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Journal of the American Society for Mass Spectrometry

David J Harvey, Weston B Struwe
There is considerable potential for the use of ion mobility mass spectrometry in structural glycobiology due in large part to the gas-phase separation attributes not typically observed by orthogonal methods. Here, we evaluate the capability of traveling wave ion mobility combined with negative ion collision-induced dissociation to provide structural information on N-linked glycans containing multiple fucose residues forming the Lewisx and Lewisy epitopes. These epitopes are involved in processes such as cell-cell recognition and are important as cancer biomarkers...
May 22, 2018: Journal of the American Society for Mass Spectrometry
Jiana Duan, I Jonathan Amster
The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2 ), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins...
May 22, 2018: Journal of the American Society for Mass Spectrometry
Wengang Chai, Yibing Zhang, Laura Mauri, Maria G Ciampa, Barbara Mulloy, Sandro Sonnino, Ten Feizi
Gangliosides, as plasma membrane-associated sialylated glycolipids, are antigenic structures and they serve as ligands for adhesion proteins of pathogens, for toxins of bacteria, and for endogenous proteins of the host. The detectability by carbohydrate-binding proteins of glycan antigens and ligands on glycolipids can be influenced by the differing lipid moieties. To investigate glycan sequences of gangliosides as recognition structures, we have underway a program of work to develop a "gangliome" microarray consisting of isolated natural gangliosides and neoglycolipids (NGLs) derived from glycans released from them, and each linked to the same lipid molecule for arraying and comparative microarray binding analyses...
May 11, 2018: Journal of the American Society for Mass Spectrometry
Thierry N J Fouquet, Robert B Cody, Yuka Ozeki, Shinya Kitagawa, Hajime Ohtani, Hiroaki Sato
The Kendrick mass defect (KMD) analysis of multiply charged polymeric distributions has recently revealed a surprising isotopic split in their KMD plots-namely a 1/z difference between KMDs of isotopes of an oligomer at charge state z. Relying on the KMD analysis of actual and simulated distributions of poly(ethylene oxide) (PEO), the isotopic split is mathematically accounted for and found to go with an isotopic misalignment in certain cases. It is demonstrated that the divisibility (resp. indivisibility) of the nominal mass of the repeating unit (R) by z is the condition for homolog ions to line up horizontally (resp...
May 11, 2018: Journal of the American Society for Mass Spectrometry
John D Benktander, Solomon T Gizaw, Stefan Gaunitz, Milos V Novotny
Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample...
May 9, 2018: Journal of the American Society for Mass Spectrometry
Ansgar Thomas Kirk, Tim Kobelt, Hauke Spehlbrink, Stefan Zimmermann
Corona discharge ionization sources are often used in ion mobility spectrometers (IMS) when a non-radioactive ion source with high ion currents is required. Typically, the corona discharge is followed by a reaction region where analyte ions are formed from the reactant ions. In this work, we present a simple yet sufficiently accurate model for predicting the ion current available at the end of this reaction region when operating at reduced pressure as in High Kinetic Energy Ion Mobility Spectrometers (HiKE-IMS) or most IMS-MS instruments...
May 8, 2018: Journal of the American Society for Mass Spectrometry
Maha T Abutokaikah, Joseph W Frye, John Tschampel, Jordan M Rabus, Benjamin J Bythell
We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2 A1 and 0,3 A1 ). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom...
May 8, 2018: Journal of the American Society for Mass Spectrometry
Andrey Dyachenko, Sem Tamara, Albert J R Heck
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Richard Y-C Huang, Steven R O'Neil, Daša Lipovšek, Guodong Chen
Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Vera B Ivleva, Nicole A Schneck, Deepika Gollapudi, Frank Arnold, Jonathan W Cooper, Q Paula Lei
CAP256 is one of the highly potent, broadly neutralizing monoclonal antibodies (bNAb) designed for HIV-1 therapy. During the process development of one of the constructs, an unexpected product-related impurity was observed via microfluidics gel electrophoresis. A panel of complementary LC-MS analyses was applied for the comprehensive characterization of CAP256 which included the analysis of the intact and reduced protein, the middle-up approach, and a set of complementary peptide mapping techniques and verification of the disulfide bonds...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Matteo T Degiacomi
Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Huong T H Nguyen, Prokopis C Andrikopoulos, Lubomír Rulíšek, Christopher J Shaffer, František Tureček
We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Zhidan Chen, Stephen L Coy, Evan L Pannkuk, Evagelia C Laiakis, Albert J Fornace, Paul Vouros
High-throughput methods to assess radiation exposure are a priority due to concerns that include nuclear power accidents, the spread of nuclear weapon capability, and the risk of terrorist attacks. Metabolomics, the assessment of small molecules in an easily accessible sample, is the most recent method to be applied for the identification of biomarkers of the biological radiation response with a useful dose-response profile. Profiling for biomarker identification is frequently done using an LC-MS platform which has limited throughput due to the time-consuming nature of chromatography...
May 7, 2018: Journal of the American Society for Mass Spectrometry
Adam Pap, Eva Klement, Eva Hunyadi-Gulyas, Zsuzsanna Darula, Katalin F Medzihradszky
A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined...
May 5, 2018: Journal of the American Society for Mass Spectrometry
(no author information available yet)
No abstract text is available yet for this article.
May 4, 2018: Journal of the American Society for Mass Spectrometry
Matthew A Downey, Maxwell J Giammona, Christian A Lang, Steven K Buratto, Ambuj Singh, Michael T Bowers
Alzheimer's disease (AD) is rapidly reaching epidemic status among a burgeoning aging population. Much evidence suggests the toxicity of this amyloid disease is most influenced by the formation of soluble oligomeric forms of amyloid β-protein, particularly the 42-residue alloform (Aβ42). Developing potential therapeutics in a directed, streamlined approach to treating this disease is necessary. Here we utilize the joint pharmacophore space (JPS) model to design a new molecule [AC0107] incorporating structural characteristics of known Aβ inhibitors, blood-brain barrier permeability, and limited toxicity...
April 30, 2018: Journal of the American Society for Mass Spectrometry
Lulu Sun, Bing Xue, Zhengxu Huang, Ping Cheng, Li Ma, Li Ding, Zhen Zhou
Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts...
April 30, 2018: Journal of the American Society for Mass Spectrometry
David J Foreman, Eric T Dziekonski, Scott A McLuckey
A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions...
April 30, 2018: Journal of the American Society for Mass Spectrometry
Wanpeng Ai, Honggang Nie, Shiyao Song, Xiaoyun Liu, Yu Bai, Huwei Liu
The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique...
April 30, 2018: Journal of the American Society for Mass Spectrometry
Yosuke Kawai, Toshinobu Hondo, Kirk R Jensen, Michisato Toyoda, Kentaro Terada
Two different types of data acquisition methods, "averaging mode" and "ion-counting mode", have been used in a time-of-flight (TOF) mass spectrometry. The most common method is an averaging mode that sums waveform signals obtained from each flight cycle. While it is possible to process many ions arriving at the same TOF in one flight cycle, low-abundance ions are difficult to measure because ion signals are overwhelmed by noises from the detection system. An ion-counting mode is suitable for the detection of such low-concentration ions, but counting loss occurs when two or more ions arrive at the detector within the dead time of the acquisition system...
April 26, 2018: Journal of the American Society for Mass Spectrometry
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