METLIN Tandem Mass Spectrometry and Neutral Loss Databases for the Identification of Microbial Natural Products and Other Chemical Entities (original) (raw)

References

1. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G., METLIN: A Metabolite Mass Spectral Database. Ther Drug Monit. 2005;27:747–51.
   CAS Google Scholar
2. Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G., An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol. 2012;30:826–8.
   CAS PubMed Google Scholar
3. Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O., Identification of small molecules using accurate mass MS/MS search. Mass Spectrom Rev. 2017; 37(4):513-532.
   Google Scholar
4. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007;35:D521–6.
   CAS PubMed Google Scholar
5. Vinaixa M, Schymanski EL, Neumann S, Navarro M, Salek RM, Yanes O., Mass spectral databases for LC/MS- and GC/MS-based metabolomics: state of the field and future prospects. TrAC Trends Anal Chem. 2016;78:23–35.
   CAS Google Scholar
6. Allen F, Greiner R, Wishart D., Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics. 2015;11:98–110.
   CAS Google Scholar
7. Duhrkop K, Shen H, Meusel M, Rousu J, Bocker S., Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A. 2015;112:12580–5.
   Google Scholar
8. Brouard C, Shen H, Duhrkop K, d'Alche-Buc F, Bocker S, Rousu J., Fast metabolite identification with Input Output Kernel Regression. Bioinformatics. 2016;32:i28–36.
   CAS PubMed Google Scholar
9. Patti GJ, Yanes O, Siuzdak G., Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol. 2012;13:263–9.
   CAS PubMed Google Scholar
10. Warth B, Spangler S, Fang M, Johnson CH, Forsberg EM, Granados A, Martin RL, Domingo-Almenara X, Huan T, Rinehart D, Montenegro-Burke JR, Hilmers B, Aisporna A, Hoang LT, Uritboonthai W, Benton HP, Richardson SD, Williams AJ, Siuzdak G., Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography–Mass Spectrometry Based Untargeted Metabolomics. Anal Chem. 2017;89:11505–13.
    CAS Google Scholar
11. Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, Ivanisevic J, Cho K, Wick EC, Hechenbleikner EM, Uritboonthai W, Goetz L, Casero RA, Pardoll DM, White JR, Patti GJ, Sears CL, Siuzdak G., Metabolism links bacterial biofilms and colon carcinogenesis. Cell Metab. 2015;21:891–7.
    CAS PubMed Google Scholar
12. Northen TR, Woo H-K, Northen MT, Nordstr­m A, Uritboonthail W, Turner KL, Siuzdak G., High surface area of porous silicon drives desorption of intact molecules. Am Soc Mass Spectrom. 2007;18(11):1945–9.
    Google Scholar
13. Robinson AR, Yousefzadeh MJ, Rozgaja TA, Wang J, Li X, Tilstra JS, Feldman CH, Gregg SQ, Johnson CH, Skoda EM, Frantz M-C, Bell-Temin H, Pope-Varsalona H, Gurkar AU, Nasto LA, Robinson RAS, Fuhrmann-Stroissnigg H, Czerwinska J, McGowan SJ, Cantu-Medellin N, Harris JB, Maniar S, Ross MA, Trussoni CE, LaRusso NF, Cifuentes-Pagano E, Pagano PJ, Tudek B, Vo NV, Rigatti LH, Opresko PL, Stolz DB, Watkins SC, Burd CE, St. Croix CM, Siuzdak G, Yates NA, Robbins PD, Wang Y, Wipf P, Kelley EE, Niedernhofer LJ., Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging. Redox Biol. 2018;17:259–73.
    Google Scholar
14. Marchetti V, Yanes O, Aguilar E, Wang M, Friedlander D, Moreno S, Storm K, Zhan M, Naccache S, Nemerow G, Siuzdak G, Friedlander M., Differential macrophage polarization promotes tissue remodeling and repair in a model of ischemic retinopathy. Sci Rep. 2011;1: 76.
    Google Scholar
15. Galmozzi A, Kok BP, Kim AS, Montonegro-Burke JR, Lee JY, Spreafico R, Mosure S, Albert V, Cintron-Colon R, Godio C, Webb WR, Conti B, Solt LA, Kojetin D, Parker CG, Peluso JJ, Pru JK, Siuzdak G, Cravatt BF, Saez E., PGRMC2 is an intracellular haem chaperone critical for adipocyte function. Nature 2019;576: 138–42.
    Google Scholar
16. Priolo C, Pyne S, Rose J, Regan ER, Zadra G, Photopoulos C, Cacciatore S, Schultz D, Scaglia N, McDunn J, De Marzo AM, Loda M., AKT1 and MYC induce distinctive metabolic fingerprints in human prostate cancer. Cancer Res. 2014;74:7198–204.
    CAS PubMed Google Scholar
17. Lim CK, Bilgin A, Lovejoy DB, Tan V, Bustamante S, Taylor BV, Bessede A, Brew BJ, Guillemin GJ., Kynurenine pathway metabolomics predicts and provides mechanistic insight into multiple sclerosis progression. Sci Rep. 2017;7:41473.
    CAS PubMed Google Scholar
18. Hocher B, Adamski J., Metabolomics for clinical use and research in chronic kidney disease. Nat Rev Nephrol. 2017;13:269–84.
    CAS PubMed Google Scholar
19. Roberts LD, Koulman A, Griffin JL., Towards metabolic biomarkers of insulin resistance and type 2 diabetes: progress from the metabolome. Lancet Diabetes Endocrinol. 2014;2:65–75.
    CAS PubMed Google Scholar
