LitCovid-sample-sentences  

PMC:7443692 / 60075-62136 JSONTXT 11 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T405 0-98 Sentence denotes Analysis of Site-Specific O-linked Glycopeptides for SARS-Cov-2 S and Human ACE2 Proteins by LC-MS
T406 99-316 Sentence denotes Three 10-μg aliquots of SARS-CoV-2 S protein and one 10-μg aliquot of ACE2 protein were reduced by incubating with 5 mM of dithiothreitol at 56°C and alkylated by 13.75 mM of iodoacetamide at room temperature in dark.
T407 317-434 Sentence denotes The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C.
T408 435-554 Sentence denotes Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®.
T409 555-778 Sentence denotes The resulting peptides were separated on an Acclaim PepMap RSLC C18 column (75 μm x 15 cm) and eluted into the nano-electrospray ion source of an Orbitrap Fusion Lumos Tribrid mass spectrometer at a flow rate of 200 nL/min.
T410 779-924 Sentence denotes The elution gradient consists of 1%–40% acetonitrile in 0.1% formic acid over 370 min followed by 10 min of 80% acetonitrile in 0.1% formic acid.
T411 925-1022 Sentence denotes The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C.
T412 1023-1297 Sentence denotes Full MS scans were acquired from m/z 200 to 2000 at 60k resolution, and MS/MS scans following higher-energy collisional dissociation (HCD) with stepped collision energy (15%, 25%, 35%) or electron transfer dissociation (ETD) were collected in the Orbitrap at 15k resolution.
T413 1298-1416 Sentence denotes The raw spectra were analyzed by Byonic (v3.8.13) with mass tolerance set as 20 ppm for both precursors and fragments.
T414 1417-1518 Sentence denotes MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed.
T415 1519-1599 Sentence denotes The search output was filtered at 1% false discovery rate and 10 ppm mass error.
T416 1600-1671 Sentence denotes The spectra assigned as O-linked glycopeptides were manually evaluated.
T417 1672-1771 Sentence denotes Quantitation was performed by calculating spectral counts for each glycan composition at each site.
T418 1772-1867 Sentence denotes Any O-linked glycan compositions identified by only one spectra were removed from quantitation.
T419 1868-2061 Sentence denotes Occupancy of each O-linked glycosylation site was calculated using spectral counts assigned to any glycosylated peptides and their unmodified counterparts from searches without MS/MS filtering.