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Journal of the American Society for Mass Spectrometry

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https://www.readbyqxmd.com/read/30414067/free-radical-initiated-peptide-sequencing-mass-spectrometry-for-phosphopeptide-post-translational-modification-analysis
#1
Inae Jang, Aeran Jeon, Suk Gyu Lim, Duk Ki Hong, Min Soo Kim, Jae Hyeong Jo, Sang Tak Lee, Bongjin Moon, Han Bin Oh
Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved...
November 9, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30414066/application-of-group-i-metal-adduction-to-the-separation-of-steroids-by-traveling-wave-ion-mobility-spectrometry
#2
Alana L Rister, Tiana L Martin, Eric D Dodds
Steroids represent an interesting class of small biomolecules due to their use as biomarkers and their status as scheduled drugs. Although the analysis of steroids is complicated by the potential for many isomers, ion mobility spectrometry (IMS) has previously shown promise for the rapid separation of steroid isomers. This work is aimed at the further development of IMS separation for the analysis of steroids. Here, traveling wave ion mobility spectrometry (TWIMS) was applied to the study of group I metal adducted steroids and their corresponding multimers for five sets of isomers...
November 9, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30411195/molecular-characterization-of-high-molecular-weight-polyesters-by-matrix-assisted-laser-desorption-ionization-high-resolution-time-of-flight-mass-spectrometry-combined-with-on-plate-alkaline-degradation-and-mass-defect-analysis
#3
Sayaka Nakamura, Thierry Fouquet, Hiroaki Sato
Matrix-assisted laser desorption ionization high-resolution time-of-flight mass spectrometry (MALDI HR TOF MS) is a powerful tool for the molecular characterization of industrial polymers. However, accurate mass determination and resolution of isobaric ions are possible for oligomer samples only typically below m/z 3000. To cut long polymer chains into oligomers suitable for high-resolution mass spectrometry, we propose a simple "on-plate" alkaline degradation of polyesters as a sample pretreatment technique prior to the MALDI TOF MS measurement...
November 8, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30402785/enhanced-desorption-electrospray-ionization-mass-spectrometry-via-synchronizing-ion-generation-and-ion-injection
#4
Zhuanghao Hou, Xingchuang Xiong, Xiang Fang, Guangming Huang
A modified version of desorption electrospray ionization mass spectrometry was developed for (i) better utilization of analyte ions and (ii) larger sampling area via synchronization the pulsed nebulizer gas with ion injection. To synchronize the sheath gas, gas flow was paused for 50 ms within each cycle, leading to solvent accumulation at the end of emitter tip. That solvent accumulation enlarged the desorption areas. As a result, the amount of analytes increased. Thus, the improved signal intensity (~ 2-5-folds for various substrates) was benefit from both better analyte ion utilization and larger desorption areas...
November 6, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30397862/editorial-and-review-30th-asms-sanibel-conference-on-mass-spectrometry-computational-modelling-in-mass-spectrometry-and-ion-mobility-methods-for-ion-structure-and-reactivity-determination
#5
EDITORIAL
Iain D G Campuzano, Frank Sobott, Michael J van Stipdonk
No abstract text is available yet for this article.
November 5, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30374663/high-resolution-hdx-ms-of-cytochrome-c-using-pepsin-fungal-protease-type-xiii-mixed-bed-column
#6
Yoshitomo Hamuro, Terry Zhang
A pepsin/FPXIII (protease from Aspergillus saitoi, type XIII) mixed bed column significantly improved the resolution of bottom-up hydrogen/deuterium exchange mass spectrometry (HDX-MS) data compared with a pepsin-only column. The HDX-MS method using the mixed bed column determined 65 amide hydrogen exchange rates out of one hundred cytochrome c backbone amide hydrogens. Different cleavage specificities of the two enzymes generated 138 unique high-quality peptic fragments, which allows fine sub-localization of deuterium...
October 29, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30374662/studying-chemistry-in-micro-compartments-by-separating-droplet-generation-from-ionization
#7
Michael I Jacobs, Ryan D Davis, Rebecca J Rapf, Kevin R Wilson
Recent studies show that reactions inside micron-sized compartments (e.g., droplets, emulsions) can proceed at significantly accelerated rates and with different mechanisms compared to the same reactions in a macroscopic container. Many of these studies use electrospray ionization (ESI) to both generate droplets and to quantify, via mass spectrometry (MS), droplet reaction kinetics. The highly charged and rapidly evaporating droplets produced in ESI make it difficult to examine precisely the underlying cause for droplet-induced rate enhancements...
