LitCovid-sample-sentences  

PMC:7443692 / 50636-53647 JSONTXT 11 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T344 0-92 Sentence denotes Analysis of N-linked and O-linked Glycans Released from SARS-Cov-2 S and Human ACE2 Proteins
T345 93-247 Sentence denotes Aliquots of approximately 25-50 μg of S or ACE2 protein were processed for glycan analysis as previously described (Aoki et al., 2007; Aoki et al., 2008).
T346 248-318 Sentence denotes For N-linked glycan analysis, the proteins were digested with trypsin.
T347 319-451 Sentence denotes Following trypsinization, glycopeptides were enriched by C18 Sep-Pak and subjected to PNGaseF digestion to release N-linked glycans.
T348 452-589 Sentence denotes Following PNGaseF digestion, released glycans were separated from residual glycosylated peptides bearing O-linked glycans by C18 Sep-Pak.
T349 590-709 Sentence denotes O-glycosylated peptides were eluted from the Sep-Pak and subjected to reductive β-elimination to release the O-glycans.
T350 710-827 Sentence denotes Another 25-50 μg aliquot of each protein was denatured with SDS and digested with PNGaseF to remove N-linked glycans.
T351 828-968 Sentence denotes The de-N-glycosylated, intact protein was precipitated with cold ethanol and then subjected to reductive β-elimination to release O-glycans.
T352 969-1069 Sentence denotes The profiles of O-glycans released from peptides or from intact protein were found to be comparable.
T353 1070-1253 Sentence denotes N- and O-linked glycans released from glycoproteins were permethylated with methyliodide according to the method of Anumula and Taylor prior to MS analysis (Anumula and Taylor, 1992).
T354 1254-1375 Sentence denotes Glycan structural analysis was performed using an LTQ-Orbitrap instrument (Orbitrap Discovery, Thermo Fisher Scientific).
T355 1376-1686 Sentence denotes Detection and relative quantification of the prevalence of individual glycans was accomplished using the total ion mapping (TIM) and neutral loss scan (NL scan) functionality of the Xcalibur software package version 2.0 (Thermo Fisher Scientific) as previously described (Aoki et al., 2007; Aoki et al., 2008).
T356 1687-1800 Sentence denotes Mass accuracy and detector response was tuned with a permethylated oligosaccharide standard in positive ion mode.
T357 1801-1922 Sentence denotes For fragmentation by collision-induced dissociation (CID in MS2 and MSn), normalized collision energy of 45% was applied.
T358 1923-2029 Sentence denotes Most permethylated glycans were identified as singly or doubly charged, sodiated species in positive mode.
T359 2030-2134 Sentence denotes Sulfated N-glycans were detected as singly or doubly charged, deprotonated species in negative ion mode.
T360 2135-2231 Sentence denotes Peaks for all charge states were deconvoluted by the charge state and summed for quantification.
T361 2232-2284 Sentence denotes All spectra were manually interpreted and annotated.
T362 2285-2409 Sentence denotes The explicit identities of individual monosaccharide residues have been assigned based on known human biosynthetic pathways.
T363 2410-2606 Sentence denotes Graphical representations of monosaccharide residues are consistent with the Symbol Nomenclature for Glycans (SNFG), which has been broadly adopted by the glycomics community (Varki et al., 2015).
T364 2607-2795 Sentence denotes The MS-based glycomics data generated in these analyses and the associated annotations are presented in accordance with the MIRAGE standards and the Athens Guidelines (Wells et al., 2013).
T365 2796-3011 Sentence denotes Data annotation and assignment of glycan accession identifiers were facilitated by GRITS Toolbox, GlyTouCan, GNOme, and GlyGen (Kahsay et al., 2020; Tiemeyer et al., 2017; Weatherly et al., 2019; York et al., 2020).