• Currently, analysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) of intact glycopeptides is often the method of choice in site-specific glycoproteomic studies ( 12 ). (frontiersin.org)
  • For glycopeptide characterization, mass spectrometry has arisen as the go-to methodology. (news-medical.net)
  • Urinary glycopeptides acquired via data-independent acquisition mass spectrometry (DIA-MS) were quantitatively analyzed, where prostatic acid phosphatase (ACPP), clusterin (CLU), alpha-1-acid glycoprotein 1 (ORM1), and CD antigen 97 (CD97) were selected to be evaluated in various combinations with and without urinary PSA. (bvsalud.org)
  • The captured glycopeptides can be further released enzymatically by wild-type endoglycosidases (EndoF3 and EndoCC) in a traceless manner for mass spectrometry (MS) analysis. (mcw.edu)
  • Then, the enzymatic reaction with galactose oxidase was utilized to specifically oxidize O-GalNAc, but not O -GlcNAc, generating the different tags between glycopeptides with O -GlcNAc and O-GalNAc that can be easily distinguishable by mass spectrometry (MS). Among O -GlcNAcylated proteins commonly identified in three types of human cells, those related to transcription and RNA binding are highly enriched. (mcw.edu)
  • The first strategy uses antibody-conjugated magnetic nanoprobes for Hp enrichment from human serum, followed by hydrophilic interaction liquid chromatography for glycopeptide enrichment and identification by mass spectrometry (NP-HILIC-MS). This strategy was employed for Hp profiling of serum from 33 individual patients: 11 HCC patients, 11 liver cirrhosis patients (LC) and 11 Hepatitis B (HBV) inactive carriers. (ntnu.edu.tw)
  • The selectivity of the amphiphilic nanoassemblies were changed by loading metal ions for the enrichment of phosphopeptides and by incorporating hydrazide functional groups for the enrichment of glycopeptides. (umass.edu)
  • In addition to developing new nanoassemblies for the enrichment of phosphopeptides and glycopeptides, we also explored how supramolecular systems could be tuned to enhance extraction selectivity and efficiency via structural variations to the amphiphilic polymers. (umass.edu)
  • The utility of these materials for the enrichment of phosphopeptides and glycopeptides from complexed samples is also demonstrated. (umass.edu)
  • The researchers then used these variants and expressed transcripts from each patient to build a sample-specific database and identified 156,135 peptides, 28,944 phosphopeptides, and 4,376 N-glycopeptides from the global proteomes, phosphoproteomes, and N-glycoproteomes, respectively. (genomeweb.com)
  • Compound classification and ensuing glycopeptide identification is executed with ProteinScape 4.0 and the embedded search algorithm GlycoQuest. (news-medical.net)
  • 1,2 discussed a new glycopeptide instant expertise method which makes use of multiple collision energies to produce glycan fragments and peptide fragments inside the same MS/MS spectrum. (news-medical.net)
  • Until recently, classification of N-glycopeptide spectra in ProteinScape (detection of glycopeptide spectra and calculation of glycan and peptide moiety mass) has centered on glycan fragment distances and oxonium ion detection when using typical CID conditions on ion trap or qTof instruments (see application note LCMS-66)4. (news-medical.net)
  • 1,2 employed synthetic, and therefore well-defined, N-glycopeptides for the optimization of CID energy parameters, so as to attain the greatest possible quantities of data on both the glycan and peptide moiety within just one tandem MS experiment. (news-medical.net)
  • Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification. (mpg.de)
  • Enrichment of glycopeptides for glycan structure and attachment site identification. (unige.ch)
  • Taking advantage of two mutant endoglycosidases (EndoF3-D165A and EndoCC-N180H), which efficiently and specifically recognize core fucose and O -GlcNAc, glycopeptides can be labeled using a biantennary N -glycan probe bearing azido and oxazoline groups. (mcw.edu)
  • PNGase F hydrolyzes nearly all types of N-glycan chains from glycopeptides/ proteins. (neb.com)
  • A highly selective hydrophilic sorbent for enrichment of N-linked glycopeptides, J. Chromatogr. (ecust.edu.cn)
  • Facile synthesis of magnetic covalent organic frameworks for hydrophilic enrichment of N-glycopeptides. (nwu.edu.cn)
