XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

Small molecule quantitative tandem mass spectrometry analysis(1) is now widely used in life sciences and medicine. Quantification is usually accomplished by prior fragmentation of standard materials and the use of commercial software to quantitate the resulting peaks(2,3). Despite its widespread application, there is a paucity of public libraries to expedite assay development. Here, we introduce a new library, METLIN-MRM, comprised of more than 15,500 optimized transitions for multiple reaction monitoring of a wide variety of low molecular weight compounds. METLIN-MRM includes (i) transitions optimized following the established protocol with standard materials and (ii) transitions computationally optimized for selectivity. This computational optimization was achieved by the analysis of a large collection of tandem mass spectrometry spectra, where an algorithm selected the most unique transitions for a given compound in comparison with other compounds with a mass within the error of the mass spectrometer. METLIN-MRM streamlines quantitative analyses with minimal resources and development time and also serves as a public repository, allowing the community to upload, share and cite experimental transitions through accession numbers. Additionally, this library has been integrated with XCMS-MRM, a cloud-based data analysis platform that allows for data analysis and sharing across different platforms and laboratories. This platform is publicly accessible at http://metlin.scripps.edu/ and http://xcmsonline-mrm.scripps.edu