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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
#1
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-ubichem-ms-enables-characterization-of-branched-ubiquitin-chains-in-cellulo
#2
Sean O Crowe, Ambar S J B Rana, Kirandeep K Deol, Ying Ge, Eric R Strieter
Ubiquitin 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 14, 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
#3
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...
March 1, 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
#4
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
https://www.readbyqxmd.com/read/28245108/determination-of-the-disulfide-structure-of-murine-meteorin-a-neurotrophic-factor-by-lc-ms-and-electron-transfer-dissociation-high-energy-collisional-dissociation-analysis-of-proteolytic-fragments
#5
Dingyi Wen, Yongsheng Xiao, Malgorzata M Vecchi, Bang Jian Gong, Jana Dolnikova, R Blake Pepinsky
Meteorin and Cometin (Meteorin-like) are secreted proteins belonging to a newly discovered growth factor family. Both proteins play important roles in neural development and may have potential as therapeutic targets or agents. Meteorin and Cometin are homologues and contain ten evolutionarily conserved Cys residues across a wide variety of species. However, the status of the Cys residues has remained unknown. Here, we have successfully determined the disulfide structure for murine Meteorin by LC-MS analysis of fragments generated by trypsin plus endoprotease-Asp-N...
March 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28242452/top-down-analysis-of-immunoglobulin-g-isotypes-1-and-2-with-electron-transfer-dissociation-on-a-high-field-orbitrap-mass-spectrometer
#6
Luca Fornelli, Daniel Ayoub, Konstantin Aizikov, Xiaowen Liu, Eugen Damoc, Pavel A Pevzner, Alexander Makarov, Alain Beck, Yury O Tsybin
The increasing importance of immunoglobulins G (IgGs) as biotherapeutics calls for improved structural characterization methods designed for these large (~150kDa) macromolecules. Analysis workflows have to be rapid, robust, and require minimal sample preparation. In a previous work we showed the potential of Orbitrap Fourier transform mass spectrometry (FTMS) combined with electron transfer dissociation (ETD) for the top-down investigation of an intact IgG1, resulting in ~30% sequence coverage. Here, we describe a top-down analysis of two IgGs1 (adalimumab and trastuzumab) and one IgG2 (panitumumab) performed with ETD on a mass spectrometer equipped with a high-field Orbitrap mass analyzer...
February 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28229292/laser-eustachian-tuboplasty-for-eustachian-tube-dysfunction-a-case-series-review
#7
REVIEW
Benjamin John Miller, Mustafa Jaafar, Hassan A Elhassan
The authors reviewed the literature regarding the safety and efficacy of Laser Eustachian Tuboplasty (LETP) in the treatment of Eustachian tube dysfunction (ETD). Medline via Pubmed, OvidSP and Science Direct were consulted, with a supplementary manual review of citations. English language case series constituted a baseline for inclusion. Primary outcome measures were pre- and post-operative tympanometry, otoscopy findings, subjective symptoms and pure tone audiometry, and findings were stratified into short term (≤6 months) and long term (>6 months-5 years)...
February 22, 2017: European Archives of Oto-rhino-laryngology
https://www.readbyqxmd.com/read/28218834/unambiguous-identification-of-serine-and-threonine-pyrophosphorylation-using-neutral-loss-triggered-electron-transfer-higher-energy-collision-dissociation
#8
Martin Penkert, Lisa M Yates, Michael Schümann, David Perlman, Dorothea Fiedler, Eberhard Krause
Tandem mass spectrometry (MS/MS) has emerged as the core technology for identification of post-translational modifications (PTMs). Here, we report the mass spectrometry analysis of serine and threonine pyrophosphorylation, a protein modification that has eluded detection by conventional MS/MS methods. Analysis of a set of synthesized, site-specifically modified peptides by different fragmentation techniques shows that pyrophosphorylated peptides exhibit a characteristic neutral loss pattern of 98, 178, and 196 Da, which enables the distinction between isobaric pyro- and diphosphorylated peptides...
March 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28205028/the-outcomes-of-initial-endoscopic-transluminal-drainage-are-superior-to-percutaneous-drainage-for-patients-with-infected-pancreatic-necrosis-a-prospective-cohort-study
#9
Wen-Hua He, Yong Zhu, Yin Zhu, Pi Liu, Hao Zeng, Liang Xia, Chen Yu, Hai-Ming Chen, Xu Shu, Zhi-Jian Liu, You-Xiang Chen, Nong-Hua Lu
BACKGROUND AND STUDY AIM: The commonly used minimally invasive methods for patients with infected pancreatic necrosis (IPN) are initial endoscopic transluminal drainage (ETD) and percutaneous catheter drainage (PCD), which are followed, if necessary, by endoscopic or surgical necrosectomy. This study intends to explore which of the two minimally invasive treatments leads to a better prognosis. PATIENTS AND METHODS: Patients with IPN and an indication for intervention were prospectively enrolled and underwent either initial ETD or PCD followed, if necessary, by endoscopic or surgical necrosectomy...
