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1.  Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine 
The journal of physical chemistry. B  2010;114(46):15092-15105.
The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc., 2009, 131, 14057–14065.). In addition to these findings we also report on the mechanisms for the formation of the b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion.
doi:10.1021/jp108452y
PMCID: PMC3664278  PMID: 20973555
Salt-bridge; proton mobility; anhydride; peptide fragmentation pathways; MALDI; modeling; gas-phase rearrangements
2.  Proteomic Analysis of Novel Marine Bacteria Using MALDI and ESI Mass Spectrometry 
The objective of this study was to develop a mass spectrometric protocol to search for proteins related to phototrophy in marine bacteria. The genes that produce proteins involved in conversion of light into energy have been detected by cloning-sequencing from some of these bacteria, but it was previously unknown if these proteins were actually expressed.
Attaining this study’s goal was complicated by the fact that the samples consisted of miniscule cell pellets, which yielded small amounts of very complex mixtures of proteins. Sample preparation and analysis were tailored to optimize the probability of detecting the proteins of interest. It has been reported that using both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) to analyze a mixture of peptides leads to the identification of more peptides that either technique alone. In order to exploit this complementarity between ESI and MALDI for proteomic analysis, samples were analyzed using both ionization techniques. With correct choices in sample preparation and ionization process, biologically relevant proteins can be identified out of small samples containing whole proteomes.
PMCID: PMC2291689  PMID: 15331585
Bacteria; MALDI; ESI; complementary; proteome
3.  Environmental proteomics of microbial plankton in a highly productive coastal upwelling system 
The ISME Journal  2010;5(5):856-865.
Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the < 1.2 μm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.
doi:10.1038/ismej.2010.168
PMCID: PMC3105774  PMID: 21068774
metaproteomics; marine plankton; OM43 clade
4.  Radio-Frequency-Free Cell for Electron Capture Dissociation in Tandem Mass Spectrometry 
Analytical chemistry  2009;81(3):1238-1243.
A radio frequency-free (RFF), analyzer-independent cell has been devised for electron-capture dissociation (ECD) of ions. The device is based on interleaving a series of electrostatic lenses with the periodic structure of magnetostatic lenses commonly found in a traveling wave tube. The RFF electrostatic/magnetostatic ECD cell was installed in a Finnigan TSQ700 ESI triple quadrupole (QqQ) spectrometer, and its performance was evaluated by recording product-ion spectra of doubly protonated substance P, doubly protonated gramicidin S, doubly protonated neurotensin, and triply protonated neurotensin. These spectra were readily obtained without recourse to a buffering gas or synchronizing electron injection with a specific phase of an RF field. The mass spectra produced with the modified instrument appear in all respects (other than resolution and mass accuracy, which were limited by the mass spectrometer used) to be at least as good for purposes of peptide identification as those recorded with Fourier transform ion cyclotron resonance (FT ICR) instruments; however, the effort and time to produce the mass spectra were much less than required to produce their FT ICR counterparts. The cell’s design and compact construction should allow it to be incorporated at relatively little cost into virtually any type of tandem mass spectrometer, for example, triple quadrupole, hybrid quadrupole ion trap, hybrid quadrupole time-of-flight, or even FT-ICR.
doi:10.1021/ac802084w
PMCID: PMC3066179  PMID: 19117494
5.  APPLICATION OF A CONGENER-SPECIFIC DEBROMINATION MODEL TO STUDY PHOTODEBROMINATION, ANAEROBIC MICROBIAL DEBROMINATION, AND FE0 REDUCTION OF POLYBROMINATED DIPHENYL ETHERS 
A model was used to predict the photodebromination of the BDE-203, 197, 196, and 153, the major components of the octa-polybrominated diphenyl ether (PBDE) technical mixture, as well as BDE-47, and the predicted results were compared to the experimental results. The predicted reaction time profiles of the photodebromination products correlate well with the experimental results. In addition, the slope of the linear regression between the measured product concentrations of the first step of the photodebromination products and their enthalpies of formation was found to be close to their theoretical value. The photodebromination results of the octa-BDE technical mixture were compared with anaerobic microbial debromination results and were found to be the same in both experiments. The debromination pathways of technical octa-BDE mixture were identified and BDE-154, 99, 47, and 31 were found to be the most abundant hexa-, penta-, tetra-, and tri-BDE debromination products, respectively. In addition to photodebromination and anaerobic biodebromination, the model prediction was also compared to the zero-valent iron reduction of BDE-209, 100, and 47 and the same debromination products were observed. Good correlation was observed between the photodebromination rate constants of fifteen PBDE congeners and their calculated lowest unoccupied molecular orbital (LUMO) energies, indicating that PBDE photodebromination is caused by electron transfer. Furthermore, the rate constants for the three different PBDE debromination processes are controlled by C–Br bond dissociation energy. With the model from the present study, the major debromination products for any PBDE congener released into the environment can be predicted.
