METLIN MS2 molecular standards database: a broad chemical and biological resource

@article{Xue2020METLINMM,
  title={METLIN MS2 molecular standards database: a broad chemical and biological resource},
  author={Jingchuan Xue and Carlos Guijas and H. Paul Benton and Benedikt Warth and Gary Siuzdak},
  journal={Nature Methods},
  year={2020},
  pages={1 - 2}
}
To the Editor — Tandem mass spectrometry (MS2) data provide high-confidence molecular identification of known molecules and preliminary characterization of novel, unknown molecules (unknowns). However, for databases to be an effective resource, broad chemical space coverage is necessary. Consequently, we have created METLIN (http://metlin.scripps.edu) a highly annotated and structurally diverse database of over 850,000 molecular standards. METLIN’s tandem mass spectral library numerically… 

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References

SHOWING 1-10 OF 10 REFERENCES

METLIN: A Technology Platform for Identifying Knowns and Unknowns.

METLIN 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, being designed to address the characterization of known and unknown molecules.

XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization.

XCMS(2) is an open source software package which has been developed to automatically search tandem mass spectrometry (MS/MS) data against high quality experimental MS/MS data from known metabolites contained in a reference library (METLIN).

Mass spectrometry searches using MASST

A webenabled mass spectrometry (MS) search engine, named Mass Spectrometry Search Tool (MASST), is introduced by enabling searches of all small-molecule tandem MS (MS/MS) data in public metabolomics repositories, it is proposed that MASST will unlock these resources for clinical, environmental and natural product applications.

HMDB 4.0: the human metabolome database for 2018

This year's update to the HMDB, HMDB 4.0, represents the most significant upgrade to the database in its history and should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.

Enhanced In-source Fragmentation Annotation Enables Novel Data Independent Acquisition and Autonomous METLIN Molecular Identification.

Enhanced ISF allowed for eISA to be used as a more sensitive alternative to other QTOF DIA and DDA approaches, and further, it enables the acquisition of ESI TOF and ESI single quadrupole mass spectrometry instrumentation spectra with improved molecular identification confidence.

Stable Isotope-Assisted Metabolomics for Deciphering Xenobiotic Metabolism in Mammalian Cell Culture

A workflow based on stable isotope-assisted metabolomics and the bioinformatics tool MetExtract II is presented for deciphering xenobiotic metabolites produced by human cells and allows the untargeted elucidation of human xenobiotics products in tissue culture.

An accelerated workflow for untargeted metabolomics using the METLIN database

Although relatively new compared to its genomic and proteomic predecessors, metabolomics has led to the discovery of biomarkers for disease, fundamental insights into cellular biochemistry, and clues related to disease pathogenesis.

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

It is found that individuals having high predose urinary levels of p-cresol sulfate had low postdose urinary ratios of acetaminophen sulfate toacetaminophen glucuronide, and this finding has important implications for certain diseases as well as for the variable responses induced by many different drugs and xenobiotics.

Global chemical effects of the microbiome include new bile-acid conjugations

It is found that the microbiota affects the chemistry of all organs, including amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic Acid, which have not previously been characterized despite extensive research on bile-acid chemistry.

Multiplexed Mass Spectrometry of Individual Ions Improves Measurement of Proteoforms and Their Complexes

Charge assignment for individual ions unlocks complex mixtures of proteoforms and their assemblies by native mass spectrometry, revealing information not obtainable by typical measurements of ensembles of ions.