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https://www.readbyqxmd.com/read/28432653/analyzing-glycopeptide-isomers-by-combining-differential-mobility-spectrometry-with-electron-and-collision-based-tandem-mass-spectrometry
#1
J Larry Campbell, Takashi Baba, Chang Liu, Catherine S Lane, J C Yves Le Blanc, James W Hager
Differential mobility spectrometry (DMS) has been employed to separate isomeric species in several studies. Under the right conditions, factors such as separation voltage, temperature, the presence of chemical modifiers, and residence time can combine to provide unique signal channels for isomeric species. In this study, we examined a set of glycopeptide isomers, MUC5AC-3 and MUC5AC-13, which bear an N-acetyl-galactosamine (GalNAc) group on either threonine-3 or threonine-13. When analyzed as a mixture, the resulting MS and MS/MS spectra yield fragmentation patterns that cannot discern these convolved species...
April 21, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28412463/frameworks-for-adaptation-of-health-guidelines-a-methodological-survey
#2
REVIEW
Andrea Darzi, Elias A Abou-Jaoude, Arnav Agarwal, Chantal Lakis, Wojtek Wiercioch, Nancy Santesso, Hneine Brax, Fadi El-Jardali, Holger J Schünemann, Elie A Akl
BACKGROUND: Our objective was to identify and describe published frameworks for adaptation of clinical, public health and health services guidelines. METHODS: We included reports describing methods of adaptation of guidelines in sufficient detail to allow its reproducibility. We searched Medline, and EMBASE databases. We also searched personal files, as well manuals and handbooks of organizations and professional societies that proposed methods of adaptation and adoption of guidelines...
April 12, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28409445/ion-mobility-spectrometry-high-resolution-ltq-orbitrap-mass-spectrometry-for-analysis-of-homemade-explosives
#3
Nathan Hagan, Ilana Goldberg, Adam Graichen, Amanda St Jean, Ching Wu, David Lawrence, Plamen Demirev
The detailed chemical characterization of homemade explosives (HMEs) and other chemicals that can mimic or mask the presence of explosives is important for understanding and improving the performance of commercial instrumentation used for explosive detection. To that end, an atmospheric-pressure drift tube ion mobility spectrometry (IMS) instrument has been successfully coupled to a commercial tandem mass spectrometry (MS) system. The tandem MS system is comprised of a linear ion trap and a high resolution Orbitrap analyzer...
April 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28404794/neprosin-a-selective-prolyl-endoprotease-for-bottom-up-proteomics-and-histone-mapping
#4
Christoph U Schraeder, Linda Lee, Martial Rey, Vladimir Sarpe, Petr Man, Seema Sharma, Vlad Zabrouskov, Brett Larsen, David C Schriemer
Trypsin dominates bottom-up proteomics, but there are reasons to consider alternative enzymes. Improving sequence coverage, exposing proteomic dark matter and clustering post-translational modifications in different ways and with higher-order drive the pursuit of reagents complementary to trypsin. Additionally, enzymes that are easy to use and generate larger peptides that capitalize upon newer fragmentation technologies should have a place in proteomics. We expressed and characterized recombinant neprosin, a novel prolyl endoprotease of the DUF239 family, which preferentially cleaves C-terminal to proline residues under highly acidic conditions...
April 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28402676/optimizing-the-parameters-governing-the-fragmentation-of-cross-linked-peptides-in-a-tribrid-mass-spectrometer
#5
Lars Kolbowski, Marta Lavouras Mendes, Juri Rappsilber
We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD...
April 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28395773/improving-data-quality-and-preserving-hcd-generated-reporter-ions-with-ethcd-for-isobaric-tag-based-quantitative-proteomics-and-proteome-wide-ptm-studies
#6
Qing Yu, Xudong Shi, Yu Feng, K Craig Kent, Lingjun Li
Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states...
May 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28383256/phosphoproteomics-with-activated-ion-electron-transfer-dissociation
#7
Nicholas M Riley, Alexander S Hebert, Gerhard Dürnberger, Florian Stanek, Karl Mechtler, Michael S Westphall, Joshua J Coon
The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods...
April 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28383247/implementation-of-activated-ion-electron-transfer-dissociation-on-a-quadrupole-orbitrap-linear-ion-trap-hybrid-mass-spectrometer
#8
Nicholas M Riley, Michael S Westphall, Alexander S Hebert, Joshua J Coon
Using concurrent IR photoactivation during electron transfer dissociation (ETD) reactions, i.e., activated ion ETD (AI-ETD), significantly increases dissociation efficiency resulting in improved overall performance. Here we describe the first implementation of AI-ETD on a quadrupole-Orbitrap-quadrupole linear ion trap (QLT) hybrid MS system (Orbitrap Fusion Lumos) and demonstrate the substantial benefits it offers for peptide characterization. First, we show that AI-ETD can be implemented in a straightforward manner by fastening the laser and guiding optics to the instrument chassis itself, making alignment with the trapping volume of the QLT simple and robust...
