James H. Scrivens

A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches

The proteome of the recently discovered bacterium Methylocella silvestris has been characterized using three profiling and comparative proteomics approaches. The organism has been grown on two different substrates enabling variations in protein expression to be identified. The results obtained using the experimental approaches have been compared with respect to number of proteins identified, confidence in identification, sequence coverage and agreement of regulated proteins. The sample preparation, instrumental time and sample loading requirements of the differing experiments are compared and discussed. A preliminary screen of the protein regulation results for biological significance has also been performed.

Characterization of Phosphorylated Peptides Using Traveling Wave-Based and Drift Cell Ion Mobility Mass Spectrometry

Phosphorylation is one the most studied and important post translational modifications. Nano electrospray mass spectrometry coupled with traveling wave (T-Wave)-based ion mobility has been used to filter for phosphorylated peptides in tryptic protein digests. T-Wave parameters have been optimized to maximize the separation between phosphorylated and non-phosphorylated peptides. A method to calibrate the T-Wave device, to provide estimates of collision cross sections, is presented, and these estimates are in excellent agreement with values obtained on drift cell instrumentation. Phosphorylated peptides have smaller cross sections which enables their separation from non-phosphorylated peptides of the same m/z. Post-mobility fragmentation is used to obtain the primary sequence for peptides of interest. This approach is shown to have potential as an additional screen for phosphorylated peptides, where up to 40% of observed peptides can be eliminated from the study.

Travelling wave ion mobility mass spectrometry studies of protein structure : biological significance and comparison with X-ray crystallography and nuclear magnetic resonance spectroscopy measurements

The three-dimensional conformation of a protein is central to its biological function. The characterisation of aspects of three-dimensional protein structure by mass spectrometry is an area of much interest as the gas-phase conformation, in many instances, can be related to that of the solution phase. Travelling wave ion mobility mass spectrometry (TWIMS) was used to investigate the biological significance of gas-phase protein structure. Protein standards were analysed by TWIMS under denaturing and near-physiological solvent conditions and cross-sections estimated for the charge states observed. Estimates of collision cross-sections were obtained with reference to known standards with published cross-sections. Estimated cross-sections were compared with values from published X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy structures. The cross-section measured by ion mobility mass spectrometry varies with charge state, allowing the unfolding transition of proteins in the gas phase to be studied. Cross-sections estimated experimentally for proteins studied, for charge states most indicative of native structure, are in good agreement with measurements calculated from published X-ray and NMR structures. The relative stability of gas-phase structures has been investigated, for the proteins studied, based on their change in cross-section with increase in charge. These results illustrate that the TWIMS approach can provide data on three-dimensional protein structures of biological relevance.

The Application of Matrix‐assisted Laser Desorption/Ionization Combined with Collision‐induced Dissociation to the Analysis of Synthetic Polymers

Matrix-assisted laser desorption/ionization combined with collision-induced dissociation (CID) has been applied to the structural determination of synthetic polymers. Post-source decay/CID experiments on a time-of-flight (TOF) instrument have been compared with CID data from a hybrid sector-TOF mass spectrometer. Fragment-ation spectra of polymers, with molecular weights of up to 4500 Da, have been shown to aid structural and end-group determination. The polymers studied were poly(methyl methacrylate), poly(ethylene glycol) and poly(ethylene terephthalate).

Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase

Flavin-containing monooxygenases (FMOs) are one of the most important monooxygenase systems in Eukaryotes and have many important physiological functions. FMOs have also been found in bacteria; however, their physiological function is not known. Here, we report the identification and characterization of trimethylamine (TMA) monooxygenase, termed Tmm, from Methylocella silvestris, using a combination of proteomic, biochemical, and genetic approaches. This bacterial FMO contains the FMO sequence motif (FXGXXXHXXXF/Y) and typical flavin adenine dinucleotide and nicotinamide adenine dinucleotide phosphate-binding domains. The enzyme was highly expressed in TMA-grown M. silvestris and absent during growth on methanol. The gene, tmm, was expressed in Escherichia coli, and the purified recombinant protein had high Tmm activity. Mutagenesis of this gene abolished the ability of M. silvestris to grow on TMA as a sole carbon and energy source. Close homologs of tmm occur in many Alphaproteobacteria, in particular Rhodobacteraceae (marine Roseobacter clade, MRC) and the marine SAR11 clade (Pelagibacter ubique). We show that the ability of MRC to use TMA as a sole carbon and/or nitrogen source is directly linked to the presence of tmm in the genomes, and purified Tmm of MRC and SAR11 from recombinant E. coli showed Tmm activities. The tmm gene is highly abundant in the metagenomes of the Global Ocean Sampling expedition, and we estimate that 20% of the bacteria in the surface ocean contain tmm. Taken together, our results suggest that Tmm, a bacterial FMO, plays an important yet overlooked role in the global carbon and nitrogen cycles.

