Peakardt - Fragmentation

Formulae to Calculate Fragment Ion Masses

[N] is the mass of N-terminal group (i.e. H₂N), [C] is the mass of C-terminal group (i.e. COOH), [M] is mass of the sum of the neutral amino acid residue masses, i.e. Σ₁^jaa_i if reading from the N-Terminus (N-terminal fragment ions: a, b, c, d), Σ_n-j+1ⁿaa_i if reading begins at the C-Terminus (C-terminal fragment ions: x, y, z, w,v).

Ion Type	Ion Mass	[1]	[2]
a_i	[N]+[M]-CO	[N]+Σ₁^jaa_i-CO	[N]+[M]-CHO
a_i*	a_i-NH₃		a_i-NH₃
a_i°	a_i-H₂O		a_i-H₂O
a^_i++	(a_i+H)/2
b_i	[N]+[M]	[N]+Σ₁^jaa_i	[N]+[M]-H
b_i*	b_i-NH₃		b_i-NH₃
b_i°	b_i-H₂O		b_i-H₂O
b_i+°	b_i+H₂O
b_i⁺⁺	(b_i+H)/2
c_i	[N]+[M]+NH₃	[N]+Σ₁^jaa_i+NH₂	[N]+[M]+NH₂
d_i		a_i-[R'_j]+H	a - partial side chain
v_i		y_i-[R_j]-H	y - complete side chain
w_i		z_i-[R'_j]+H	z - partial side chain
x_i	[C]+[M]+CO	[C]+Σ_n-j+1ⁿaa_i+CO	[C]+[M]+CO-H
y_i	[C]+[M]+H₂	[C]+Σ_n-j+1ⁿaa_i+NH₂	[C]+[M]+H
y_i*	y_i-NH₃		y_i-NH₃
y_i°	y_i-H₂O		y_i-H₂O
y^_i++	(y_i+H)/2
Y_i	[C]+[M]
z_i	[C]+[M]-NH	[C]+Σ_n-j+1ⁿaa_i-NH	[C]+[M]-NH₂
immonium	AA-CO+H

[1] Papayannopoulos, IA, The interpretation of collision induced dissociation tandem mass spectra of peptides. Mass Spectrom. Rev., 14(1) 49-73 (1995).

[2] Cottrell, J, Database Searching for Protein Identification and Characterization, ASMS Tutorial 2005