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Jennifer S. Brodbelt - One of the best experts on this subject based on the ideXlab platform.

  • Publication No._____________
    2014
    Co-Authors: Jennifer S. Brodbelt, Matthew Cooper Crowe, James A. Holcombe, David Vanden Bout, Edward M. Marcotte, Mike Dicaprio, Ph. D, Supervisor Jennifer
    Abstract:

    (IRMPD) and Collisionally Activated Dissociation (CAD) in

  • Characterization of flavonoids by aluminum complexation and Collisionally Activated Dissociation.
    Journal of Mass Spectrometry, 2005
    Co-Authors: Junmei Zhang, Junmei Wang, Jennifer S. Brodbelt
    Abstract:

    Aluminum complexes of the type [Al(III) (flavonoid-H)2]+ are generated by electrospray ionization in order to allow differentiation of isomeric flavonoids by tandem mass spectrometry. The dominant species observed from the aluminum complexation reaction has a 1:2 aluminum(III):flavonoid stoichiometry. Differentiation of 18 flavonoids constituting seven isomeric series was achieved based on the Collisionally Activated Dissociation patterns of the aluminum complexes. Characteristic fragmentation pathways allow identification of the site of glycosylation, the type of saccharide (rutinose versus neohesperidose) and the type of bond between the C-2 and C-3 atoms (thus distinguishing flavanones from flavonols and flavones). Two stable coordination geometries of the aluminum complex of apigenin were identified. The non-planar structure with a plane-angle of nearly 90 degrees is 25.3 kcal mol-1 more favorable than the planar structure. The conformations of the complexes, which involve multiple interactions between the aglycone and disaccharide portions of the flavonoid with the metal ion, are significantly different for the isomeric flavonoids.

  • Comparison of sustained off-resonance irradiation Collisionally Activated Dissociation and multipole storage-assisted Dissociation for top-down protein analysis.
    Journal of mass spectrometry : JMS, 2004
    Co-Authors: Karin M. Keller, Jennifer S. Brodbelt, Robert {bob} L Hettich, Gary J Van Berkel
    Abstract:

    Tandem mass spectrometric data acquired for small (8-18 kDa) intact proteins by sustained off-resonance irradiation Collisionally Activated Dissociation (SORI-CAD) and multipole storage-assisted Dissociation (MSAD) were compared, and the results indicate that the two activation methods do not always provide the same fragmentation patterns. In MSAD experiments, the charge state distribution made available by the ionization conditions may dictate the range of fragment ions that can be generated. In addition, conditions of high space charge within the hexapole impair transmission and/or trapping of high m/z species, which can result in loss of important precursor and product ions. Finally, the non-resonant nature of activation in MSAD can provide access to secondary Dissociation processes that are not available by SORI. Because of these considerations, MSAD is less reliable than SORI for generating sequence tag data. However, it appears that MSAD samples 'preferred' cleavage processes (i.e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses.

  • Collisionally Activated Dissociation and infrared multiphoton Dissociation of oligonucleotides in a quadrupole ion trap.
    Analytical Biochemistry, 2004
    Co-Authors: Karin M. Keller, Jennifer S. Brodbelt
    Abstract:

    Infrared multiphoton Dissociation (IRMPD) of deprotonated and protonated oligonucleotides ranging from 5 to 40 residues has been performed in a quadrupole ion trap mass spectrometer at normal operating pressure and temperature. Only moderate exposure times and laser powers were required to achieve efficient Dissociation. In general, IRMPD and Collisionally Activated Dissociation (CAD) produce comparable sequencing information, indicating that IRMPD is a viable alternative to CAD for oligonucleotide analysis in the quadrupole ion trap. Two major characteristics distinguish CAD and IRMPD spectra for a given parent ion. First, structurally uninformative M-B ions that dominate CAD spectra are generally only low-intensity species in IRMPD spectra because nonresonant activation causes these species to dissociate to backbone cleavage products. Second, phosphate and nucleobase ions can be observed directly in IRMPD experiments because the low-mass cutoff can be set to trap small fragment ions. For this reason IRMPD can sometimes facilitate analysis of sequences containing modified bases.

