Ion Types

Standard Fragment Ions

These are the most commonly used fragment ions in peptide mass spectrometry:

Ion Type	String Value	Delta Formula	Description
Precursor	"p"	H₂O	Intact peptide with water addition
Neutral	"n"	(none)	Neutral peptide backbone (no modifications)
a-ion	"a"	C⁻¹O⁻¹	N-terminal fragment
b-ion	"b"	(none)	N-terminal fragment
c-ion	"c"	H₃N	N-terminal fragment
x-ion	"x"	CO₂	C-terminal fragment
y-ion	"y"	H₂O	C-terminal fragment
z-ion	"z"	H⁻¹N⁻¹O	C-terminal fragment
z• radical	"z."	N⁻¹O	Radical z-ion
z+H	"z+H"	HN⁻¹O	Protonated z-ion (additional H from c-ion)
c-H	"c-H"	H₂N	Dehydrogenated c-ion (loss of H from z-ion)
Immonium	"i"	C⁻¹O⁻¹	Amino acid immonium ions (residue-specific)

Side-Chain Fragment Ions

These ions involve side-chain cleavage and are residue-specific:

Ion Type	String Value	Delta Formula	Description
d-ion	"d"	C₂H₃N	General side-chain loss from a-ion
d-ion (Val)	"d-valine"	C₃H₆N	Valine-specific d-ion
da-ion	"da"		General da-ion (side-chain loss)
da-ion (Thr)	"da-threonine"	C₂H₄NO	Threonine-specific da-ion
da-ion (Ile)	"da-isoleucine"	C₄H₈N	Isoleucine-specific da-ion
db-ion	"db"		General db-ion (side-chain loss)
db-ion (Thr)	"db-threonine"	C₃H₆N	Threonine-specific db-ion
db-ion (Ile)	"db-isoleucine"	C₃H₆N	Isoleucine-specific db-ion
v-ion	"v"	C₂H₂NO	Side-chain retention (complement of d-ion)
w-ion	"w"	C₃H₃O	General side-chain retention from x-ion
w-ion (Val)	"w-valine"	C₄H₆O	Valine-specific w-ion
wa-ion	"wa"		General wa-ion (side-chain retention)
wa-ion (Thr)	"wa-threonine"	C₃H₄O₂	Threonine-specific wa-ion
wa-ion (Ile)	"wa-isoleucine"	C₅H₈O	Isoleucine-specific wa-ion
wb-ion	"wb"		General wb-ion (side-chain retention)
wb-ion (Thr)	"wb-threonine"	C₄H₆O	Threonine-specific wb-ion
wb-ion (Ile)	"wb-isoleucine"	C₄H₆O	Isoleucine-specific wb-ion

Internal Fragment Ions

Internal fragments result from cleavage at both N- and C-termini. Formulas are based on the mzPAF specification.

Ion Type	String Value	Delta Formula	Description
by	"by"	C⁻¹O⁻¹	N-terminal b-ion, C-terminal y-ion
ax	"ax"	C⁻¹O⁻¹	N-terminal a-ion, C-terminal x-ion
cz	"cz"	C⁻¹O⁻¹	N-terminal c-ion, C-terminal z-ion
ay	"ay"	C⁻²O⁻²	N-terminal a-ion, C-terminal y-ion
az	"az"	C⁻²H⁻¹N⁻¹O⁻²	N-terminal a-ion, C-terminal z-ion
bx	"bx"	(none)	N-terminal b-ion, C-terminal x-ion
bz	"bz"	C⁻¹H⁻¹N⁻¹O⁻¹	N-terminal b-ion, C-terminal z-ion
cx	"cx"	N	N-terminal c-ion, C-terminal x-ion
cy	"cy"	C⁻¹H⁻¹NO⁻¹	N-terminal c-ion, C-terminal y-ion