April 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28381646/analysis-of-phosphoinositide-3-kinase-inhibitors-by-bottom-up-electron-transfer-dissociation-hydrogen-deuterium-exchange-mass-spectrometry
#9
Glenn Robert Masson, Sarah L Maslen, Roger L Williams
Until recently, one of the major limitations of Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) was the peptide-level resolution afforded by proteolytic digestion. This limitation can be selectively overcome through the use of Electron Transfer Dissociation (ETD) to fragment peptides in a manner that allows the retention of the deuterium signal to produce Hydrogen Deuterium Exchange Tandem Mass Spectrometry (HDX-MS/MS). Here we describe the application of HDX-MS/MS to structurally screen inhibitors of the oncogene phosphoinositide 3-kinase (PI3K) catalytic p110α subunit...
April 5, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28377194/applying-grade-to-coverage-decisions-results-of-a-stakeholder-survey-and-workshop
#10
Philipp Dahm, Andrew D Oxman, Benjamin Djulbegovic, Gordon H Guyatt, M Hassan Murad, Laura Amato, Elena Parmelli, Marina Davoli, Rebecca L Morgan, Reem A Mustafa, Shahnaz Sultan, Yngve Falck-Ytter, Elie A Akl, Holger J Schünemann
BACKGROUND: Coverage decisions are complex and require the consideration of many factors. A well-defined, transparent process could improve decision-making and facilitate decision-maker accountability. METHODS: We surveyed key United States (U.S.)-based stakeholders regarding their current approaches for coverage decisions. Then we held a workshop to test an evidence-to-decision (EtD) framework for coverage based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria...
April 1, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28374314/leveraging-electron-transfer-dissociation-for-site-selective-radical-generation-applications-for-peptide-epimer-analysis
#11
Yana A Lyon, Gregory Beran, Ryan R Julian
Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer...
April 3, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28368811/novoexd-de-novo-peptide-sequencing-for-etd-ecd-spectra
#12
Yan Yan, Anthony J Kusalik, Fang-Xiang Wu
De novo peptide sequencing using tandem mass spectrometry (MS/MS) data has become a major computational method for sequence identification in recent years. With the development of new instruments and technology, novel computational methods have emerged with enhanced performance. However, there are only a few methods focusing on ECD/ETD spectra, which mainly contain variants of c -ions and z-ions. Here, a de novo sequencing method for ECD/ETD spectra, NovoExD, is presented. NovoExD applies a new form of spectrum graph with multiple edge types (called a GMET), considers multiple peptide tags, and integrates amino acid combination (AAC) and fragment ion charge information...
March 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28361174/eustachian-tuboplasty-and%C3%A2-shrinkage-of-ostial-mucosa-with-new-devices-including-a-proposal-of-a-classification%C3%A2-system
#13
L Di Rienzo Businco, A Di Mario, M Tombolini, A Mattei, M Lauriello
OBJECTIVE: A new combined approach to Eustachian tube dysfunction (ETD) employing new minimally invasive devices is described. STUDY DESIGN: An anatomoclinical classification of ETD was conceived to allow correct categorization of patients and enable comparative studies to be performed. Herein, the authors report on their experience with a consecutive series of obstructive ETD patients treated by balloon dilation of the Eustachian tube using AERA (Acclarent, Menlo Park, CA, USA), combined with a quantic molecular resonance (QMR)-mediated rhinopharyngeal tubal ostial mucosa shrinkage technique with a dedicated "Mitto" hand piece (Telea, Sandrigo-Vicenza, Italy)...
March 30, 2017: HNO
https://www.readbyqxmd.com/read/28356319/fast-acting-insulin-aspart-improves-glycemic-control-in-basal-bolus-treatment-for-type-1-diabetes-results-of-a-26-week-multicenter-active-controlled-treat-to-target-randomized-parallel-group-trial-onset-1
#14
David Russell-Jones, Bruce W Bode, Christophe De Block, Edward Franek, Simon R Heller, Chantal Mathieu, Athena Philis-Tsimikas, Ludger Rose, Vincent C Woo, Anne Birk Østerskov, Tina Graungaard, Richard M Bergenstal
OBJECTIVE: This multicenter, treat-to-target, phase 3 trial evaluated the efficacy and safety of fast-acting insulin aspart (faster aspart) versus conventional insulin aspart (IAsp) in adults with type 1 diabetes. RESEARCH DESIGN AND METHODS: The primary end point was change from baseline in HbA1c after 26 weeks. After an 8-week run-in, subjects were randomized (1:1:1) to double-blind mealtime faster aspart (n = 381), IAsp (n = 380), or open-label postmeal faster aspart (n = 382)-each with insulin detemir...