  • Evaluation of noncovalent interactions between peptides and polyether compounds via energy-variable Collisionally Activated Dissociation
    Journal of the American Society for Mass Spectrometry, 2003
    Co-Authors: Matthew C. Crowe, Jennifer S. Brodbelt
    Abstract:

    Energy-variable Collisionally Activated Dissociation (CAD) was used to analyze noncovalent interactions of protonated peptide/polyether complexes in a quadrupole ion trap complexes were formed with a series of four polyether host molecules and thirteen peptide molecules. Comparison of Dissociation thresholds revealed correlations between the gas-phase basicities of the peptides and polyether molecules and the onset of Dissociation. The Dissociation thresholds of complexes containing the tripeptides or pentapeptides were inversely proportional to the gas-phase basicities of the sites of protonation of the peptides. Intramolecular hydrogen bonding of the pentapeptides affected the observed Dissociation thresholds as well. The Dissociation thresholds also scaled proportionally to the gas-phase basicities of the polyethers in the complexes, and the importance of the conformational flexibility of the polyether ligand was confirmed for one of the histidine-containing tripeptide complexes.

Myung Soo Kim - One of the best experts on this subject based on the ideXlab platform.

Young Jin Lee - One of the best experts on this subject based on the ideXlab platform.

Erwin J. Alvarez - One of the best experts on this subject based on the ideXlab platform.

  • Collisionally Activated Dissociation of transition metal ion polyether complexes in a quadrupole ion trap
    Journal of the American Chemical Society, 1996
    Co-Authors: Erwin J. Alvarez, Chien Chung Liou, Jennifer S. Brodbelt
    Abstract:

    For a series of polyether/transition metal ion complexes, Collisionally Activated Dissociation reactions that are mediated by the flexibility of the polyether and the number of coordination sites are reported. The metal ions are generated by a pulsed laser desorption technique, and collision-Activated Dissociation methods are used to characterize the structures of the resulting metal/polyether complexes. The CAD patterns for the different polyether/metal ion complexes show striking variations depending on the flexibility of the ether, its number of coordination sites, and the type of metal ion. For example, (18-crown-6 + Co+) dissociates by loss of CHCH• or C2H3O• radicals, each pathway in conjunction with multiple losses of C2H4O, and resulting in products incorporating one covalent or ionic bond between the Co+ ion and the crown ether. In contrast, (12-crown-4 + Co+) dissociates by loss of CH2CH2 or C2H4O closed shell neutrals, each pathway in conjunction with additional losses of C2H4O and resulting in...

  • Collisionally Activated Dissociation of Transition Metal Ion/Polyether Complexes in a Quadrupole Ion Trap
    Journal of the American Chemical Society, 1996
    Co-Authors: Erwin J. Alvarez, Chien Chung Liou, Jennifer S. Brodbelt
    Abstract:

    For a series of polyether/transition metal ion complexes, Collisionally Activated Dissociation reactions that are mediated by the flexibility of the polyether and the number of coordination sites are reported. The metal ions are generated by a pulsed laser desorption technique, and collision-Activated Dissociation methods are used to characterize the structures of the resulting metal/polyether complexes. The CAD patterns for the different polyether/metal ion complexes show striking variations depending on the flexibility of the ether, its number of coordination sites, and the type of metal ion. For example, (18-crown-6 + Co+) dissociates by loss of CHCH• or C2H3O• radicals, each pathway in conjunction with multiple losses of C2H4O, and resulting in products incorporating one covalent or ionic bond between the Co+ ion and the crown ether. In contrast, (12-crown-4 + Co+) dissociates by loss of CH2CH2 or C2H4O closed shell neutrals, each pathway in conjunction with additional losses of C2H4O and resulting in...