February 15, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28196325/decoding-of-o-linked-glycosylation-by-mass-spectrometry
#10
SriHariRaju Mulagapati, Veerendra Koppolu, T Shantha Raju
Protein glycosylation (N- and O-linked) plays an important role in many biological processes, including protein structure and function. However, the structural elucidation of glycans, specifically O-linked glycans, remains a major challenge and is often overlooked during protein analysis. Recently, mass spectrometry (MS) has matured as a powerful technology for high-quality analytical characterization of O-linked glycans. This review summarizes the recent developments and insights of MS-based glycomics technologies, with a focus on mucin-type O-glycan analysis...
February 27, 2017: Biochemistry
https://www.readbyqxmd.com/read/28194953/click-chemistry-reagent-for-identification-of-sites-of-covalent-ligand-incorporation-in-integral-membrane-proteins
#11
Melissa M Budelier, Wayland W L Cheng, Lucie Bergdoll, Zi-Wei Chen, Jeff Abramson, Kathiresan Krishnan, Mingxing Qian, Douglas F Covey, James W Janetka, Alex S Evers
Identifying sites of protein-ligand interaction is important for structure-based drug discovery and understanding protein structure-function relationships. Mass spectrometry (MS) has emerged as a useful tool for identifying residues covalently modified by ligands. Current methods use database searches that are dependent on acquiring interpretable fragmentation spectra (MS2) of peptide-ligand adducts. This is problematic for identifying sites of hydrophobic ligand incorporation in integral membrane proteins (IMPs), where poor aqueous solubility and ionization of peptide-ligand adducts and collision-induced adduct loss hinder the acquisition of quality MS2 spectra...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193068/high-confidence-sequencing-of-phosphopeptides-by-electron-transfer-dissociation-mass-spectrometry-using-dinuclear-zinc-ii-complex
#12
Daiki Asakawa, Issey Osaka
Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS(2)) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn2L)(3+) (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS(2) analysis...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28179079/exploiting-charge-differences-for-the-analysis-of-challenging-post-translational-modifications-by-capillary-electrophoresis-mass-spectrometry
#13
Klaus Faserl, Bettina Sarg, Verena Maurer, Herbert H Lindner
Reversed-phase high-performance liquid chromatography (RP-HPLC) in combination with mass spectrometry (MS) is typically employed for mapping modifications in proteins and peptides. Here we applied a low-flow capillary electrophoresis (CE) -electrospray ionization interface coupled to Orbitrap mass spectrometers to analyze challenging modifications such as asparagine deamidation, aspartate isomerization, arginine citrullination, and phosphopeptide isomers. We achieved excellent resolution of asparagine (Asn), aspartic acid (Asp) and isoaspartic acid (iso-Asp) containing peptides using a synthetic peptide mixture...
February 1, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28178175/the-effect-of-nicardipine-on-the-surgical-pleth-index-during-thyroidectomy-under-general-anesthesia-a-prospective-double-blind-randomized-controlled-trial
#14
RANDOMIZED CONTROLLED TRIAL
Young Ju Won, Byung Gun Lim, Gwi Eun Yeo, Min Ki Lee, Dong Kyu Lee, Heezoo Kim, Il Ok Lee, Myoung Hoon Kong
BACKGROUND: The effectiveness of surgical pleth index (SPI) for managing nociception-antinociception balance during general anesthesia with vasodilators, including nicardipine has not been demonstrated. We aimed to compare the time course during surgery in SPI values in patients receiving nicardipine or remifentanil infusion during thyroidectomy. METHODS: Forty patients undergoing thyroidectomy were randomly assigned to receive nicardipine (group N; n = 19) or remifentanil (group R; n = 21) along with induction (propofol, fentanyl, and rocuronium) and maintenance (50% desflurane/nitrous oxide in oxygen) anesthesia (goal bispectral index [BIS] ∼50)...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28177774/proteomics-analysis-of-latex-from-hevea-brasiliensis-clone-rrim-600
#15
Mohd Afiq Hazlami Habib, Chee Yuen Gan, Fazilah Othman, Nurul Nabilah Zainudin, Aishah Abdul Latiff, Mohd Nazri Ismail
The natural rubber latex extracted from the bark of Hevea brasiliensis plays various important roles in today's modern society. Following ultracentrifugation, the latex can be separated into 3 layers; C-serum, lutoids, and rubber particle. Previous studies showed that a large number of proteins were present inside these three layers. However, a complete proteome for this important plant is still unavailable. Protein sequences have been recently translated from the completed draft genome database of H. brasiliensis leading to the creation of annotated protein databases of H...
