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Journal of the American Society for Mass Spectrometry

Yoshitomo Hamuro
A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism...
January 20, 2017: Journal of the American Society for Mass Spectrometry
Mellie June Paulines, Patrick A Limbach
Even with the advent of high throughput methods to detect modified ribonucleic acids (RNAs), mass spectrometry remains a reliable method to detect, characterize, and place post-transcriptional modifications within an RNA sequence. Here we have developed a stable isotope labeling comparative analysis of RNA digests (SIL-CARD) approach, which improves upon the original (18)O/(16)O labeling CARD method. Like the original, SIL-CARD allows sequence or modification information from a previously uncharacterized in vivo RNA sample to be obtained by direct comparison with a reference RNA, the sequence of which is known...
January 19, 2017: Journal of the American Society for Mass Spectrometry
K Ilker Sen, Wilfred H Tang, Shruti Nayak, Yong J Kil, Marshall Bern, Berk Ozoglu, Beatrix Ueberheide, Darryl Davis, Christopher Becker
Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation...
January 19, 2017: Journal of the American Society for Mass Spectrometry
Rong-Sheng Yang, Huaming Sheng, Katrina W Lexa, Edward C Sherer, Li-Kang Zhang, Bangping Xiang, Roy Helmy, Bing Mao
An unusual in-source fragmentation pattern observed for 14 doubly quaternized cinchona alkaloid-based phase-transfer catalysts (PTC) was studied using (+)-ESI high resolution mass spectrometry. Loss of the substituted benzyl cation (R1 or R2) was found to be the major product ion [M(2+) - R1(+) or R2(+)](+) in MS spectra of all PTC compounds. A Hofmann elimination product ion [M - H](+) was also observed. Only a small amount of the doubly charged M(2+) ions were observed in the MS spectra, likely due to strong Columbic repulsion between the two quaternary ammonium cations in the gas phase...
January 18, 2017: Journal of the American Society for Mass Spectrometry
Randy W Purves, Satendra Prasad, Michael Belford, Albert Vandenberg, Jean-Jacques Dunyach
The implementation of an aerodynamic mechanism to improve ion sampling between nanoelectrospray (n-ESI) and FAIMS was recently reported for proteomic analyses. This investigation explores the new FAIMS interface for small molecule analysis at high liquid flow rates and includes an examination of key differences in ionization between heated-ESI (HESI) and n-ESI. The sheath gas, critical for desolvation with HESI, affects FAIMS operation as higher FAIMS gas flow rates are required to achieve sufficient desolvation...
January 17, 2017: Journal of the American Society for Mass Spectrometry
Pengfei Li, Glen P Jackson
1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways...
January 13, 2017: Journal of the American Society for Mass Spectrometry
David Z Keifer, Andrew W Alexander, Martin F Jarrold
Spontaneous mass and charge losses from individual multi-megadalton ions have been observed with charge detection mass spectrometry (CDMS) by trapping single hepatitis B virus (HBV) capsids for 3 s. Gradual increases in the oscillation frequency of single ions in the ion trap are attributed mainly to mass loss (probably solvent, water, and/or salt). The total mass lost during the 3 s trapping period peaks at around 20 kDa for 4 MDa HBV T = 4 capsids. Discrete frequency drops punctuate the gradual increases in the oscillation frequencies...
January 12, 2017: Journal of the American Society for Mass Spectrometry
Hongyan Ma, Daniel G Delafield, Zhe Wang, Jianlan You, Si Wu
The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated...
January 12, 2017: Journal of the American Society for Mass Spectrometry
Juha-Pekka Hieta, Anu Vaikkinen, Samuli Auno, Heikki Räikkönen, Markus Haapala, Gianmario Scotti, Jaakko Kopra, Petteri Piepponen, Tiina J Kauppila
In mass spectrometry imaging of tissues, the size of structures that can be distinguished is determined by the spatial resolution of the imaging technique. Here, the spatial resolution of IR laser ablation is markedly improved by increasing the distance between the laser and the focusing lens. As the distance between the laser and the lens is increased from 1 to 18 m, the ablation spot size decreases from 440 to 44 μm. This way, only the collimated center of the divergent laser beam is directed on the focusing lens, which results in better focusing of the beam...
January 11, 2017: Journal of the American Society for Mass Spectrometry
Candice Z Ulmer, Jeremy P Koelmel, Jared M Ragland, Timothy J Garrett, John A Bowden
Lipidomics, the comprehensive measurement of lipid species in a biological system, has promising potential in biomarker discovery and disease etiology elucidation. Advances in chromatographic separation, mass spectrometric techniques, and novel substrate applications continue to expand the number of lipid species observed. The total number and type of lipid species detected in a given sample are generally indicative of the sample matrix examined (e.g., serum, plasma, cells, bacteria, tissue, etc.). Current exact mass lipid libraries are static and represent the most commonly analyzed matrices...
