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https://www.readbyqxmd.com/read/28518125/glycoproteomics-of-the-extracellular-matrix-a-method-for-intact-glycopeptide-analysis-using-mass-spectrometry
#1
Javier Barallobre-Barreiro, Ferheen Baig, Marika Fava, Xiaoke Yin, Manuel Mayr
Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). Using proteomics, we have previously identified more than 150 ECM and ECM-associated proteins in cardiovascular tissues. Notably, many ECM proteins are glycosylated. This post-translational modification affects protein folding, solubility, binding, and degradation. We have developed a sequential extraction and enrichment method for ECM proteins that is compatible with the subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of intact glycopeptides...
April 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28501617/biochemical-and-biophysical-characterization-of-ruthenation-of-brca1-ring-protein-by-rapta-complexes-and-its-e3-ubiquitin-ligase-activity
#2
Pornvichai Temboot, Ronald F S Lee, Laure Menin, Luc Patiny, Paul J Dyson, Adisorn Ratanaphan
RAPTA compounds, ([Ru(η(6)-arene)(PTA)X2], PTA = 1,3,5-triaza-7-phosphaadamantane), have been reported to overcome drug resistance in cisplatin resistant cells. However, the exact mechanism of these complexes is still largely unexplored. In this study, the interaction of some RAPTA compounds with the N-terminal region of the BRCA1 RING domain protein was investigated. The binding of the RAPTA compounds to the BRCA1 protein results in the release of Zn(2+) ions in a dose and time dependent manner, as well as thermal alteration of ruthenated-BRCA1 proteins...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28485292/assessment-and-management-of-retraction-pockets
#3
Alper Cuneyt, Ewa Olszewska
This manuscript intends to review types, pathogenesis, associated risk factors, and potential methods of prevention and treatment of the retraction pockets in adults and children. The importance of retraction pockets (RP) lies in loss of original histological and anatomical structure which is associated with development of ossicular chain erosion, cho¬lesteatoma formation and potentially life threatening complications of cholesteatoma. The trans-mucosal exchange each gas in the middle ear (ME) is towards equalizing its partial pressures with the partial pressure in the environ¬ment...
February 28, 2017: Otolaryngologia Polska
https://www.readbyqxmd.com/read/28483786/faster-aspart-versus-insulin-aspart-as-part-of-a-basal-bolus-regimen-in-inadequately-controlled-type-2-diabetes-the-onset-2-trial
#4
Keith Bowering, Christopher Case, John Harvey, Michael Reeves, Michael Sampson, Robert Strzinek, Ditte-Marie Bretler, Rikke Beck Bang, Bruce W Bode
OBJECTIVE: This multicenter, double-blind, treat-to-target, phase 3 trial evaluated the efficacy and safety of fast-acting insulin aspart (faster aspart) versus insulin aspart (IAsp) in adults with type 2 diabetes receiving basal insulin and oral antidiabetic agents. RESEARCH DESIGN AND METHODS: The primary end point was HbA1c change from baseline after 26 weeks' treatment. After an 8-week run-in to optimize basal insulin, subjects were randomized (1:1) to mealtime faster aspart (n = 345) or IAsp (n = 344), titrated using a simple daily patient-driven algorithm, plus insulin glargine U100 and metformin...
May 8, 2017: Diabetes Care
https://www.readbyqxmd.com/read/28460638/using-patient-values-and-preferences-to-inform-the-importance-of-health-outcomes-in-practice-guideline-development-following-the-grade-approach
#5
Yuan Zhang, Pablo Alonso Coello, Jan Brożek, Wojtek Wiercioch, Itziar Etxeandia-Ikobaltzeta, Elie A Akl, Joerg J Meerpohl, Waleed Alhazzani, Alonso Carrasco-Labra, Rebecca L Morgan, Reem A Mustafa, John J Riva, Ainsley Moore, Juan José Yepes-Nuñez, Carlos Cuello-Garcia, Zulfa AlRayees, Veena Manja, Maicon Falavigna, Ignacio Neumann, Romina Brignardello-Petersen, Nancy Santesso, Bram Rochwerg, Andrea Darzi, Maria Ximena Rojas, Yaser Adi, Claudia Bollig, Reem Waziry, Holger J Schünemann
BACKGROUND: There are diverse opinions and confusion about defining and including patient values and preferences (i.e. the importance people place on the health outcomes) in the guideline development processes. This article aims to provide an overview of a process for systematically incorporating values and preferences in guideline development. METHODS: In 2013 and 2014, we followed the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to adopt, adapt and develop 226 recommendations in 22 guidelines for the Ministry of Health of the Kingdom of Saudi Arabia...
May 2, 2017: Health and Quality of Life Outcomes
https://www.readbyqxmd.com/read/28453255/characterization-and-identification-of-dityrosine-cross-linked-peptides-using-tandem-mass-spectrometry
#6
Soumya Mukherjee, Eugene A Kapp, Amber Lothian, Anne M Roberts, Yury Vasilev, Berin Boughton, Kevin Jeffrey Barnham, W Mei Kok, Craig A Hutton, Colin L Masters, Ashley Bush, Joseph S Beckman, Somdatta Ghosh Dey, Blaine R Roberts
The use of mass spectrometry coupled with chemical cross-linking of proteins has become a powerful tool for proteins structure and interactions studies. Unlike structural analysis of proteins using chemical reagents specific for lysine or cysteine residues, identification of gas-phase fragmentation patterns of endogenous dityrosine cross-linked peptides have not been investigated. Dityrosine cross-linking in proteins and peptides are clinical markers of oxidative stress, ageing and neurodegenerative diseases including Alzheimer's disease and Parkinson's disease...
April 28, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28447219/an-ethcd-based-method-for-discrimination-of-leucine-and-isoleucine-residues-in-tryptic-peptides
#7
Sergey S Zhokhov, Sergey V Kovalyov, Tatiana Yu Samgina, Albert T Lebedev
An EThcD-based approach for the reliable discrimination of isomeric leucine and isoleucine residues in peptide de novo sequencing procedure has been proposed. A multistage fragmentation of peptide ions was performed with Orbitrap Elite mass spectrometer in electrospray ionization mode. At the first stage, z-ions were produced by ETD or ETcaD fragmentation of doubly or triply charged peptide precursor ions. These primary ions were further fragmented by HCD with broad-band ion isolation, and the resulting w-ions showed different mass for leucine and isoleucine residues...
April 26, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28432653/analyzing-glycopeptide-isomers-by-combining-differential-mobility-spectrometry-with-electron-and-collision-based-tandem-mass-spectrometry
#8
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
#9
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
#10
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
#11
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
#12
Lars Kolbowski, Marta L 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...
May 16, 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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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