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Journal of the American Society for Mass Spectrometry

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https://www.readbyqxmd.com/read/28717933/a-novel-ms-cleavable-azo-cross-linker-for-peptide-structure-analysis-by-free-radical-initiated-peptide-sequencing-frips
#1
Claudio Iacobucci, Christoph Hage, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28717932/a-w-geometry-ortho-tof-ms-with-high-resolution-and-up-to-100-duty-cycle-for-ms-ms
#2
Igor V Chernushevich, Samuel I Merenbloom, Suya Liu, Nic Bloomfield
Orthogonal injection time-of-flight (orthoTOF) mass spectrometry (MS) is the most prevalent form of TOFMS, owing to its greater control over incoming ion energy, the ability to correct for aberrations in incoming ion velocity and position, and its ability to provide an entire mass spectrum within a single scan. However, the duty cycle of orthoTOFMS is low compared with scanning analyzers, which can have 100% duty cycle when measuring a single type of ion. Typical duty cycles for orthoTOFMS range from 1% to 30%, depending on instrument geometry...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28717931/noncovalent-halogen-bonding-as-a-mechanism-for-gas-phase-clustering
#3
Christina Wegeberg, William A Donald, Christine J McKenzie
Gas-phase clustering of nonionizable iodylbenzene (PhIO2) is attributed to supramolecular halogen bonding. Electrospray ionization results in the formation of ions of proton-charged and preferably sodium-charged clusters assignable to [H(PhIO2) n ](+), n = 1-7; [Na(PhIO2) n ](+), n = 1-6; [Na2(PhIO2) n ](2+), n = 7-20; [HNa(PhIO2) n ](2+), n = 6-19; [HNa2(PhIO2) n ](3+), n = 15-30; and [Na3(PhIO2) n ](3+), n = 14-30. The largest cluster detected has a supramolecular mass of 7147 Da. Electronic structure calculations using the M06-2X functional with the 6-311++G(d,p) basis set for C, H, and O, and LANL2DZ basis set for I and Na predict 298 K binding enthalpies for the protonated and sodiated iodylbenzene dimers and trimers are greater than 180 kJ/mol...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28710594/addressing-a-common-misconception-ammonium-acetate-as-neutral-ph-buffer-for-native-electrospray-mass-spectrometry
#4
Lars Konermann
Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pKa ± 1 pH unit...
July 14, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28707193/laser-pulse-width-dependence-and-ionization-mechanism-of-matrix-assisted-laser-desorption-ionization
#5
Sheng-Ping Liang, I-Chung Lu, Shang-Ting Tsai, Jien-Lian Chen, Yuan Tseh Lee, Chi-Kung Ni
Ultraviolet laser pulses at 355 nm with variable pulse widths in the region from 170 ps to 1.5 ns were used to investigate the ionization mechanism of matrix-assisted laser desorption/ionization (MALDI) for matrices 2,5-dihydroxybenzoic acid (DHB), α-cyano-4-hydroxycinnamic acid (CHCA), and sinapinic acid (SA). The mass spectra of desorbed ions and the intensity and velocity distribution of desorbed neutrals were measured simultaneously for each laser shot. These quantities were found to be independent of the laser pulse width...
July 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28702929/the-mechanism-behind-top-down-uvpd-experiments-making-sense-of-apparent-contradictions
#6
Ryan R Julian
Top-down ultraviolet photodissociation (UVPD) allows greater sequence coverage than any other currently available method, often fracturing the vast majority of peptide bonds in whole proteins. At the same time, UVPD can be used to dissociate noncovalent complexes assembled from multiple proteins without breaking any covalent bonds. Although the utility of these experiments is unquestioned, the mechanism underlying these seemingly contradictory results has been the subject of many discussions. Herein, some fundamental considerations of photochemistry are briefly summarized within the context of a proposed mechanism that rationalizes the experimental results obtained by UVPD...
July 12, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28699065/n-protonated-isomers-and-coulombic-barriers-to-dissociation-of-doubly-protonated-ala8arg
#7
Fredrik Haeffner, Karl K Irikura
Collision-induced dissociation (or tandem mass spectrometry, MS/MS) of a protonated peptide results in a spectrum of fragment ions that is useful for inferring amino acid sequence. This is now commonplace and a foundation of proteomics. The underlying chemical and physical processes are believed to be those familiar from physical organic chemistry and chemical kinetics. However, first-principles predictions remain intractable because of the conflicting necessities for high accuracy (to achieve qualitatively correct kinetics) and computational speed (to compensate for the high cost of reliable calculations on such large molecules)...
