Kristen A.; Siuzdak, Gary (August 2022). "Drug-Initiated Activity Metabolomics Identifies Myristoylglycine as a Potent Endogenous Metabolite for Human Brown Fat Differentiation". Metabolites. 12 (8): 749. doi: 10.3390/metabo12080749 . ISSN   2218-1989. PMC   9415469 . PMID   36005620.
  9. 1 2 "The Analytical Scientist Innovation Awards 2023". The Analytical Scientist. 2023-12-12. Retrieved 2023-12-14.
  10. Heim, Wilasinee; Aisporna, Aries; Hoang, Linh; Benton, H. Paul; Siuzdak, Gary (2023), Ivanisevic, Julijana; Giera, Martin (eds.), "METLIN Tandem Mass Spectrometry and Neutral Loss Databases for the Identification of Microbial Natural Products and Other Chemical Entities" , A Practical Guide to Metabolomics Applications in Health and Disease: From Samples to Insights into Metabolism, Cham: Springer International Publishing, pp. 105–124, doi:10.1007/978-3-031-44256-8_5, ISBN   978-3-031-44256-8 , retrieved 2024-03-27
  11. 1 2 Benton HP, Wong DM, Trauger SA, Siuzdak G (August 2008). "XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization". Analytical Chemistry. 80 (16): 6382–9. doi:10.1021/ac800795f. PMC   2728033 . PMID   18627180.
  12. 1 2 Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G (September 2012). "An accelerated workflow for untargeted metabolomics using the METLIN database". Nature Biotechnology. 30 (9): 826–8. doi:10.1038/nbt.2348. PMC   3666346 . PMID   22965049.
  13. 1 2 Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Ivanisevic, Julijana; Thomas, Aurelien; Sidibé, Jonathan; Teav, Tony; Guijas, Carlos; Aisporna, Aries E.; Rinehart, Duane; Hoang, Linh; Nordström, Anders (September 2018). "XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules". Nature Methods. 15 (9): 681–684. doi:10.1038/s41592-018-0110-3. ISSN   1548-7105. PMC   6629029 . PMID   30150755.
  14. Majumder, Erica L.-W.; Billings, Elizabeth M.; Benton, H. Paul; Martin, Richard L.; Palermo, Amelia; Guijas, Carlos; Rinschen, Markus M.; Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Tagtow, Bradley A.; Plumb, Robert S. (2021-01-22). "Cognitive analysis of metabolomics data for systems biology". Nature Protocols. 16 (3): 1376–1418. doi:10.1038/s41596-020-00455-4. ISSN   1754-2189. OSTI   1774918. PMC   10357461 . PMID   33483720. S2CID   231687415.
  15. Heim, Wilasinee; Aisporna, Aries; Hoang, Linh; Benton, H. Paul; Siuzdak, Gary (2023), Ivanisevic, Julijana; Giera, Martin (eds.), "METLIN Tandem Mass Spectrometry and Neutral Loss Databases for the Identification of Microbial Natural Products and Other Chemical Entities" , A Practical Guide to Metabolomics Applications in Health and Disease: From Samples to Insights into Metabolism, Learning Materials in Biosciences, Cham: Springer International Publishing, pp. 105–124, doi:10.1007/978-3-031-44256-8_5, ISBN   978-3-031-44256-8 , retrieved 2024-03-01