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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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METLIN 960 K: An Empirical Tandem Mass Spectrometry Data Resource.

Winnie Uritboonthai1, Aries E Aisporna1, Linh Hoang1

  • 1Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Analytical Chemistry
|April 21, 2026
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The METLIN 960 K platform now offers the largest collection of over 960,000 experimentally acquired small-molecule tandem mass spectrometry (MS/MS) spectra. This comprehensive, standardized database aids in high-confidence metabolite identification for mass spectrometry workflows.

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Area of Science:

  • Analytical Chemistry
  • Metabolomics
  • Biochemistry

Background:

  • Mass spectrometry (MS/MS) is crucial for identifying small molecules.
  • Existing spectral databases lack scale and standardization, hindering accurate identification.
  • The METLIN database has been expanded to address these limitations.

Purpose of the Study:

  • To introduce the reengineered METLIN 960 K platform, the largest public collection of experimentally acquired MS/MS spectra.
  • To provide a standardized, high-resolution MS/MS dataset for over 960,000 molecular standards.
  • To enhance metabolite annotation and quantitative method development in mass spectrometry.

Main Methods:

  • Implemented a high-throughput experimental framework using acoustic droplet ejection and LC-MS/MS.
  • Acquired MS/MS spectra for 960,000+ authentic standards under controlled conditions.
  • Generated data across positive/negative ionization modes and four collision energies (0-40 eV).

Main Results:

  • Established METLIN 960 K as the largest public empirical MS/MS database (>960,000 spectra).
  • Ensured standardized data acquisition for reproducible spectral comparison and machine learning.
  • Provided empirically derived MRM transitions for quantitative analysis.
  • Developed an enhanced interface for efficient querying and access to curated spectra and metadata.

Conclusions:

  • METLIN 960 K significantly advances small-molecule identification in mass spectrometry.
  • The standardized, large-scale dataset supports high-confidence annotation for untargeted and targeted workflows.
  • The platform facilitates reproducible research and the development of new analytical methods.