  • We identified a total of 587 glycoproteins, including 1239 glycopeptides, 526 monosaccharide components, and 8326 intact glycopeptides in glycoproteomics, as well as a total of 4496 proteins identified in proteomic analysis. (frontiersin.org)
  • The influence of two different sample treatments comprising the enrichment of glycoproteins by boronic acid and dynamic range compression by hexapeptide libraries, on the detection of stress markers in saliva of pigs was evaluated in this study. (biomedcentral.com)
  • Although from a practical point of view, the use of saliva without further treatment as well as the enrichment of glycoproteins are less expensive and easy to do procedures. (biomedcentral.com)
  • Dynamic range compression (DRC) by hexapeptide libraries and enrichment of glycoproteins by boronic acid are techniques that have been used for sample enrichment. (biomedcentral.com)
  • Enrichment of glycoproteins could increase the sensitivity in the detection of carbohydrate-based markers. (biomedcentral.com)
  • The objective of this study was to evaluate how the enrichment of glycoproteins using the phenyl boronic acid (PBA) ligand or DRC by hexapeptide libraries could affect the identification of acute stress markers in porcine saliva. (biomedcentral.com)
  • Here, we developed an effective method benefiting from selective enrichment and the enzymatic specificity to simultaneously identify and distinguish glycoproteins with O -GlcNAc and O-GalNAc. (mcw.edu)
  • On the other hand, enrichment by boronic acid was selected since previous works have confirmed it as a valid non-destructive glycoprotein enrichment methodology for complex samples such as whole saliva in humans [ 7 ]. (biomedcentral.com)
  • Validation was performed by glycoprotein enrichment and analysing the input, the flow through and the bound fraction. (analyteguru.com)
  • Affinisep offers ready-to-use BioSPE™ kits specially developed for various applications in proteomics (peptide desalting, peptide fractionation, glycopeptide enrichment, intact protein purification, removal of magnetic beads after SP3 procedure) or metabolomics. (msacl.org)
  • It is possible to achieve glycopeptide fragmentation under standard collision induced dissociation (CID) conditions, in which the glycosidic bonds between carbohydrate bonds are favourably cleaved. (news-medical.net)
  • To find a way around this issue, deeper investigation of the fragmentation of N-glycopeptides was carried out using Bruker oTOF instruments. (news-medical.net)
  • In the case of N-glycopeptide fragmentation, the higher collision energies, which are required for peptide moiety fragmentation, also bring about a characteristic fragmentation pattern, which has earlier been described for MALDI fragmentation 3 . (news-medical.net)
  • The former detected predominantly high intensity, multiply charged glycopeptides while the latter preferentially selected precursors with complex / hybrid glycans for fragmentation. (analyteguru.com)
  • were easily recovered on CNA and M agar with or without selective enrichment in Enterococcus broth. (vin.com)
  • Yang's group developed a fine-tuned MS/MS acquisition method and pGlyco 2.0 search engine to perform confident intact glycopeptide characterization ( 13 ). (frontiersin.org)
  • This poster demonstrates how the NP-based proteomics workflow enables the investigation of plasma glycoproteome without subsequent enrichment of glycopeptides while facilitating deep access to the proteome. (seer.bio)
  • 2022. MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses . (wisc.edu)
  • This dissertation describes the use of supramolecular nanoassemblies, formed by amphiphilic polymers, as novel enrichment tools for the detection and analysis of peptides and proteins that are phosphorylated and glycosylated. (umass.edu)
  • Compared to glycopeptides from the post-DRE urine data, humoral immunity-related proteins were enriched in pre-DRE urine samples, whereas cell mediated immune response proteins were enriched in post-DRE urine samples. (bvsalud.org)
  • Glycopeptides were enriched by ZIC-HILIC resins and were either treated with PNGase F and H(2)(18)O or directly analysed using a recently developed HCD-ETD workflow for a hybrid linear ion trap-orbitrap MS. After deglycosylation with PNGase F in the presence of H(2)(18)O, 123 unique peptides displayed (18)O-deamidation of asparagine, corresponding to 86 proteins with a total of 121 glycosylation sites. (analyteguru.com)