Neil L Kelleher - One of the best experts on this subject based on the ideXlab platform.

  • *Corresponding author: #Current address:
    2016
    Co-Authors: Neil L Kelleher, Benjamin A. Garcia, James A. Streeky, Craig A, C. A. Mizzen, James J. Pesavento
    Abstract:

    modification); MS/MS (tandem mass spectrometry); RP-HPLC (reverse-phase high performance liquid chromatography); ESI-FTMS (electrospray ionization Fourier transform mass spectrometry); MPA (mild performic acid); OCAD (octupole Collisionally Activated Dissociation); ECD (electron capture Dissociation); SWIFT (stored waveform inverse Fourier transform); aK16 (Lysine 16 ε-N-acetylation); aαS1 (α-N-acetyl on Serine 1

  • top down mass spectrometry of 60 kda proteins from methanosarcina acetivorans using quadrupole ftms with automated octopole Collisionally Activated Dissociation
    Molecular & Cellular Proteomics, 2006
    Co-Authors: Steven M Patrie, Dana E Robinson, Jonathan T Ferguson, Dave Whipple, Michael Rother, William W Metcalf, Neil L Kelleher
    Abstract:

    : A fragmentation geometry based upon axial acceleration of m/z-selected protein ions into a linear octopole ion trap allowed simultaneous production and external accumulation of fragment ions prior to m/z measurement in a FT mass spectrometer. Improved dynamic range resulting from this octopole Collisionally Activated Dissociation resulted in a 2.5x increase in experimental throughput and a 2x increase in fragment ion matches to gene products identified and characterized in the top down fashion. The acceleration voltage for optimal fragmentation has a m/z and mass dependence, knowledge of which facilitated an automated platform for top down MS/MS on a quadrupole FT hybrid mass spectrometer. Controlled by improved software for data acquisition (e.g. using dynamic exclusion of previously identified species), automated octopole Collisionally Activated Dissociation of samples fractionated using chromatofocusing and reversed-phase liquid chromatography achieved a significant increase in protein identification rate versus previous benchmarks. Also a batch analysis version of ProSight PTM facilitated probability-based identification of intact proteins obtained in a higher throughput fashion. In total, 101 unique proteins (5-59 kDa) were identified from whole cell lysates of Methanosarcina acetivorans grown anaerobically, including the characterization of several mispredicted start sites and biologically relevant mass discrepancies.

  • Top Down Mass Spectrometry of
    Molecular & cellular proteomics : MCP, 2006
    Co-Authors: Steven M Patrie, Dana E Robinson, Jonathan T Ferguson, Dave Whipple, Michael Rother, William W Metcalf, Neil L Kelleher
    Abstract:

    A fragmentation geometry based upon axial acceleration of m/z-selected protein ions into a linear octopole ion trap allowed simultaneous production and external accumulation of fragment ions prior to m/z measurement in a FT mass spectrometer. Improved dynamic range resulting from this octopole Collisionally Activated Dissociation resulted in a 2.5x increase in experimental throughput and a 2x increase in fragment ion matches to gene products identified and characterized in the top down fashion. The acceleration voltage for optimal fragmentation has a m/z and mass dependence, knowledge of which facilitated an automated platform for top down MS/MS on a quadrupole FT hybrid mass spectrometer. Controlled by improved software for data acquisition (e.g. using dynamic exclusion of previously identified species), automated octopole Collisionally Activated Dissociation of samples fractionated using chromatofocusing and reversed-phase liquid chromatography achieved a significant increase in protein identification rate versus previous benchmarks. Also a batch analysis version of ProSight PTM facilitated probability-based identification of intact proteins obtained in a higher throughput fashion. In total, 101 unique proteins (5-59 kDa) were identified from whole cell lysates of Methanosarcina acetivorans grown anaerobically, including the characterization of several mispredicted start sites and biologically relevant mass discrepancies.