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https://www.readbyqxmd.com/read/28218834/unambiguous-identification-of-serine-and-threonine-pyrophosphorylation-using-neutral-loss-triggered-ethcd-mass-spectrometry
#1
Martin Penkert, Lisa M Yates, Michael Schuemann, David H Perlman, Dorothea Fiedler, Eberhard Krause
Tandem mass spectrometry (MS/MS) has emerged as the core technology for identification of posttranslational 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...
February 20, 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
#2
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
#3
SriHariRaju Mulagapati, Veerendra Koppolu, T Shantha Raju
Protein glycosylation (N-, and O- linked) plays an important role in many biological processes including the 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) is maturing as a powerful technology for high-quality analytical characterization of O-linked glycans. This article summarizes the recent developments and insights of MS based glycomics technology, which focus on mucin type O-glycan analysis...
February 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28194953/click-chemistry-reagent-for-identification-of-sites-of-covalent-ligand-incorporation-in-integral-membrane-proteins
#4
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 9, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28116997/the-burden-and-epidemiology-of-eustachian-tube-dysfunction-in-adults
#14
Peter M Vila, Tom Thomas, Carrie Liu, Dennis Poe, Jennifer J Shin
Objectives Pediatric eustachian tube dysfunction (ETD), otitis media with effusion (OME), and tympanic membrane retraction (TMR) have been well studied, but no large analyses have described the associated burden beyond childhood. The potential impact and feasibility of prospective trials designed to optimize management of affected adults are thus unclear. Our objectives were therefore (1) to determine the national visit burden associated with ETD/OME/TMR beyond childhood and (2) to examine risk factors specific to adults, highlighting differences in comparison with children...
February 2017: Otolaryngology—Head and Neck Surgery
https://www.readbyqxmd.com/read/28111955/opposite-electron-transfer-dissociation-and-higher-energy-collisional-dissociation-fragmentation-characteristics-of-proteolytic-k-r-x-n-and-x-nk-r-peptides-provide-benefits-for-peptide-sequencing-in-proteomics-and-phosphoproteomics
#15
Liana Tsiatsiani, Piero Giansanti, Richard A Scheltema, Henk van den Toorn, Christopher M Overall, A F Maarten Altelaar, Albert J R Heck
A key step in shotgun proteomics is the digestion of proteins into peptides amenable for mass spectrometry. Tryptic peptides can be readily sequenced and identified by collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) because the fragmentation rules are well-understood. Here, we investigate LysargiNase, a perfect trypsin mirror protease, because it cleaves equally specific at arginine and lysine residues, albeit at the N-terminal end. LysargiNase peptides are therefore practically tryptic-like in length and sequence except that following ESI, the two protons are now both positioned at the N-terminus...
December 2, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/28091811/charge-transfer-dissociation-ctd-mass-spectrometry-of-peptide-cations-study-of-charge-state-effects-and-side-chain-losses
#16
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
https://www.readbyqxmd.com/read/28055230/improved-postprandial-glycemic-control-with-faster-acting-insulin-aspart-in-patients-with-type-1-diabetes-using-continuous-subcutaneous-insulin-infusion
#17
Bruce W Bode, Joseph A Johnson, Liselotte Hyveled, Søren C Tamer, Marek Demissie
BACKGROUND: Faster aspart is insulin aspart (IAsp) in a new formulation, which in continuous subcutaneous insulin infusion (CSII) in subjects with type 1 diabetes has shown a faster onset and offset of glucose-lowering effect than IAsp. METHODS: This double-blind, randomized, crossover active-controlled trial compared 2-h postprandial plasma glucose (PPG) response, following 2 weeks of CSII with faster aspart or IAsp. Primary endpoint: mean change in PPG 2 h after a standardized meal test (ΔPGav,0-2h)...
January 2017: Diabetes Technology & Therapeutics
https://www.readbyqxmd.com/read/28035802/rapid-distinction-of-leucine-and-isoleucine-in-monoclonal-antibodies-using-nanoflow-lcms-n
#18
Dhanashri Bagal, Eddie Kast, Ping Cao
Monoclonal antibodies (mAbs) are large heterogeneous molecules that represent a growing class of therapeutics. De novo sequencing of mAbs becomes necessary when the original cell line or the cDNA is unavailable. An important feature in sequencing of mAbs is the discrimination of isobaric residues (Xle): leucine (Leu) and isoleucine (Ile). An incorrect identification of the Xle site, especially in the complementarity determining regions (CDRs), can result in the production of an antibody with severely compromised efficacy...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27992946/balloon-tuboplasty-in-patients-with-eustachian-tube-dysfunction-a-prospective-study-in-39-patients-55-ears
#19
P F Bowles, S Agrawal, M A Salam
No abstract text is available yet for this article.
December 19, 2016: Clinical Otolaryngology
https://www.readbyqxmd.com/read/27989944/top-down-protein-identification-using-isotopic-envelope-fingerprinting
#20
Kaijie Xiao, Fan Yu, Zhixin Tian
: For top-down protein database search and identification from tandem mass spectra, our isotopic envelope fingerprinting search algorithm and ProteinGoggle search engine have demonstrated their strength of efficiently resolving heavily overlapping data as well separating non-ideal data with non-ideal isotopic envelopes from ideal ones with ideal isotopic envelopes. Here we report our updated ProteinGoggle 2.0 for intact protein database search with full-capacity. The indispensable updates include users' optional definition of dynamic post-translational modifications and static chemical labeling during database creation, comprehensive dissociation methods and ion series, as well as a Proteoform Score for each proteoform...
January 30, 2017: Journal of Proteomics
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