  • Direct glycopeptides analysis by HCD-ETD identified 131 glycopeptides from 59 proteins and 118 glycosylation sites, of which 41 were known, 51 were predicted and 26 were novel. (analyteguru.com)
  • In the present study, we demonstrate a significantly improved O -GlcNAc protein enrichment procedure, which exploits metabolic labeling of cells by azide-modified GlcNAc and copper-mediated Click chemistry for purification of modified proteins on an alkyne-resin. (mcw.edu)
  • Targeted parallel reaction monitoring (PRM) assays of the glycopeptides from urinary ACPP and CLU were investigated along with urinary PSA for the ability of aggressive PCa detection. (bvsalud.org)
  • If you are developing novel glycoproteomics workflows or looking into quantifying novel glycopeptide biomarkers ask for our custom Glycopeptide synthesis service with optional stable isotope labeling. (aspariaglycomics.com)
  • A Bacterial Mannose Binding Lectin as a Tool for the Enrichment of C- and O-Mannosylated Peptides. (mpg.de)
  • We offer tailored custom synthesis services for complex oligosaccharides, glycopeptides, glycoconjugates and glyconanoparticles from mg to multigram scale for applications ranging from novel biomarker development to preclinical studies. (aspariaglycomics.com)
  • As well as the instrumental arrangement, a suitable software solution is essential to enable glycopeptide identification and cut laborious processing and de novo analysis time. (news-medical.net)
  • GlycoQuest (search algorithm in ProteinScape) is Bruker's proven solution and delivers dependable results with regards to glycopeptide identification. (news-medical.net)
  • There, her thesis work focused on enrichment and mass spectrometric identification of glycopeptides presented by the MHC class I and II processing pathways. (malakerlab.com)
  • This article discusses a novel, enhanced classification workflow for glycopeptides evaluated with the Glycopeptide Instant Expertise™ acquisition method (QTof series). (news-medical.net)
  • We achieved site-specific glycosylation profiling for total of 183, 169 and 164 intact glycopeptides in HCC, LC, and HBV serum samples, respectively from Asn184, Asn207, Asn211 and Asn241 sites. (ntnu.edu.tw)
  • In the second part, we developed a novel method to improve sensitivity for detecting specific glycopeptides: we developed a One Pot enrichment strategy for concomitant purification and glycosylation profiling of biomarker candidates in serum. (ntnu.edu.tw)
  • This approach takes advantages of dual nanoprobes: hemoglobin-conjugated silica nanoparticle (Hb@SiO2) for enrichment of target protein and ligand-conjugated magnetic nanoparticle (ligand@MNP) for enrichment of target glycopeptide. (ntnu.edu.tw)
  • Any variety of glycopeptide sample can be employed in this workflow - low complex and high complex, with and without glycopeptide enrichment. (news-medical.net)
  • Despite the fact that the classification workflow in ProteinScape has an explicit parameter to address this issue, the peptide mass of low abundant N-glycopeptides can be miscalculated at times, which can result in no or incorrect identifications. (news-medical.net)
  • More importantly, 28 unique glycopeptides containing 5 core fucosylated bi- and tri-antennary structures, were uniquely discovered in HCC, suggesting that the site-specific unique glycoforms might be used to discriminate HCC from LC and HBV patients. (ntnu.edu.tw)
  • Then, a temperature-sensitive poly( N -isopropylacrylamide) polymer functionalized with dibenzocyclooctyne was introduced to facilitate the enrichment of the labeled glycopeptides from the complex mixture. (mcw.edu)
  • Collision energy stepping implemented in the Glycopeptide Instant Expertise™ method. (news-medical.net)
  • Typical glycopeptide CID spectrum achieved by using the Glycopeptide Instant Expertise™ method. (news-medical.net)
  • After optimization, this one pot method enhanced the number (2-fold) and abundance (2-fold) of glycopeptides. (ntnu.edu.tw)
  • Quantitative sialylated glycopeptide standard. (ludger.com)
  • In this study, we investigated urinary marker panels composed of urinary glycopeptides and/or urinary prostate-specific antigen (PSA) for their clinical utility in distinguishing non-aggressive (Grade Group 1) from aggressive (Grade Group ≥ 2) PCa. (bvsalud.org)