The following table summarizes the types of fragment ions that appear in the spectra in the MS2 Spectra pane.
Fragment | Description | Color |
Ion series | ||
a | A ion with a charge on the N-terminal side | Light blue |
b | B ion with a charge on the N-terminal side | Dark blue |
c | C ion with a charge on the N-terminal side | Dark green |
c· | C ion with a charge on the N-terminal side, one less proton (c−1.0078) | Light green |
x | X ion with a charge on the C-terminal side | Orange |
y | Y ion with a charge on the C-terminal side | Red |
z | Z ion with a charge on the C-terminal side | Purple |
z· | Z ion with a charge on the C-terminal side, one more proton (z+1.0078) | Light purple |
z·· | Z ion with a charge on the C-terminal side, two more protons (z+2(1.0078)) | Lighter purple |
Neutral losses | ||
−H2O | Fragment that has lost water (−18 Da) | |
−NH3 | Fragment that has lost ammonia (−17 Da) | |
Post-translational modifications (PTMs) | ||
H3PO4 | Phosphorylation loss (designated −P) | |