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)

Other

Immonium

Immonium ion

M

Precursor ion, M

Neutral loss, for example:

  • Water loss, M-H20
  • Loss from phosphorylated residues, M-98

R

Neutral loss from arginine with a minus mass value, for example, R-44

Glycans

There are several types of glycan labels:

  • Glycan fragments, which appear in parentheses, for example, (Gn)
  • Glycan fragment losses, for example, −A2S1G1F
  • Glycan core cleavages labeled with the B or Y convention, for example, Bn, Bn1, Y0, Y1
  • Common glycan structure, for example, GlcNAc

Each type can have a charge associated with it. Glycan labels include capital letters to distinguish them from ion series labels.

See Appendix: Glycans.