July 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28699064/joule-heating-and-thermal-denaturation-of-proteins-in-nano-esi-theta-tips
#8
Feifei Zhao, Sarah M Matt, Jiexun Bu, Owen G Rehrauer, Dor Ben-Amotz, Scott A McLuckey
Electro-osmotically induced Joule heating in theta tips and its effect on protein denaturation were investigated. Myoglobin, equine cytochrome c, bovine cytochrome c, and carbonic anhydrase II solutions were subjected to electro-osmosis in a theta tip and all of the proteins were denatured during the process. The extent of protein denaturation was found to increase with the applied square wave voltage and electrolyte concentration. The solution temperature at the end of a theta tip was measured directly by Raman spectroscopy and shown to increase with the square wave voltage, thereby demonstrating the effect of Joule heating through an independent method...
July 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28699063/determination-of-collision-cross-sections-using-a-fourier-transform-electrostatic-linear-ion-trap-mass-spectrometer
#9
Eric T Dziekonski, Joshua T Johnson, Kenneth W Lee, Scott A McLuckey
Collision cross sections (CCSs) were determined from the frequency-domain linewidths in a Fourier transform electrostatic linear ion trap. With use of an ultrahigh-vacuum precision leak valve and nitrogen gas, transients were recorded as the background pressure in the mass analyzer chamber was varied between 4× 10(-8) and 7 × 10(-7) Torr. The energetic hard-sphere ion-neutral collision model, described by Xu and coworkers, was used to relate the recorded image charge to the CCS of the molecule. In lieu of our monoisotopically isolating the mass of interest, the known relative isotopic abundances were programmed into the Lorentzian fitting algorithm such that the linewidth was extracted from a sum of Lorentzians...
July 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28699062/rapid-analysis-of-ingredients-in-cream-using-ultrasonic-mist-direct-analysis-in-real-time-time-of-flight-mass-spectrometry
#10
Haruo Shimada, Katsuyuki Maeno, Kazumasa Kinoshita, Yasuo Shida
A novel method for the simultaneous detection of ingredients in pharmaceutical applications such as creams and lotions was developed. An ultrasonic atomizer has been used to produce a mist containing ingredients. The analyte molecules in the mist can be ionized by using direct analysis in real time (DART) at lower temperature than traditionally used, and we thus solved the problem of normal DART-MS measurement using a high-temperature gas. Thereby, molecular-related ions of heat-unstable components and nonvolatile components became detectable...
July 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28695533/electron-transfer-higher-energy-collision-dissociation-ethcd-enabled-intact-glycopeptide-glycoproteome-characterization
#11
Qing Yu, Bowen Wang, Zhengwei Chen, Go Urabe, Matthew S Glover, Xudong Shi, Lian-Wang Guo, K Craig Kent, Lingjun Li
Protein glycosylation, one of the most heterogeneous post-translational modifications, can play a major role in cellular signal transduction and disease progression. Traditional mass spectrometry (MS)-based large-scale glycoprotein sequencing studies heavily rely on identifying enzymatically released glycans and their original peptide backbone separately, as there is no efficient fragmentation method to produce unbiased glycan and peptide product ions simultaneously in a single spectrum, and that can be conveniently applied to high throughput glycoproteome characterization, especially for N-glycopeptides, which can have much more branched glycan side chains than relatively less complex O-linked glycans...
July 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28695532/improved-precision-and-accuracy-of-quantification-of-rare-earth-element-abundances-via-medium-resolution-la-icp-ms
#12
Rebecca Funderburg, Ricardo Arevalo, Marek Locmelis, Tomoko Adachi
Laser ablation ICP-MS enables streamlined, high-sensitivity measurements of rare earth element (REE) abundances in geological materials. However, many REE isotope mass stations are plagued by isobaric interferences, particularly from diatomic oxides and argides. In this study, we compare REE abundances quantitated from mass spectra collected with low-resolution (m/Δm = 300 at 5% peak height) and medium-resolution (m/Δm = 2500) mass discrimination. A wide array of geological samples was analyzed, including USGS and NIST glasses ranging from mafic to felsic in composition, with NIST 610 employed as the bracketing calibrating reference material...
