Mass Spectrometry Metabolite Library Protocol

Supplied by IROA Technologies

Catalog Number MSMLS
Storage Temperature -20 ⁰C

Product Description

MSMLS (Mass Spectrometry Metabolite Library) is a collection of high quality small biochemical molecules that span a broad range of primary metabolism. These are high purity (>95%) compounds supplied in an economical, ready-to-use format.

The library is most commonly used to provide retention times and spectra for key metabolic compounds, help optimize analytical mass spectrometry protocols, and qualify and quantify mass spectrometry sensitivity and limit of detection.

MSMLS comes with MSMLSDiscovery™, a software tool to support the extraction, manipulation, and storage of the data generated when using the MSMLS. For further information on the software, to download, and for manual and video links please visit: MSMLS


MSMLS contains over 600 unique small molecule metabolites, conveniently provided at 5 μg per well, enough for multiple injections, suitable for manual and automated workflow.

The Library is intended to be used for mass spectrometry metabolomics applications and provides a broad representation of primary metabolism.

Occasionally the plate map will change due to the availability of compounds. Although we try to make sure the compounds of each row have distinct molecular weights and can be multiplexed, users should refer to the plate map before proceeding.

The plate map contains descriptors and represents information gathered from multiple databases. We try to ensure the accuracy of the data but it may contain errors. We suggest that the information provided is carefully reviewed. To help build a better database, please report any discrepancies.

MSMLS includes:

  • 7 polypropylene plates in 96 well format
  • 5 μg (dried weight) of each metabolite
  • Polypropylene deepwell (1.2 mL, total volume per well) plates (MasterBlock, Greiner #780215) in combination with seals (VIEWseal, Greiner #676070)
  • Plate map
  • Alphanumeric assigned position


  • Name
  • Parent CID
  • KEGG ID where available or ChemSpider ID
  • molecular formula
  • molecular weight
  • CAS
  • ChEBI
  • PubChem Compound and Substance ID
  • Metlin ID

Precautions and Disclaimer

This product is for R&D use only, not for drug, household, or other uses. Please consult the Safety Data Sheet for information regarding hazards and safe handling practices.

Product Profile

The compounds of the MSMLS can either be used as standards and injected individually, or mixed in such a way that the entire library may be examined with reasonable efficiency. Mixing compounds by row mixtures allows multiple compounds to be analyzed per injection. Be sure to check the plate map to ensure you can adequately separate the compounds using your chromatographic system prior to pooling. Note that plate 6 contains water soluble sugar compounds, which have masses too close in range to inject together.

The following are only suggestions and depend on user chromatography and instrumentation.

  1. Individual Injections As standards, each well represents a single compound. The entire library may be examined in great detail with 612 injections, one for each of the unique metabolites (Total volumes for each well of 250 μL–1 mL may be considered).
  2. Simple multiplex injections If the rows of each plate are pooled, then the entire collection may be analyzed with 56 injections of simple mixtures (Keep the total volume for each well to 500 μL or less to prevent loss due to dilution). Be sure to check the individual masses across plate rows to ensure these compounds can be separated with the chromatographic system employed.
  3. Complex multiplex injections If the rows across all plates are pooled, then the entire library may be analyzed with 8 injections, but the mixtures will be complex and may be dilute (Keep the total volume for each well to 200 μL or less to prevent loss due to dilution).

Preparation Instructions

The following are suggestions and dependent on user chromatography and instrumentation.

Plates 1-5: Add 5% of final volume (up to 20 μL) of high purity methanol (MeOH) to every well of every plate. Add ultrapure water to make up the desired volume. The addition of water ensures the solubilization of the more polar compounds. A final 5% methanol solution is suggested. Pipette liquid up and down in the well 2-3 times to facilitate solubilization.

Plates 6 and 7: These plates contain primarily lipid-like compounds (with the exception of the water soluble sugar compounds in plate 6). It is recommended to solubilize these compounds in a solvent with a 1:1:0.3 ratio of chloroform:methanol:water.

Pool compounds for multiplexing. Again, be sure to check the plate map to ensure you can adequately separate the compounds using your chromatographic system prior to pooling.

Note: There are 34 “duplicate” compounds for QC/QA purposes. Some pairs differ in salt and/or hydration form or CAS number.


Store plates at -20 °C. Once diluted the plates should be resealed and kept at -20 °C or -80 °C for long-term storage protected from moisture and light. Avoid repeated freeze/thaw cycles. 

Legal Information

MSMLS and MSMLSDiscovery are trademarks of IROA Technologies, LLC.




  1. Wishart, D.S. et al., HMDB: the Human Metabolome Database. Nucleic Acids Res., 2007 Jan; 35 (Database issue):D521-6. 17202168.
  2. Wishart, D.S. et al., HMDB: a knowledge base for the human metabolome. Nucleic Acids Res., 2009 37 (Database issue):D603-610. 18953024.
  3. Wishart, D.S. et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res., 2013. Jan 1;41(D1):D801-7. 23161693
  4. Hastings, J. et al., The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res., 2013.
  5. Kanehisa, M., and Goto, S., "KEGG: Kyoto Encyclopedia of Genes and Genomes". Nucleic Acids Res., 2000 28 (1): 27– 30. doi:10.1093/nar/28.1.27. PMC 102409.PMID 10592173.
  6. Tautenhahn, R. et al., An accelerated workflow for untargeted metabolomics using the METLIN database. Nature Biotechnology, 2012 30: 826–828. doi:10.1038/nbt.2348.
  7. Smith, C.A. et al., METLIN: a metabolite mass spectral database. The Drug Monit., 2005 27 (6): 747–51. doi:10.1097/01.ftd.0000179845.53213.39. PMID 16404815.
  8. Bolton, E. et al., PubChem: Integrated Platform of Small Molecules and Biological Activities. Chapter 12 IN Annual Reports in Computational Chemistry, Volume4, American Chemical Society, Washington, DC. 2008 Apr [free author manuscript]
  9. YMDB 2.0: A Significantly Expanded Version of the Yeast Metabolome Database. Ramirez-Guana M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Y, Arndt D and Wishart DS. Nucleic Acids Res. 2016
  10. YMDB: The Yeast Metabolome Database. Jewison T, Neveu V, Lee J, Knox C, Liu P, Mandal R, Murthy RK, Sinelnikov I, Guo AC, Wilson M, Djoumbou Y and Wishart DS. Nucleic Acids Res. 2012 Jan;40(Database ussue):D815-20 PubMed: 22064855


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