Gas chromatography with quadrupole time-of-flight mass spectrometry (GC-QTOFMS) and soft ionization generated by a rare-gas plasma is described here for the determination of various chlorophenoxy acid methyl esters and a few chlorinated herbicides. This plasma-based, wavelength-selectable ionization source, which can use Xe, Kr, Ar, Ne, or He as the plasma gas, enables ionization of GC-amenable compounds with ionization energies below 8.4, 10, 11.6, 16.5, or 22.4 eV, respectively. The advantages of soft ionization include enhanced molecular ions, reduced fragmentation, and reduced background noise as compared to electron ionization. In the study presented here for two plasma gases, we demonstrate that Kr plasma, which is softer than Ar plasma, yields molecular ions with a relative intensity >60% for 11 of the 16 test compounds. When using this “tunable” plasma to ionize the analytes, there is the possibility for selective ionization and less fragmentation, which may lead to increased sensitivity and may help structure elucidation, especially when using high-resolution mass spectrometry that generates accurate masses within a few parts per million (ppm) mass errors. Data generated with the Ar plasma and real matrices such as a peppermint extract, a plum extract, and an orange peel extract, spiked with 16 test compounds, indicate that the test compounds can be detected at 1-10 pg/µL of extract, and compounds such as menthone, limonene, eucalyptol, pinene, caryophylene, and other C15H24 isomers, which are present in the peppermint and the orange peel extracts at ppm to percent levels, do not appear to interfere with the determination of the chlorophenoxy acid methyl esters or the chlorinated herbicides, although there were matrix effects when the test compounds were spiked at 1-10 pg/µL of extract.

Complementary methods of high-resolution mass spectrometry and microspectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene SOA (LSOA) and α-pinene SOA (PSOA). The LSOA compounds readily formed adducts with Na(+) under electrospray ionization conditions, with only a small fraction of compounds detected in the protonated form. In contrast, a significant fraction of PSOA compounds appeared in the protonated form because of their increased molecular rigidity. Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas was detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl-imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the α-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.

Soft ionization used with gas chromatography time-of-flight mass spectrometry (GC–TOFMS) allows for the selective ionization of aliphatic hydrocarbons and polycyclic aromatic sulfur heterocycles in certified standard reference oil (NIST SRM2721) and coal tar (NIST SRM1597a). Soft ionization is accomplished by photoionization from vacuum ultraviolet resonance lines produced by Xe, Kr, and Ar microplasmas. Molecular ion fragmentation of an aliphatic hydrocarbon C24H50 in a TOF mass spectrometer and a QTOF mass spectrometer using Ar and Kr are compared. The advantage of using soft ionization, as compared with the more commonly used electron ionization, lies in the enhancement of the relative intensity of molecular ions, which can be controlled by the choice of plasma gas. Furthermore, the enhanced selectivity provided by the ability to select the ionization wavelength is demonstrated through the qualitative analysis of a series of polycyclic aromatic sulfur heterocycles including dibenzothiophene, naphthothiophene, benzonaphthothiophene, and various methylated derivatives of these compounds.

Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097–1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.