doi:10.1002/etc.119
PMCID: PMC3059408  PMID: 20821505
Polybrominated diphenyl ether; Model; Photodegradation; Anaerobic microbial debromination
7.  A comparison of relative quantification with isobaric tags on a subset of the murine hepatic proteome using electrospray ionization quadrupole time-of-flight and matrix-assisted laser desorption/ionization tandem time-of-flight 
The use of isobaric tagging for relative and absolute quantification (iTRAQ) has increased dramatically over the past few years. Many factors can affect the accuracy of quantification. Some of these include the number of biological/technical replicates, sample complexity, instrumentation, method of peptide/protein identification and the statistical techniques used for data analysis. It has been observed that the low collision energies normally used in electrospray ionization quadrupole time-of-flight (ESI QTOF) can result in low iTRAQ reporter ion abundances. We used two-way analysis of variance (ANOVA) to compare the iTRAQ ratios that were generated on an ESI QTOF and a matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI TOF/TOF). It appears that iTRAQ analyses performed on an ESI QTOF without any special modifications to instrumental parameters produce essentially the same protein ratios as those obtained on a MALDI TOF/TOF.
doi:10.1002/rcm.3719
PMCID: PMC3057221  PMID: 18798194
8.  Occurrence and Mass Flows of Fluorochemicals in the Glatt Valley Watershed, Switzerland 
Environmental science & technology  2008;42(17):6369-6377.
Fluorochemicals are persistent contaminants that are globally distributed in air, water, sediments, and biota. Wastewater treatment plants (WWTPs) play an important role in mitigating pollutant releases from municipalities to aquatic and terrestrial environments. However, because WWTPs are point sources of fluorochemicals, it is important to understand their contribution to fluorochemical burdens in the greater context of watersheds. To this end, over a 1 week period, the mass flows of 11 fluorochemicals from seven WWTPs that discharge effluent into the Glatt River in Switzerland were measured and compared to the measured mass flows within the Glatt River. Overall, the fluorochemicals were not removed efficiently during wastewater treatment. Effluents from WWTPs and Glatt River water were dominated by perfluorooctane sulfonate, which was detected in all samples, followed by perfluorohexane sulfonate and perfluorooctanoate. The mass flows of fluorochemicals emanating from WWTPs were found to be conserved within the 35 km Glatt River, which indicates that input from the WWTPs is additive and that removal within the Glatt River is not significant. Per capita discharges of fluorochemicals were calculated from the populations served by the WWTPs studied; the values determined also account for the fluorochemical content of Lake Greifen (Greifensee), which is a lake at the headwaters of the Glatt River that also receives treated wastewater.
PMCID: PMC3056649  PMID: 18800503
9.  DEVELOPMENT AND VALIDATION OF A CONGENER-SPECIFIC PHOTODEGRADATION MODEL FOR POLYBROMINATED DIPHENYL ETHERS 
With the phaseout of the manufacture of some polybrominated diphenyl ether (PBDE) formulations, namely penta-brominated diphenyl ether (BDE) and octa-BDE, and the continued use of the deca-BDE formulation, it is important to be able to predict the photodegradation of the more highly brominated congeners. A model was developed and validated to predict the products and their relative concentrations from the photodegradation of PBDEs. The enthalpies of formation of the 209 PBDE congeners were calculated, and the relative reaction rate constants were obtained. The predicted reaction rate constants for PBDEs show linear correlation with previous experimental results. Because of their large volume use, their presence in the environment, and/or importance in the photodegradation of the deca-BDE formulation, BDE-209, BDE-184, BDE-100, and BDE-99 were chosen for further ultraviolet photodegradation experiments in isooctane. The photodegradation model successfully predicted the products of the photochemical reactions of PBDEs in experimental studies. A gas chromatography retention time model for PBDEs was developed using a multiple linear regression analysis and, together with the photodegradation model and additional PBDE standards, provided a way to identify unknown products from PBDE photodegradation experiments. Based on the results of the photodegradation experiments, as well as the model predictions, it appears that the photodegradation of PBDEs is a first-order reaction and, further, that the rate-determining step is the stepwise loss of bromine. Our results suggest that, based on photodegradation, over time, BDE-99 will remain the most abundant penta-BDE, while BDE-49 and BDE-66 will increase greatly and will be comparable in abundance to BDE-47.
