The Ion Series page in the Fragment Matches ion table is selected by default. See Use the Peptide Spectrum Match Identification Details view for an example of this page. The ion series in this table appears in the following default colors:

  • Red: a, b, c–1, c, and c+1 fragment ions
  • Blue: x, y, z, z+1, and z+2 fragment ions
  • Magenta: immonium ions
  • Green: precursor ions
  • Yellow background: phosphorylation losses

NOTE

The application automatically chooses the colors of PTMs and neutral loss ions based on the colors of the ion series that they belong to.

The following table summarizes the types of fragment ions that appear on the pages of the ion table and in the extracted data plot of the Peptide Spectrum Match Identification Details view.

Fragment ions

Fragment

Description

Ion series

 

a

A ion with a charge on the N-terminal side

b

B ion with a charge on the N-terminal side

c

C ion with a charge on the N-terminal side

c–1

C ion with a charge on the N-terminal side, one fewer hydrogen

c+1

C ion with a charge on the N-terminal side, one more hydrogen

x

X ion with a charge on the C-terminal side

y

Y ion with a charge on the C-terminal side

z

Z ion with a charge on the C-terminal side

z+1

Z ion with a charge on the C-terminal side, one more hydrogen

z+2

Z ion with a charge on the C-terminal side, two more hydrogens

Neutral losses

 

–H2O

Fragment that has lost water (–18 Da)

–NH3

Fragment that has lost ammonia (–17 Da)

PTMs

 

H3PO4

Phosphorylation loss (designated –P)

Other

 

Immonium

Immonium ion

Precursor

Precursor ion