Precision mapping of the metabolome

Abstract

The global study of the structure and dynamics of metabolic networks has been hindered by a lack of techniques that identify metabolites and their biochemical relationship in complex mixtures. The recent application of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to metabolomic analysis suggests a way to tackle the problem. A lower-cost alternative to high-field FTICR-MS, the Orbitrap mass analyzer, promises accelerated activity in this area. Here, we show how the ultra-high mass accuracy and resolution provided by this new generation of mass spectrometers can help to identify metabolites and connect them into metabolic networks. Data from perturbation studies and isotope-tracking experiments can complement this information to create metabolic maps de novo and chart unexplored areas of metabolism.

Exploring metallodrug–protein interactions by mass spectrometry: comparisons between platinum coordination complexes and an organometallic ruthenium compound

“…High-resolution ESI MS has previously been used to study covalent and non-covalent ligand-biomolecule interactions [37,38] and to screen complex mixtures of metabolites [39][40][41], often without the need for chromatographic separation of the adducts prior to analysis. Hence, this method allows the simultaneous screening of complicated mixtures of compounds with the direct (Ub), cytochrome c (cyt c) and superoxide dismutase (SOD) (1:1:1) in tetramethylammonium acetate (TMeAmAc) buffer pH 7.4 and the same protein mixture after 24-h incubation at 37°C with cisplatin, transplatin and RAPTA-C, respectively (5:1 metal-to-protein ratio).…”

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

“…Another field that benefits from the accurate mass measurements and high resolving power MS/MS features of the LTQ-Orbitrap is metabolomics-the comprehensive identification and quantification of all metabolites and their inter-relationships in a biological sample (Breitling, Pitt, & Barrett, 2006). The immense diversity of small biomolecules, coupled with their wide concentration range in a sample, makes analysis very tedious using conventional mass spectrometric instrumentation and methods.…”

“…The degree of chromatographic separation required to characterize a sample could be significantly minimized by using a mass spectrometer with high resolving power and mass accuracy. Since metabolites are typically small molecules <1,500 Da, a mass accuracy of approximately 1 ppm can significantly reduce the number of possibilities in assigning molecular formulae, assuming a composition of only the most common biological elements C, H, O, N, S, and P (Breitling, Pitt, & Barrett, 2006). Such high accuracy is routinely achieved by the orbitrap and FT-ICR mass analyzers.…”

“…Such high accuracy is routinely achieved by the orbitrap and FT-ICR mass analyzers. Coupling these high performance features with MS/MS capabilities further facilitates the identification and structure elucidation of a large number of metabolites and also provides information about the biochemical connectivity between them (Breitling, Pitt, & Barrett, 2006).…”

“…The LTQOrbitrap has also been used to analyze intact small (3-10 kDa) (Bredehöft, Schänzer, & Thevis, 2008;Thevis et al, 2006a;Thevis, Thomas, & Schänzer, 2008b), medium (10-25 kDa) (Macek et al, 2006;Waanders, Hanke, & Mann, 2007) and large ($150 kDa) (Zhang & Shah, 2007) proteins where the MS n capability of the LIT coupled with the high performance features of the orbitrap can facilitate unambiguous determination of the charge states of fragment ions, as well as identification of PTMs by database searching. The high performance attributes of this hybrid mass spectrometer have also found applications in environmental chemistry (Barceló & Petrovic, 2007;Krauss & Hollender, 2008), drug and metabolite analysis (Breitling, Pitt, & Barrett, 2006;Cuyckens et al, 2008;Ding et al, 2007;Karu et al, 2007;Li et al, 2007a;Lim et al, 2007Lim et al, , 2008Madalinski et al, 2008;Nielen et al, 2007;Peterman et al, 2006;Ruan et al, 2008;Thevis et al, 2005;Thevis, Kamber, & Schänzer, 2006b;Thevis, Krug, & Schänzer, 2006c;Thevis et al, 2006dThevis et al, ,e, 2007aThevis et al, , 2008aZhu et al, 2007), lipidomics (Davis et al, 2008;Ejsing et al, 2006;Schwudke et al, 2007;Silipo et al, 2008), small-molecule (Chen et al, 2007b) and reaction product (Jamin et al, 2007) identification, as well as molecular structure characterization using hydrogen/deuterium exchange measurements (Chen et al, 2007a;...…”