Id |
Subject |
Object |
Predicate |
Lexical cue |
T406 |
0-217 |
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 |
218-335 |
Sentence |
denotes |
The four aliquots were then digested respectively using trypsin, Lys-C, Arg-C, or a combination of trypsin and Lys-C. |
T408 |
336-455 |
Sentence |
denotes |
Following digestion, the proteins were deglycosylated by PNGaseF treatment and then digested with O-protease OpeRATOR®. |
T409 |
456-679 |
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 |
680-825 |
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 |
826-923 |
Sentence |
denotes |
The spray voltage was set to 2.2 kV and the temperature of the heated capillary was set to 280°C. |
T412 |
924-1198 |
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 |
1199-1317 |
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 |
1318-1419 |
Sentence |
denotes |
MS/MS filtering was applied to only allow for spectra where the oxonium ions of HexNAc were observed. |
T415 |
1420-1500 |
Sentence |
denotes |
The search output was filtered at 1% false discovery rate and 10 ppm mass error. |
T416 |
1501-1572 |
Sentence |
denotes |
The spectra assigned as O-linked glycopeptides were manually evaluated. |
T417 |
1573-1672 |
Sentence |
denotes |
Quantitation was performed by calculating spectral counts for each glycan composition at each site. |
T418 |
1673-1768 |
Sentence |
denotes |
Any O-linked glycan compositions identified by only one spectra were removed from quantitation. |
T419 |
1769-1962 |
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. |