doi:10.1897/07-570.1
PMCID: PMC3056650  PMID: 18613751
Polybrominated diphenyl ether; Photodegradation; Model; Theoretical calculation
11.  Resonant electron capture by some amino acids esters† 
Resonant electron capture by Gly, Ala and Phe esters have shown that the most efficient negative ion (NI) fragmentations are associated with the C-termini. A new mechanism for the negative ion-forming processes at energies lower than those associated with the π*OO shape resonance involves coupling between dipole-bound and valence negative ion states of the same symmetry for amino acid conformers with high permanent dipoles. The interaction avoids crossing of the NI states and instead leads to formation of two adiabatic potential energy surfaces. Underivatized amino acids most effectively fragment from the bottom adiabatic surface via generation of [M-H]− carboxylate anions by hydrogen-atom tunneling through the barrier; fragmentation of the their esters with formation of analogues [M-X]− NIs occurs through the upper adiabatic state without penetration of the barrier in which the energy of the valence σ*OX resonance exceeds the bond dissociation energy of the neutral molecule. Low and high temperature resonant electron capture experiments point to the importance of conformational preferences of the amino acids for optimum dissociation of the parent NIs in the gas phase.
doi:10.1016/j.ijms.2007.07.006
PMCID: PMC2762707  PMID: 19838328
Resonant electron capture mass spectrometry; negative ions; amino acids; esterification
12.  Proteomic analysis of native metabotropic glutamate receptor 5 protein complexes reveals novel molecular constituents 
Journal of neurochemistry  2004;91(2):438-450.
We used a proteomic approach to identify novel proteins that may regulate metabotropic glutamate receptor 5 (mGluR5) responses by direct or indirect protein interactions. This approach does not rely on the heterologous expression of proteins and offers the advantage of identifying protein interactions in a native environment. The mGluR5 protein was immunoprecipitated from rat brain lysates; co-immunoprecipitating proteins were analyzed by mass spectrometry and identified peptides were matched to protein databases to determine the correlating parent proteins. This proteomic approach revealed the interaction of mGluR5 with known regulatory proteins, as well as novel proteins that reflect previously unidentified molecular constituents of the mGluR5-signaling complex. Immunoblot analysis confirmed the interaction of high confidence proteins, such as phosphofurin acidic cluster sorting protein 1, microtubule-associated protein 2a and dynamin 1, as mGluR5-interacting proteins. These studies show that a proteomic approach can be used to identify candidate interacting proteins. This approach may be particularly useful for neurobiology applications where distinct protein interactions within a signaling complex can dramatically alter the outcome of the response to neurotransmitter release, or the disruption of normal protein interactions can lead to severe neurological and psychiatric disorders.
doi:10.1111/j.1471-4159.2004.02735.x
PMCID: PMC2747775  PMID: 15447677
mass spectrometry; metabotropic glutamate receptor; protein interaction; proteomics
13.  Proteomic Analysis of Stationary Phase in the Marine Bacterium “Candidatus Pelagibacter ubique”▿  
Applied and Environmental Microbiology  2008;74(13):4091-4100.
“Candidatus Pelagibacter ubique,” an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome reveals no evidence of global regulatory mechanisms for adaptation to stationary phase. High-resolution capillary liquid chromatography coupled online to an LTQ mass spectrometer was used to build an accurate mass and time (AMT) tag library that enabled quantitative examination of proteomic differences between exponential- and stationary-phase “Ca. Pelagibacter ubique” cells cultivated in a seawater medium. The AMT tag library represented 65% of the predicted protein-encoding genes. “Ca. Pelagibacter ubique” appears to respond adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis rather than undergoing a major remodeling of its proteome. Stationary-phase abundances increased significantly for OsmC and thioredoxin reductase, which may mitigate oxidative damage in “Ca. Pelagibacter,” as well as for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in ρ-dependent transcription termination, and the signal transduction enzyme CheY-FisH. We speculate that this limited response may enable “Ca. Pelagibacter ubique” to cope with ambient conditions that deprive it of nutrients for short periods and, furthermore, that the ability to resume growth overrides the need for a more comprehensive global stationary-phase response to create a capacity for long-term survival.