September 6, 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28170125/effects-of-acidic-peptide-size-and-sequence-on-trivalent-praseodymium-adduction-and-electron-transfer-dissociation-mass-spectrometry
#16
Juliette J Commodore, Carolyn J Cassady
Using the lanthanide ion praseodymium, Pr(III), metallated ion formation and electron transfer dissociation (ETD) were studied for 25 biological and model acidic peptides. For chain lengths of seven or more residues, even highly acidic peptides that can be difficult to protonate by electrospray ionization will metallate and undergo abundant ETD fragmentation. Peptides composed of predominantly acidic residues form only the deprotonated ion, [M + Pr - H](2+) ; this ion yields near complete ETD sequence coverage for larger peptides...
February 7, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28167002/intranasal-fluticasone-associated-with-delayed-tympanostomy-tube-placement-in-children-with-eustachian-tube-dysfunction
#17
Matthew G Crowson, Marisa A Ryan, Vaibhav H Ramprasad, Kevin J Choi, Eileen Raynor
OBJECTIVES: Pediatric patient caregivers may prefer to avoid a surgical intervention and request a medical management option for eustachian tube dysfunction (ETD). However, there are limited published data evaluating the efficacy of intranasal fluticasone in the medical management of ETD as an alternative to tympanostomy tube placement. The objectives of this study were to: 1) determine if intranasal fluticasone (INF) prevented tympanostomy tube placement in children with ETD, and 2) describe differences in patient response to INF related to cleft lip and/or palate (CLP) and Down syndrome...
March 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28155636/spectra-library-assisted-de-novo-peptide-sequencing-for-hcd-and-etd-spectra-pairs
#18
Yan Yan, Kaizhong Zhang
BACKGROUND: De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance of de novo sequencing is greatly improved. Currently, with large amount of spectra sequenced everyday, spectra libraries containing tens of thousands of annotated experimental MS/MS spectra become available. These libraries provide information of the spectra properties, thus have the potential to be used with de novo sequencing to improve its performance...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28154306/taste-masking-effect-of-chlorogenic-acid-cga-on-bitter-drugs-evaluated-by-taste-sensor-and-surface-plasmon-resonance-on-the-basis-of-cga-drug-interactions
#19
Sayuko Shiraishi, Tamami Haraguchi, Saki Nakamura, Dahong Li, Honami Kojima, Miyako Yoshida, Takahiro Uchida
The purpose of this study was to evaluate the taste-masking effects of chlorogenic acid (CGA) on bitter drugs using taste sensor measurements and surface plasmon resonance (SPR) analysis of CGA-drug interactions. Six different bitter drugs were used: amlodipine besylate (AMD), diphenhydramine hydrochloride (DPH), donepezil hydrochloride (DNP), rebamipide (RBM), diclofenac sodium (DCF) and etodolac (ETD). Taste sensor outputs were significantly inhibited by the addition of CGA to all drugs. The inhibition ratio of the taste sensor output decreased in the following order DPH>DNP>AMD≈DCF≈RBM≈ETD...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28150883/analysis-of-protein-o-glcnacylation-by-mass-spectrometry
#20
Junfeng Ma, Gerald W Hart
O-linked β-D-N-acetyl glucosamine (O-GlcNAc) addition (O-GlcNAcylation), a post-translational modification of serine/threonine residues of proteins, is involved in diverse cellular metabolic and signaling pathways. Aberrant O-GlcNAcylation underlies the initiation and progression of multiple chronic diseases including diabetes, cancer, and neurodegenerative diseases. Numerous methods have been developed for the analysis of protein O-GlcNAcylation, but instead of discussing the classical biochemical techniques, this unit covers O-GlcNAc characterization by combining several enrichment methods and mass spectrometry detection techniques [including collision-induced dissociation (CID), higher energy collision dissociation (HCD), and electron transfer dissociation (ETD) mass spectrometry]...
February 2, 2017: Current Protocols in Protein Science
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