July 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28695531/gain-switching-for-a-detection-system-to-accommodate-a-newly-developed-maldi-based-quantification-method
#13
Sung Hee Ahn, Taeghwan Hyeon, Myung Soo Kim, Jeong Hee Moon
In matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF), matrix-derived ions are routinely deflected away to avoid problems with ion detection. This, however, limits the use of a quantification method that utilizes the analyte-to-matrix ion abundance ratio. In this work, we will show that it is possible to measure this ratio by a minor instrumental modification of a simple form of MALDI-TOF. This involves detector gain switching. Graphical Abstract ᅟ.
July 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28695530/the-synthesis-and-structural-characterization-of-graft-copolymers-composed-of-%C3%AE-pga-backbone-and-oligoesters-pendant-chains
#14
Iwona Kwiecień, Iza Radecka, Marek Kowalczuk, Katarzyna Jelonek, Arkadiusz Orchel, Grażyna Adamus
The novel copolymers composed of poly-γ-glutamic acid (γ-PGA) and oligoesters have been developed. The structures of the obtained copolymers including variety of end groups were determined at the molecular level with the aid of electrospray ionization multistage mass spectrometry (ESI-MS(n)). The fragmentation experiment performed for the selected sodium adducts of the copolymers confirmed that the developed methods lead to the formation of graft copolymers composed of poly-γ-glutamic acid (γ-PGA) backbone and oligoesters pendant chains...
July 10, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28685494/the-impact-of-phosphorylation-on-electron-capture-dissociation-of-proteins-a-top-down-perspective
#15
Bifan Chen, Xiao Guo, Trisha Tucholski, Ziqing Lin, Sean McIlwain, Ying Ge
Electron capture dissociation (ECD) is well suited for the characterization of phosphoproteins, with which labile phosphate groups are generally preserved during the fragmentation process. However, the impact of phosphorylation on ECD fragmentation of intact proteins remains unclear. Here, we have performed a systematic investigation of the phosphorylation effect on ECD of intact proteins by comparing the ECD cleavages of mono-phosphorylated α-casein, multi-phosphorylated β-casein, and immunoaffinity-purified phosphorylated cardiac troponin I with those of their unphosphorylated counterparts, respectively...
July 6, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28681361/top-down-lesa-mass-spectrometry-protein-analysis-of-gram-positive-and-gram-negative-bacteria
#16
Klaudia I Kocurek, Leanne Stones, Josephine Bunch, Robin C May, Helen J Cooper
We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS...
July 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28681360/intact-protein-analysis-at-21-tesla-and-x-ray-crystallography-define-structural-differences-in-single-amino-acid-variants-of-human-mitochondrial-branched-chain-amino-acid-aminotransferase-2-bcat2
#17
Lissa C Anderson, Maria Håkansson, Björn Walse, Carol L Nilsson
Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments...
July 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28681359/intramolecular-halogen-atom-coordinated-h-transfer-via-ion-neutral-complex-in-the-gas-phase-dissociation-of-protonated-dichlorvos-derivatives
#18
Xiaoping Zhang, Shuai Cheng
Intramolecular halogen atom coordinated H transfer reaction in the gas phase dissociation of protonated dichlorvos derivatives has been explored by electrospray ionization tandem mass spectrometry. Upon collisional activation, protonated dichlorvos underwent dissociation reaction via cleavage of the P-O bond to give reactive ion-neutral complex (INC) intermediate, [dimethoxylphosphinoylium + dichloroacetaldehyde]. Besides direct dissociation of the complex, intramolecular chlorine atom coordinated H transfer reaction within the complex takes place, leading to the formation of protonated dimethyl chlorophosphate...
July 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28681358/delivering-transmembrane-peptide-complexes-to-the-gas-phase-using-nanodiscs-and-electrospray-ionization
#19
Jun Li, Michele R Richards, Elena N Kitova, John S Klassen
The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)(2+) ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å(2) (conformation 1, C1), 708 Å(2) (C2), and 737 Å(2) (C3)...
July 5, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28664477/maximizing-ion-transmission-in-differential-mobility-spectrometry
#20
Bradley B Schneider, Frank Londry, Erkinjon G Nazarov, Yang Kang, Thomas R Covey
We provide modeling and experimental data describing the dominant ion-loss mechanisms for differential mobility spectrometry (DMS). Ion motion is considered from the inlet region of the mobility analyzer to the DMS exit, and losses resulting from diffusion to electrode surfaces, insufficient effective gap, ion fragmentation, and fringing field effects are considered for a commercial DMS system with 1-mm gap height. It is shown that losses due to diffusion and radial oscillations can be minimized with careful consideration of residence time, electrode spacing, gas flow rate, and waveform frequency...
June 29, 2017: Journal of the American Society for Mass Spectrometry
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