Time-lag focusing and cation attachment in the analysis of synthetic polymers by matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry

Ultraviolet matrix-assisted laser desorption/ionization-mass spectrometry has been employed with time-lag focusing to explore its utility for the characterization of synthetic polymers with broad distributions. Mixtures of five polymer standards with narrow molecular weight distributions were analyzed. The spectra were found to be broadly those expected for three different types of polymer systems—poly(styrene), poly(methyl methacrylate), and poly(ethylene glycol)—when equimass mixtures were used. Large changes in the apparent molecular weight distribution of poly(ethylene terephthalate) were observed when the cation was varied. The shift in the envelope was found to be related to the size and the ability of the oligomers to solvate the cation.

Protomers of Benzocaine: Solvent and Permittivity Dependence

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid that finds an application as a local anesthetic, is found to adopt in its protonated form at least two populations of distinct structures in the gas phase, and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization process. Here, we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry to yield gas-phase IR spectra of simultaneously m/z and drift-time-resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species: the N- and O-protonated forms. Density functional theory calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution-phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation have been suggested.

Probing hemoglobin structure by means of traveling-wave ion mobility mass spectrometry.

Hemoglobin (Hb) is a tetrameric noncovalent complex consisting of two α- and two β-globin chains each associated with a heme group. Its exact assembly pathway is a matter of debate. Disorders of hemoglobin are the most common inherited disorders and subsequently the molecule has been extensively studied. This work attempts to further elucidate the structural properties of the hemoglobin tetramer and its components. Gas-phase conformations of hemoglobin tetramers and their constituents were investigated by means of traveling-wave ion mobility mass spectrometry. Sickle (HbS) and normal (HbA) hemoglobin molecules were analyzed to determine whether conformational differences in their quaternary structure could be observed. Rotationally averaged collision cross sections were estimated for tetramer, dimer, apo-, and holo-monomers with reference to a protein standard with known cross sections. Estimates of cross section obtained for the tetramers were compared to values calculated from X-ray crystallographic structures. HbS was consistently estimated to have a larger cross section than that of HbA, comparable with values obtained from X-ray crystallographic structures. Nontetrameric species observed included apo- and holo- forms of α- and β-monomers and heterodimers; α- and β-monomers in both apo- and holo- forms were found to have similar cross sections, suggesting they maintain a similar fold in the gas phase in both the presence and the absence of heme. Heme-deficient dimer, observed in the spectrum when analyzing commercially prepared Hb, was not observed when analyzing fresh blood. This implies that holo-α-apo-β is not an essential intermediate within the Hb assembly pathway, as previously proposed.

Structural Analysis of Synthetic Polymer Mixtures Using Ion Mobility and Tandem Mass Spectrometry

Ion mobility (IM) combined with tandem mass spectrometry (MS/MS) has been employed to separate and differentiate between polyether oligomers with the same nominal molecular weights. Poly(ethylene glycol)s with the same nominal mass-to-charge ratio (m/z), but with differing structures, were separated using ion mobility. IM-MS/MS data were able to aid identification of the backbone and end groups of the four individual polyethers in the two sets of isobaric mixtures. The MS/MS data from the resolved oligomers enabled a detailed structural characterization of the polyether mixtures to be completed in one experiment.

Characterisation of synthetic polymer systems

Abstract Mass spectrometry has been used in the study of synthetic polymer systems since the 1960s. The application has been, for the most part, limited to the characterisation of polymer additive systems and polymers that had either been chemically or thermally degraded. The advent of newer ionisation approaches, coupled with the development of analyser technology, has led to the reappraisal of mass spectrometry for this work. Molecular weight distributions have been obtained and information on end groups and chemical variation with molecular weight has been measured. Polymer microstructure has been probed with information obtained on partial and, in some cases, complete sequence for oligomeric systems. Fundamental work to support these developments is needed and is being carried out. Information on gas-phase polymer conformations has been obtained and an important link with calculation established. The future of the approach, particularly when used in conjunction with other complimentary chromatographic and spectroscopic techniques, looks promising.