March 29, 2017: Diabetes Care
https://www.readbyqxmd.com/read/28351064/the-early-tech-development-course-experiential-commercialization-education-for-the-medical-academician
#15
Jonathan Servoss, Connie Chang, Jonathan Fay, Kevin Ward
PROBLEM: Research produced by medical academicians holds promise for developing into biomedical innovations in therapeutics, devices, diagnostics, and health care information technology; however, the road to biomedical innovation is fraught with risk, including the challenge of moving from basic research insight onto a viable commercialization path. Compounding this challenge is the growing demand on medical academicians to be more productive in their clinical, teaching, and research duties within a resource-constrained environment...
April 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/28346764/mapping-the-interactions-of-selective-biochemical-probes-of-antibody-conformation-by-hydrogen-deuterium-exchange-mass-spectrometry
#16
Ulrike Leurs, Hermann Beck, Lea Bonnington, Ingo Lindner, Ewa Pol, Kasper Dyrberg Rand
Protein-based pharmaceuticals represent the fastest growing group of drugs in development in the pharmaceutical industry. One of the major challenges in the discovery, development and distribution of biopharmaceuticals is the assessment of changes in their higher-order structure due to chemical modifications. Here, we investigate the interactions of three different biochemical probes (Fabs) generated to detect conformational changes in a therapeutic IgG1 antibody (mAbX) by local hydrogen-deuterium exchange mass spectrometry (HDX-MS)...
March 27, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28315238/comprehensive-gas-phase-peptide-ion-structure-studies-using-ion-mobility-techniques-part-2-gas-phase-hydrogen-deuterium-exchange-for-ion-population-estimation
#17
Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Amirmahdi Tafreshian, Stephen J Valentine
Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data...
March 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28291339/ubiquitin-chain-enrichment-middle-down-mass-spectrometry-enables-characterization-of-branched-ubiquitin-chains-in-cellulo
#18
Sean O Crowe, Ambar S J B Rana, Kirandeep K Deol, Ying Ge, Eric R Strieter
Ubiquitin (Ub) has a broad functional range that has been ascribed to the formation of an array of polymeric ubiquitin chains. Understanding the precise roles of ubiquitin chains, however, is difficult due to their complex chain topologies. Branched ubiquitin chains are particularly challenging, as multiple modifications on a single ubiquitin preclude the use of standard bottom-up proteomic approaches. Developing methods to overcome these challenges is crucial considering evidence suggesting branched chains regulate the stability of proteins...
March 29, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28248111/inclusion-complexation-of-etodolac-with-hydroxypropyl-beta-cyclodextrin-and-auxiliary-agents-formulation-characterization-and-molecular-modeling-studies
#19
Atul P Sherje, Vaidehi Kulkarni, Manikanta Murahari, Usha Y Nayak, Pritesh Bhat, Vasanti Suvarna, Bhushan Dravyakar
The present investigation was aimed to prepare inclusion complexes of a therapeutically important nonsteroidal anti-inflammatory drug, etodolac (ETD) with hydroxypropyl-beta-cyclodextrin (HP-β-CD) and to study the effect of l-arginine (l-Arg) as an auxiliary agent on the complexation efficiency of HP-β-CD to improve aqueous solubility and the dissolution property of ETD. The binary and ternary complexes were prepared by physical mixing, coevaporation, and spray drying methods. The complexes were characterized using differential scanning colorimetry (DSC), Fourier transform-infrared spectroscopy (FT-IR), and powder X-ray diffraction (PXRD) studies...
April 3, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28247191/a-lc-ms-all-in-one-workflow-for-site-specific-location-identification-and-quantification-of-n-o-glycosylation-in-human-chorionic-gonadotropin-drug-products
#20
Hongbin Zhu, Chen Qiu, Ashley C Ruth, David A Keire, Hongping Ye
Site-specific characterization of the N- and O-linked glycosylation on a set of different human chorionic gonadotropin (hCG) drug products was performed by a LC-MS method combining high resolution (120K at m/z 200) mass spectrometry, multiple dissociation methods, tandem mass tag (TMT 10plex) labeling, and partial least squares-discriminant analysis (PLS-DA). In total, the data provided identification, relative quantification, and comparison of site-specific glycosylation of protein therapeutics with a single experiment...
February 28, 2017: AAPS Journal
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