Table 2.
Sum of the relative peak intensities of the highest (first peptide sequence) and second highest (second peptide sequence) abundance peptide groups, each group including peptides with the same peptide sequence but with different N-glycansa
| Site | Protease(s)b | D614G | Alpha | Beta | Gamma | Delta | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1st peptide | 2nd peptidec | 1st peptide | 2nd peptide | 1st peptide | 2nd peptide | 1st peptide | 2nd peptide | 1st peptide | 2nd peptide | ||
| N17 | Lys-C | 99.6% | 99.6% | 99.5% | |||||||
| N20 | Lys-C/CHTR | 58.9% | 34.0% | ||||||||
| N61 | Lys-C/aLP | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | |||||
| N74 | Asp-N/CHTR | 86.4% | 93.7% | 87.0% | 85.9% | 81.1% | |||||
| N122 | Lys-C/CHTR | 75.6% | 22.3% | 56.4% | 35.6% | 52.1% | 38.9% | 53.7% | 37.6% | 55.0% | 37.4% |
| N165 | Lys-C | 76.7% | 12.0% | 80.4% | 73.2% | 10.1% | 78.9% | 6.6% | 83.7% | ||
| N188 | Lys-C | 99.6% | |||||||||
| N234 | Lys-C/CHTR | 66.1% | 17.2% | 89.1% | 85.6% | 84.9% | 86.9% | ||||
| N282 | Lys-C/CHTR | 83.0% | 82.5% | 84.3% | 85.5% | 85.0% | |||||
| N331 | Lys-C/CHTR | 48.1% | 45.6% | 69.2% | 22.0% | 66.6% | 22.6% | 62.5% | 27.7% | 64.3% | 25.5% |
| N343 | Lys-C/aLP | 94.6% | 93.6% | 94.5% | 91.4% | 97.6% | |||||
| N603 | Lys-C/CHTR | 76.7% | 23.3% | 74.3% | 25.7% | 78.6% | 25.0% | 76.1% | 23.9% | 64.0% | 17.4% |
| N616 | Lys-C/CHTR | 72.2% | 16.3% | 71.1% | 20.7% | 70.1% | 21.2% | 71.1% | 21.7% | 73.3% | 19.5% |
| N657 | Lys-C/CHTR | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | |||||
| N709 | Lys-C/aLP | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | |||||
| N717 | Lys-C/aLP | 100.0% | 100.0% | 85.3% | 100.0% | ||||||
| N801 | Lys-C/aLP | 51.9% | 22.2% | 52.1% | 22.3% | 65.3% | 11.0% | 72.0% | 4.4% | 70.6% | 4.0% |
| N1074 | Lys-C | 99.1% | 99.1% | 99.4% | 99.6% | 99.9% | |||||
| N1098 | Lys-C/CHTR | 79.4% | 10.4% | 74.3% | 15.3% | 76.8% | 13.1% | 76.5% | 14.4% | 77.2% | 14.5% |
| N1134 | Asp-N/CHTR | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | |||||
| N1158 | Asp-N/CHTR, aLP for Delta | 80.7% | 85.1% | 87.0% | 80.0% | 93.6% | |||||
| N1173 | Lys-C/aLP, trypsin/Asp-N for Delta | 100.0% | 100.0% | 100.0% | 100.0% | 78.9% | 21.1% | ||||
| N1194 | Lys-C | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | |||||
aEach value was calculated by dividing the sum of the intensities of target glycopeptides by the total intensity of all peptides containing a specific glycosylation site. The glycosylation on N149, N17 in Gamma and N717 in Delta was not determined due to lack of valid data
bIn sequential enzyme digestion, for example, Lys-C/CHTR, the first (Lys-C) and second (CHTR) digestions were conducted at 52 °C/1 h and 37 °C/overnight, respectively. CHTR represents chymotrypsin; aLP represents alpha lytic protease
cThe amino acid sequence of the 2nd peptide form of a glycosylation site (if any) overlaps with most of the region of the 1st peptide, but differs by 1–3 residues at the N-terminal or C-terminal end