October 29, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30353292/whole-cell-maldi-fingerprinting-is-a-robust-tool-for-differential-profiling-of-two-component-mammalian-cell-mixtures
#8
Valentina Z Petukhova, Alexandria N Young, Jian Wang, Mingxun Wang, Andras Ladanyi, Rajul Kothari, Joanna E Burdette, Laura M Sanchez
MALDI fingerprinting was first described two decades ago as a technique to identify microbial cell lines. Microbial fingerprinting has since evolved into an automated platform for microorganism identification and classification, which is now routinely used in clinical and environmental sectors. The extension of fingerprinting to mammalian cells has yet to progress partly due to compartmentalization of eukaryotic cells and overall higher cellular complexity. A number of publications on mammalian whole cell fingerprinting suggest that the method could be useful for classification of different cell types, cell states, and monitoring cell differentiation...
October 23, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30353291/characterization-of-electrospray-ionization-esi-parameters-on-in-esi-hydrogen-deuterium-exchange-of-carbohydrate-metal-ion-adducts
#9
O Tara Liyanage, Matthew R Brantley, Emvia I Calixte, Touradj Solouki, Kevin L Shuford, Elyssia S Gallagher
The conformations of glycans are crucial for their biological functions. In-electrospray ionization (ESI) hydrogen/deuterium exchange-mass spectrometry (HDX-MS) is a promising technique for studying carbohydrate conformations since rapidly exchanging functional groups, e.g., hydroxyls, can be labeled on the timeframe of ESI. However, regular application of in-ESI HDX to characterize carbohydrates requires further analysis of the in-ESI HDX methodology. For instance, in this method, HDX occurs concurrently to the analyte transitioning from solution to gas-phase ions...
October 23, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30353290/quantifying-sims-of-organic-mixtures-and-depth-profiles-characterizing-matrix-effects-of-fragment-ions
#10
M P Seah, R Havelund, S J Spencer, I S Gilmore
Sets of matrix factors, Ξ, are reported for the first time for secondary ions in secondary ion mass spectrometry for several binary organic systems. These show the interplay of the effects of ion velocity, fragment chemistry, and the secondary ion point of origin. Matrix factors are reported for negative ions for Irganox 1010 with FMOC or Irganox 1098 and, for both positive and negative ions, with Ir(ppy)2(acac). For Irganox 1010/FMOC, the Ξ values for Irganox 1010 fall with m/z, whereas those for FMOC rise...
October 23, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30341582/sputter-coated-metal-screening-for-small-molecule-analysis-and-high-spatial-resolution-imaging-in-laser-desorption-ionization-mass-spectrometry
#11
Rebecca L Hansen, Maria Emilia Dueñas, Young Jin Lee
Nanoparticles are efficient matrices in laser desorption/ionization (LDI) mass spectrometry (MS), especially for the profiling or imaging of small molecules. Recently, solvent-free physical vapor desorption (PVD), or sputter coating, was adopted as a homogenous method to rapidly apply metal nanoparticles (NPs) in situ to samples prior to LDI MS or MS imaging analysis. However, there has been no systematic study comparing different metal targets for the analysis of a variety of small molecule metabolites. Here, we present a screening and optimization of various sputter-coated metals, including Ag, Au, Cu, Pt, Ni, and Ti, for LDI analysis of small molecules in both positive and negative ion modes...
October 19, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30341581/gas-phase-ion-ion-chemistry-as-a-probe-for-the-presence-of-carboxylate-groups-in-polypeptide-cations
#12
Anthony M Pitts-McCoy, Christopher P Harrilal, Scott A McLuckey
The reactivity of 1-hydroxybenzoyl triazole (HOBt) esters with the carboxylate functionality present in peptides is demonstrated in the gas phase with a doubly deprotonated dianion. The reaction forms an anhydride linkage at the carboxylate site. Upon ion trap collisional-induced dissociation (CID) of the modified peptide, the resulting spectrum shows a nominal loss of the mass of the reagent and a water molecule. Analogous phenomenology was also noted for model peptide cations that likely contain zwitterionic/salt-bridged motifs in reactions with a negatively charged HOBt ester...
October 19, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30341580/ion-mobility-mass-spectrometry-reveals-details-of-formation-and-structure-for-gaa%C3%A2-tcc-dna-and-rna-triplexes
#13
Jiawei Li, Alexander Begbie, Belinda J Boehm, Alexander Button, Charles Whidborne, Yannii Pouferis, David M Huang, Tara L Pukala
DNA and RNA triplexes are thought to play key roles in a range of cellular processes such as gene regulation and epigenetic remodeling and have been implicated in human disease such as Friedreich's ataxia. In this work, ion mobility-mass spectrometry (IM-MS) is used with supporting UV-visible spectroscopy to investigate DNA triplex assembly, considering stability and specificity, for GAA·TTC oligonucleotide sequences of relevance to Friedreich's ataxia. We demonstrate that, contrary to other examples, parallel triplex structures are favored for these sequences and that stability is enhanced by increasing oligonucleotide length and decreasing pH...