doi:10.1128/AEM.00599-08
PMCID: PMC2446508  PMID: 18469119
14.  Quantitative Determination of Fluorinated Alkyl Substances by Large-Volume-Injection LC/MS/MS—Characterization of Municipal Wastewaters 
A quantitative method was developed for the determination of fluorinated alkyl substances in municipal wastewater influents and effluents. The method consisted of centrifugation followed by large-volume injection (500 μL) of the supernatant onto a liquid chromatograph with a reverse-phase column and detection by electrospray ionization, and tandem mass spectrometry (LC/MS/MS). The fluorinated analytes studied include perfluoroalkyl sulfonates, fluorotelomer sulfonates, perfluorocarboxylates, and select fluorinated alkyl sulfonamides. Recoveries of the fluorinated analytes from wastewater treatment plant (WWTP) raw influents and final effluent ranged from 77% – 96% and 80% – 99%, respectively. The lower limit of quantitation ranged from 0.5 to 3.0 ng/L depending on the analyte. The method was applied to flow-proportional composites of raw influent and final effluent collected over a 24 hr period from ten WWTPs nationwide. Fluorinated alkyl substances were observed in wastewater at all treatment plants and each plant exhibited unique distributions of fluorinated alkyl substances despite similarities in treatment processes. In nine out of the ten plants sampled, at least one class of fluorinated alkyl substances exhibited increased concentrations in the effluent as compared to the influent concentrations. In some instances, decreases in certain fluorinated analyte concentrations were observed and attributed to sorption to sludge.
PMCID: PMC2597010  PMID: 16433363
15.  Fluorochemical Mass Flows in a Municipal Wastewater Treatment Facility 
Environmental science & technology  2006;40(23):7350-7357.
Fluorochemicals have widespread applications and are released into municipal wastewater treatment plants via domestic wastewater. A field study was conducted at a full-scale municipal wastewater treatment plant to determine the mass flows of selected fluorochemicals. Flow-proportional, 24-h samples of raw influent, primary effluent, trickling filter effluent, secondary effluent, and final effluent and grab samples of primary, thickened, activated, and anaerobically-digested sludge were collected over ten days and analyzed by liquid chromatography electrospray-ionization tandem mass spectrometry. Significant decreases in the mass flows of perfluorohexane sulfonate and perfluorodecanoate occurred during trickling filtration and primary clarification, while activated sludge treatment decreased the mass flow of perfluorohexanoate. Mass flows of the 6:2 fluorotelomer sulfonate and perfluorooctanoate were unchanged as a result of wastewater treatment, which indicates that conventional wastewater treatment is not effective for removal of these compounds. A net increase in the mass flows for perfluorooctane and perfluorodecane sulfonates occurred from trickling filtration and activated sludge treatment. Mass flows for perfluoroalkylsulfonamides and perfluorononanoate also increased during activated sludge treatment and are attributed to degradation of precursor molecules.
PMCID: PMC2556954  PMID: 17180988
16.  Comparison of ESI MS Interfaces for the Analysis of UV-crosslinked Peptide-Nucleic Acid Complexes 
In this report, the effectiveness of high performance liquid chromatography (HPLC) in conjunction with electrospray ionization mass spectrometry (ESI-MS) is examined as a tool for identifying the sites of crosslinking in a protein that has been photoreacted with a non-photolabeled oligonucleotide. ESI-MS and MALDI-MS analyses preceded by off-line microflow and nanoflow HPLC, on-line microflow HPLC/ESI, and on-line nanoflow HPLC/ESI interfaces were performed in order to determine their relative effectiveness in separating mixtures of nucleopeptides and identifying sites of crosslinking on the individual components. The characteristics of these four techniques as well as possibilities for improving the analysis of nucleopeptides by ESI MS are compared and discussed.
doi:10.1016/j.jchromb.2007.09.029
PMCID: PMC2238692  PMID: 18042442
17.  The 64-Kilodalton Capsid Protein Homolog of Beet Yellows Virus Is Required for Assembly of Virion Tails 
Journal of Virology  2003;77(4):2377-2384.
The filamentous virion of the closterovirus Beet yellows virus (BYV) consists of a long body formed by the major capsid protein (CP) and a short tail composed of the minor capsid protein (CPm) and the virus-encoded Hsp70 homolog. By using nano-liquid chromatography-tandem mass spectrometry and biochemical analyses, we show here that the BYV 64-kDa protein (p64) is the fourth integral component of BYV virions. The N-terminal domain of p64 is exposed at the virion surface and is accessible to antibodies and mild trypsin digestion. In contrast, the C-terminal domain is embedded in the virion and is inaccessible to antibodies or trypsin. The C-terminal domain of p64 is shown to be homologous to CP and CPm. Mutation of the signature motifs of capsid proteins of filamentous RNA viruses in p64 results in the formation of tailless virions, which are unable to move from cell to cell. These results reveal the dual function of p64 in tail assembly and BYV motility and support the concept of the virion tail as a specialized device for BYV cell-to-cell movement.
doi:10.1128/JVI.77.4.2377-2384.2003
PMCID: PMC141117  PMID: 12551975

Results 1-17 (17)