Table 1.
Variable modificaitons monitored in the global characterization assay.
| Cysteine 12,13 | Tryptophan 12-15 | Methionine 12,13 | Histidine 12,13, 16-18 | Tyrosine 17-19 | Phenylalanine 17, 18 | Leucine/Isoleucine 17, 18 | Valine 17, 18 | Serine 17, 18 |
|---|---|---|---|---|---|---|---|---|
| carbamidomethylation (+57.0516)a | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) |
| oxidation (+15.9949) | dioxidation (+31.9898) | dioxidation (+31.9898) | dioxidation (+31.9898) | dioxidation (+31.9898) | dioxidation (+31.9898) | carbonylation (+13.9793) | carbonylation (+13.9793) | carbonylation (+13.9793) |
| dioxidation (+31.9898) | trioxidation (+47.9847) | trioxidation (+47.9847) | dopa-derrived quinone (+13.9793) | |||||
| trioxidation (+47.9847) | kynurenin (+3.9949) | ring opening 1 (-23.0160) | quinone (+29.9742) | |||||
| hydroxykynurenin (+19.9898) | ring opening 2 (-22.0320) | |||||||
| trptoline (+12.0000) | ring opening 3 (+4.9790) | |||||||
| quinone (+29.9742) | ring opening 4 (-10.0320) | |||||||
| unsaturated tryptophandione (+27.9585) | hydroxy-dioxidiation (+34.0055) | |||||||
| hydroxytryptophandione (+43.9534) |
| Threonine 12, 13, 17, 18 | Asparagine 17, 18 | Aspartic acid 17, 18 | Glutamine 17, 18 | Glutamic Acid 12, 13, 17, 18 | Arginine 17, 18 | Lysine 17, 18 | Proline 17, 18 |
|---|---|---|---|---|---|---|---|
| oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) | oxidation (+15.9949) |
| carbonylation (+13.9793) | demaidation (+0.9849) | decarboxylation (-30.0105) | demaidation (+0.9849) | carbonylation (+13.9793) | carbonylation (+13.9793) | carbonylation (+13.9793) | |
| pyro-glutamate (-18.0105) | decarboxylation (-30.0105) | GluSA (-43.0534) | |||||
| pyro-glutamate (-18.0105) |
The following Skyline filters were used: precursor ions, 5 ppm mass error, 0.95 isotope dot product; product ions, 10 ppm mass errors. Up to 3 modifications per peptide and a maximum of 4 miscleavages were monitored. Very few tryptic peptides above 1 miscleavages or chymotryptic peptides above 2 miscleavages were observed.
aCysteine carbamidomethylation was selected as variable modification during peptide search on Skyline, so that other cysteine modifications could be searched at equal weight. But it is selected as constant modification during data analysis on the Global Characterization Data Processing Site, so that it is not calculated as a stressed modification.