October 19, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30338451/poppet-a-new-method-to-predict-the-protection-factor-of-backbone-amide-hydrogens
#14
Jürgen Claesen, Argyris Politis
Hydrogen exchange (HX) has become an important tool to monitor protein structure and dynamics. The interpretation of HX data with respect to protein structure requires understanding of the factors that influence exchange. Simulated protein structures can be validated by comparing experimental deuteration profiles with the profiles derived from the modeled protein structure. To do this, we propose here a new method, POPPeT, for protection factor prediction based on protein motions that enable HX. By comparing POPPeT with two existing methods, the phenomenological approximation and COREX, we show enhanced predictability measured at both protection factor and deuteration level...
October 18, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30328005/exposure-of-solvent-inaccessible-regions-in-the-amyloidogenic-protein-human-sod1-determined-by-hydroxyl-radical-footprinting
#15
Yuewei Sheng, Joseph Capri, Alan Waring, Joan Selverstone Valentine, Julian Whitelegge
Solvent-accessibility change plays a critical role in protein misfolding and aggregation, the culprit for several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Mass spectrometry-based hydroxyl radical (·OH) protein footprinting has evolved as a powerful and fast tool in elucidating protein solvent accessibility. In this work, we used fast photochemical oxidation of protein (FPOP) hydroxyl radical (·OH) footprinting to investigate solvent accessibility in human copper-zinc superoxide dismutase (SOD1), misfolded or aggregated forms of which underlie a portion of ALS cases...
October 16, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30324263/evaluation-of-digital-image-recognition-methods-for-mass-spectrometry-imaging-data-analysis
#16
Måns Ekelöf, Kenneth P Garrard, Rika Judd, Elias P Rosen, De-Yu Xie, Angela D M Kashuba, David C Muddiman
Analyzing mass spectrometry imaging data can be laborious and time consuming, and as the size and complexity of datasets grow, so does the need for robust automated processing methods. We here present a method for comprehensive, semi-targeted discovery of molecular distributions of interest from mass spectrometry imaging data, using widely available image similarity scoring algorithms to rank images by spatial correlation. A fast and powerful batch search method using a MATLAB implementation of structural similarity (SSIM) index scoring with a pre-selected reference distribution is demonstrated for two sample imaging datasets, a plant metabolite study using Artemisia annua leaf, and a drug distribution study using maraviroc-dosed macaque tissue...
October 15, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30324262/conditions-for-analysis-of-native-protein-structures-using-uniform-field-drift-tube-ion-mobility-mass-spectrometry-and-characterization-of-stable-calibrants-for-twim-ms
#17
Julian A Harrison, Celine Kelso, Tara L Pukala, Jennifer L Beck
Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes...
October 15, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30324261/comparison-of-peptide-ion-conformers-arising-from-non-helical-and-helical-peptides-using-ion-mobility-spectrometry-and-gas-phase-hydrogen-deuterium-exchange
#18
Ahmad Kiani Karanji, Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Sandra N Majuta, Kushani Attanayake, Stephen J Valentine
The dominant gas-phase conformer of [M+3H]3+ ions of the model peptide acetyl-PSSSSKSSSSKSSSSKSSSSK has been examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. The [M+3H]3+ peptide ions are observed predominantly as a relatively compact conformer type. Upon subjecting these ions to electron transfer dissociation (ETD), the level of protection for each amino acid residue in the peptide sequence is assessed. The overall per-residue deuterium uptake is observed to be relatively more efficient for the neutral residues than for the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK...
October 15, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30291556/initial-benchmarking-of-the-liquid-sampling-atmospheric-pressure-glow-discharge-orbitrap-system-against-traditional-atomic-mass-spectrometry-techniques-for-nuclear-applications
#19
Edward D Hoegg, Benjamin T Manard, E Miller Wylie, K J Mathew, Chelsea F Ottenfeld, R Kenneth Marcus
The integration of the liquid sampling-atmospheric pressure glow discharge (LS-APGD) ion source with Orbitrap mass spectrometers has resulted in new opportunities in the field of isotope ratio mass spectrometry. In a field that has been dominated by thermal ionization mass spectrometry (TIMS) and inductively coupled plasma mass spectrometry (ICP-MS) on quadrupole and scanning-mode sector field analyzer platforms for highly accurate and precise measurements, the LS-APGD-Orbitrap system offers a benchtop instrument capable of meeting the rigorous International Target Values for measurement uncertainty for uranium (U)...
October 5, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/30284205/sequence-ion-structures-and-dissociation-chemistry-of-deprotonated-sucrose-anions
#20
Benjamin J Bythell, Jordan M Rabus, Ashley R Wagoner, Maha T Abutokaikah, Philippe Maître
We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1 -Y1 and C1 -Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]- , C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol-1 ) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm-1 ...
October 3, 2018: Journal of the American Society for Mass Spectrometry
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