Mass Spectrometry and Metabolomics in Chemical Ecology

A. Daniel Jones


215A BCH


Prof.Director, Mass Spec /Metabolomics Core

Primary Research Area

Analytical (An)

Other Area(s) of Interest

Biological (Bi)


(Research Description PDF)

Global profiling of metabolites, the small molecules produced by living things, provides one of the most powerful strategies for learning about gene and protein functions. This approach, known as metabolomics, is generating information that will serve as the foundation for engineering of plants and microbes to produce renewable feedstocks for high-value bioactive chemicals and biofuels. Metabolite profiles also are important indicators of health and disease, and many metabolites serve important signaling functions that regulate physiological states ranging from inflammation to resolution

Schematic of UHPLC-TOF MS analysis using multiplexed collision induced dissociation showing time-dependence of collision potential.


Research in the Jones laboratory is driven by a desire to understand how genetics and environment combine to influence biological chemistry by: (1) developing analytical and biochemical tools for deep profi and spatial localization of specialized metabolites, (2) developing experimental and data mining approaches to accelerate discoveries of natural products in medicinal and non-model plants and the genes involved in their accumulation, (3) deployment of mass spectrometry strategies to identify and quantify byproducts generated during processing of lignocellulosic biomass for conversion into renewable fuels and chemicals, and (4) measurements of metabolic biomarkers of inflammation, analgesia, and resolution of disease.

Laser desorption ionization mass spectrometry imaging of two insecticidal acylsugar metabolites in leaf trichomes of the wild tomato relative Solanum habrochaites LA1777.


Many plants accumulate large quantities of bioactive phytochemicals in specialized epidermal cells known as glandular trichomes, which are prolific biochemical fac- tories. Our laboratory has pioneered rapid metabolite profiling protocols based on ultrahigh performance liquid chromatography (UHPLC) coupled to time-of-flight mass spectrometry (MS). By employing rapid gradients and by multiplexing collision potentials across a lens between the mass spectrometer ion source and mass analyzer, ~500 metabolites are measured in a 5-minute analysis. This allows for large-scale guide gene function discoveries. Trichomes are also amenable to mass spectrometry imaging, allowing for extensive chemical interrogation of individual trichomes across plant tissues. Ongoing research involves labeling metabolites using 13C to investigate metabolic dynam- ics coupled with elucidation of metabolite structures using MS and NMR.

We also investigate whether inflammatory, anti-inflammatory, and analgesic lipid metabolite biomarkers in the blood of COPD patients indicate mechanisms underlying pulmonary rehabilitation and osteopathic manipulative treatments (OMT). Since more diseases are associated with environment and lifestyle than specifi genetic factors, our lab is beginning to adapt our analytical methods to investigate the exposome, which is the entire range of molecules (e.g. from foods, environment, gut microbes) to which individuals are exposed.

Selected Publications

Metabolite diversity in alkaloid biosynthesis – a multi-lane highway for camptothecin production in Camptotheca acuminata, R. Sadre, M. Magallanes-Lundback, S. Pradhan, V. Salim, A. Mesberg, A. D. Jones, and D. DellaPenna, The Plant Cell, 2016, 28, 1926-1944.

In vitro reconstruction and analysis of evolutionary variation of the tomato acylsucrose metabolic network, P. X. Fan, A. M. Miller, A. L. Schilmiller, X. X. Liu, I. Ofner, A. D. Jones, D. Zamir, and R. L. Last, Proc. Natl. Acad. Sci. USA 2016, 113, E239-E248.

Profiling of stable isotope enrichment in specialized metabolites using liquid chromatography and multiplexed non-selective collision-induced dissociation, Z. Wang and A. D. Jones, Anal. Chem. 2014, 86, 10600-10607.

Chemical imaging of trichome specialized metabolites using contact printing and laser desorption/ionization mass spectrometry, C. Li, Z. Wang, and A. D. Jones, Anal. Bioanal. Chem. 2014, 406, 171-182.

Comparative structural profiling of trichome specialized metabolites in tomato (Solanum lycopersicum) and S. habrochaites: acylsugar profiles revealed by UHPLC/MS and NMR, B. Ghosh, T. C. Westbrook, and A. D. Jones, Metabolomics 2014, 10, 496-507.

Towards the plant metabolome and beyond, R. L. Last, A. D. Jones, and Y. Shachar-Hill, Nature Rev. Mol. Cell Biol. 2007, 8, 167-174.


B.S., 1976, Harvey Mudd College

Ph.D., 1984,The Pennsylvania State Univ.

Director, 1984-1998, Facility for Advanced Instrumentation, Univ. of California, Davis

Senior Scientist, 1998-2005, Dept. of Chemistry, The Pennsylvania State Univ.


2012 CNS Distinguished Faculty Award