January 10, 2017: Journal of the American Society for Mass Spectrometry
Santosh Karki, Habiballah Sistani, Jieutonne J Archer, Fengjian Shi, Robert J Levis
Charge state distributions are measured using mass spectrometry for both native and denatured cytochrome c and myoglobin after laser vaporization from the solution state into an electrospray (ES) plume consisting of a series of solution additives differing in gas-phase basicity. The charge distribution depends on both the pH of the protein solution prior to laser vaporization and the gas-phase basicity of the solution additive employed in the ES solvent. Cytochrome c (myoglobin) prepared in solutions with pH of 7...
January 6, 2017: Journal of the American Society for Mass Spectrometry
Sung-Gun Park, Gordon A Anderson, James E Bruce
FT-based high performance mass analyzers yield increased resolving power and mass measurement accuracy, yet require increased duration of signal acquisition that can limit many applications. The implementation of stronger magnetic fields, multiple detection electrodes for harmonic signal detection, and an array of multiple mass analyzers arranged along the magnetic field axis have been used to decrease required acquisition time. The results presented here show that multiple ion cyclotron resonance (ICR) mass analyzers can also be implemented orthogonal to the central magnetic field axis...
January 5, 2017: Journal of the American Society for Mass Spectrometry
Sheng Wang, Chunsheng Xiao, Ying Li, Ling Ling, Xuesi Chen, Xinhua Guo
We report a novel strategy to achieve simultaneous one-step in-situ self-desalting and enrichment (OISE) of peptides/proteins on a facilely fabricated patterned MALDI steel plate with a circular paraffin-steel-polystyrene structure. The OISE plate could efficiently segregate salts from both analytes and matrices while retaining both analyte and matrix concentrate, and facilitating them to form homogeneous co-crystals on the centrally located polystyrene pattern. With the OISE plate, high quality and reproducible spectra could be obtained for low abundance peptides even in the presence of high salt concentrations (200 mM NH4HCO3, 1 M NaCl, or 400 mM urea)...
January 5, 2017: Journal of the American Society for Mass Spectrometry
Yanglan Tan, Ning Zhao, Jinfeng Liu, Pengfei Li, Corey N Stedwell, Long Yu, Nicolas C Polfer
Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations...
January 3, 2017: Journal of the American Society for Mass Spectrometry
Jack Henion, Russell Grant
No abstract text is available yet for this article.
January 3, 2017: Journal of the American Society for Mass Spectrometry
Mathilde Farenc, Matthias Witt, Kirsten Craven, Caroline Barrère-Mangote, Carlos Afonso, Pierre Giusti
Polyolefins such as polyethylene (PE) and polypropylene (PP) are often characterized from their pyrolysis products by Py-MS. Nowadays the development of plasma-based direct probe atmospheric pressure sources allow the direct analysis of these polymers. These sources operate at atmospheric pressure, which implies a limited control of the ionization conditions. It was shown that side reactions could occur with species present in air, such as O2, which may lead to the formation of oxidized compounds. In this work, ion mobility-mass spectrometry (IM-MS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR) were used for the exhaustive characterization of the PP and PE pyrolysis ions produced using plasma-based atmospheric pressure ion sources...
January 3, 2017: Journal of the American Society for Mass Spectrometry
Adam D Feenstra, Maria Emilia Dueñas, Young Jin Lee
High-spatial resolution mass spectrometry imaging (MSI) is crucial for the mapping of chemical distributions at the cellular and subcellular level. In this work, we improved our previous laser optical system for matrix-assisted laser desorption ionization (MALDI)-MSI, from ~9 μm practical laser spot size to a practical laser spot size of ~4 μm, thereby allowing for 5 μm resolution imaging without oversampling. This is accomplished through a combination of spatial filtering, beam expansion, and reduction of the final focal length...
January 3, 2017: Journal of the American Society for Mass Spectrometry
Alice L Pilo, Feifei Zhao, Scott A McLuckey
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O](+) derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O](+), [M-H](+), and [M-H-NH3](+) species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared...
January 3, 2017: Journal of the American Society for Mass Spectrometry
Majors J Badgett, Barry Boyes, Ron Orlando
Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein's function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts...
January 3, 2017: Journal of the American Society for Mass Spectrometry
Paula M Ladwig, David R Barnidge, Maria A V Willrich
As therapeutic monoclonal antibodies (mAbs) become more humanized, traditional tryptic peptide approaches used to measure biologics in serum become more challenging since unique clonotypic peptides used for quantifying the mAb may also be found in the normal serum polyclonal background. An alternative approach is to monitor the unique molecular mass of the intact light chain portion of the mAbs using liquid chromatography-mass spectrometry (LC-MS). Distinguishing a therapeutic mAb from a patient's normal polyclonal immunoglobulin (Ig) repertoire is the primary limiting factor when determining the limit of quantitation (LOQ) in serum...
December 21, 2016: Journal of the American Society for Mass Spectrometry
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