LitCovid-sentences  

PMC:7253482 / 29924-32503 JSONTXT 19 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T175 0-107 Sentence denotes Aliquots of 30–50 μg of coronavirus spikes were denatured, reduced and alkylated as described previously36.
T176 108-252 Sentence denotes Proteins were proteolytically digested with trypsin (Promega), chymotrypsin (Promega), alpha-lytic protease (Sigma-Aldrich) and Glu-C (Promega).
T177 253-396 Sentence denotes Reaction mixtures were dried and peptides/glycopeptides were extracted using C18 Zip-tip (MerckMilipore) following the manufacturer’s protocol.
T178 397-608 Sentence denotes Samples were resuspended in 0.1% formic acid prior to analysis by liquid chromatography-mass spectrometry using an Easy-nLC 1200 system coupled to an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific).
T179 609-837 Sentence denotes Glycopeptides were separated using an EasySpray PepMap RSLC C18 column (75 μm × 75 cm) with a 240-min linear solvent gradient of 0–32% acetonitrile in 0.1% formic acid, followed by 35 min of 80% acetonitrile in 0.1% formic acid.
T180 838-985 Sentence denotes Other settings include an LC flow rate of 200 nL/min, spray voltage of 2.8 kV, capillary temperature of 275 °C, and an HCD collision energy of 50%.
T181 986-1117 Sentence denotes Precursor and fragmentation detection were performed using an Orbitrap at the following resolution: MS1 = 100,000 and MS2 = 30,000.
T182 1118-1236 Sentence denotes The automatic gain control (AGC) targets were MS1 = 4e5 and MS2 = 5e4, and injection times were MS1 = 50 and MS2 = 54.
T183 1237-1379 Sentence denotes The following cleavage sites were used for the respective proteases; trypsin=R/K, chymotrypsin=F/Y/W, alpha lytic protease=T/A/S/V, Glu C=E/D.
T184 1380-1421 Sentence denotes Number of missed cleavages were set at 3.
T185 1422-1469 Sentence denotes The following modifications were also included:
T186 1470-1767 Sentence denotes Carbamidomethyl (+57.021464, target=C, fine control=fixed), Oxidation (+15.994915, target=M, fine control=variable rare 1), Glu to pyro-Glu (−18.010565, target=peptide N-term E, fine control=variable rare 1), and Gln to pyro-Glu (−17.026549, target peptide N-term Q, fine control=variable rare 1).
T187 1768-1915 Sentence denotes Glycopeptide fragmentation data were extracted form raw files using ByonicTM (Version 3.5.0) and ByologicTM (Version 3.5-15; Protein Metrics Inc.).
T188 1916-2127 Sentence denotes Glycopeptide fragmentation data were manually evaluated with true-positive assignments given when correct b- and y-fragments and oxonium ions corresponding to the peptide and glycan, respectively, were observed.
T189 2128-2222 Sentence denotes The precursor mass tolerance was set at 4 ppm for precursor ions and 10 ppm for fragment ions.
T190 2223-2316 Sentence denotes MS data were searched using a glycan library (SI Fig. 9) with the identical peptide sequence.
T191 2317-2361 Sentence denotes A 1% false discovery rate (FDR) was applied.
T192 2362-2579 Sentence denotes The extracted ion chromatographic areas for each true-positive glycopeptide, with the same amino-acid sequence, were compared to determine the relative quantitation of glycoforms at each specific N-linked glycan site.