20. Armitage EG, Southam AD., Monitoring cancer prognosis, diagnosis and treatment efficacy using metabolomics and lipidomics. Metabolomics. 2016;12:146.
    PubMed Google Scholar
21. Warth B, Raffeiner P, Granados A, Huan T, Fang M, Forsberg EM, Benton HP, Goetz L, Vogt P, Johnson CH, Siuzdak G., Metabolomics Reveals that Dietary Xenoestrogens Alter Cellular Metabolism Induced by Palbociclib/Letrozole Combination Cancer Therapy. Cell Chem Biol. 2018;25(3):291–300.e3..
    Google Scholar
22. Yanes O, Clark J, Wong DM, Patti GJ, Sanchez-Ruiz A, Benton HP, Trauger SA, Desponts C, Ding S, Siuzdak G. Nat Chem Biol., Metabolic oxidation regulates embryonic stem cell differentiation. 2010;6:411–7.
    CAS Google Scholar
23. Beyer BA, Fang M, Sadrian B, Montenegro-Burke JR, Plaisted WC, Kok BPC, Saez E, Kondo T, Siuzdak G, Lairson LL., Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation. Nat Chem Biol. 2018;14:22–8.
    CAS PubMed Google Scholar
24. Guijas C, Montenegro-Burke JR, Warth B, Spilker ME, Siuzdak G., Metabolomics activity screening for identifying metabolites that modulate phenotype. Nat Biotechnol. 2018;36:316–20.
    CAS PubMed Google Scholar
25. Aisporna A, Benton HP, Chen A, Derks RJE, Galano JM, Giera M, Siuzdak G., Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in METLIN. JASMS. 2022;33:530–4.
    CAS Google Scholar
26. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006;78:779–87.
    Article CAS PubMed Google Scholar
27. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G., Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. PNAS. 2009;106:3698–703.
    CAS PubMed Google Scholar
28. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–20.
    Article PubMed Google Scholar
29. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3:213–23.
    Article CAS PubMed PubMed Central Google Scholar
30. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122:107–18.
    Article CAS PubMed Google Scholar
31. Alverdy JC, Chang EB. The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away. J Leukoc Biol. 2008;83:461–6.
    Article CAS PubMed Google Scholar
32. Frank DN, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104:13780–5.
    Article CAS PubMed PubMed Central Google Scholar
33. Hord NG. Eukaryotic-microbiota crosstalk: potential mechanisms for health benefits of prebiotics and probiotics. Annu Rev Nutr. 2008;28:215–31.
    Article CAS PubMed Google Scholar
34. Zaneveld J, et al. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008;12:109–14.
    Article CAS PubMed PubMed Central Google Scholar
35. Gill SR, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–9.
    Article CAS PubMed PubMed Central Google Scholar
36. Turnbaugh PJ, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–31.
    Article PubMed Google Scholar
37. Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A. 2008;105:13580–5.
    Article CAS PubMed PubMed Central Google Scholar
38. Karbownik M, Reiter RJ, Garcia JJ, Cabrera J, Burkhardt S, Osuna C, Lewinski A. Indole-3-propionic acid, a melatonin-related molecule, protects hepatic microsomal membranes from iron-induced oxidative damage: relevance to cancer reduction. J Cell Biochem. 2001;81:507–13.
    Article CAS PubMed Google Scholar
39. Elsden SR, Hilton MG, Waller JM. The end products of the metabolism of aromatic amino acids by clostridia. Arch Microbiol. 1976;107:283–8.
    Article CAS PubMed Google Scholar
40. Young SN, Anderson GM, Gauthier S, Purdy WC. The origin of indoleacetic acid and indolepropionic acid in rat and human cerebrospinal fluid. J Neurochem. 1980;34:1087–92.
    Article CAS PubMed Google Scholar
41. Siuzdak G, Ichikawa Y, Caulfield TJ, Munoz B, Wong C-H, Nicolaou KC. Evidence of calcium(2+)-dependent carbohydrate association through ion spray mass spectrometry. J Am Chem Soc. 1993;115:2877–81.
    Article CAS Google Scholar
42. Chatman K, Hollenbeck T, Hagey L, Vallee M, Purdy R, Weiss F, Siuzdak G. Nanoelectrospray mass spectrometry and precursor ion monitoring for quantitative steroid analysis and Attomole sensitivity. Anal Chem. 1999;71:2358–63.
    Article CAS PubMed Google Scholar
43. Go EP, Uritboonthai W, Apon JV, Trauger SA, Nordstrom A, O'Maille G, Brittain SM, Peters EC, Siuzdak G. Selective metabolite and peptide capture/mass detection using fluorous affinity tags. J Proteome Res. 2007;6:1492–14999.
    Article CAS PubMed PubMed Central Google Scholar
44. Benton HP, Wong DM, Trauger SA, Siuzdak G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem. 2008;80:6382–9.
    Article CAS PubMed PubMed Central Google Scholar
45. Xue J, Guijas C, Benton HP, Warth B, Siuzdak G. METLIN MS2 molecular standards database; a broad chemical and biological resource. Nat Methods. 2020;17:953–4.
    Article CAS PubMed PubMed Central Google Scholar

Download references