Fragment Ion Types

The ion types module provides lookups for peptide fragment ion types.

class tacular.ion_types.FragmentIonInfo(id, name, formula, monoisotopic_mass, average_mass, dict_composition, properties=<IonTypeProperty.NONE: 0>)

Bases: object

Information about a fragment ion

Parameters:

• id (str)

• name (str)

• formula (str | None)

• monoisotopic_mass (float | None)

• average_mass (float | None)

• dict_composition (Mapping[str, int] | None)

• properties (IonTypeProperty)

average_mass: float | None

property composition: Counter[ElementInfo]

Get the composition as a Counter

dict_composition: Mapping[str, int] | None

formula: str | None

get_mass(monoisotopic=True)

Get the mass of the fragment ion

Return type:

float

Parameters:

monoisotopic (bool)

id: str

property ion_type: IonType

property is_aa_specific_backward: bool

Check if ion is an amino acid-specific backward ion (v, w, wa, wb)

property is_aa_specific_forward: bool

Check if ion is an amino acid-specific forward ion (d, da, db)

property is_backward: bool

Check if ion is a backward ion type (x, y, z)

property is_forward: bool

Check if ion is a forward ion type (a, b, c)

property is_intact: bool

Check if ion is an intact ion (precursor, neutral)

property is_internal: bool

Check if ion is an internal fragment

monoisotopic_mass: float | None

name: str

properties: IonTypeProperty = 0

to_dict(float_precision=6)

Convert the FragmentIonInfo to a dictionary

Return type:

dict[str, object]

Parameters:

float_precision (int)

class tacular.ion_types.FragmentIonLookup(fragment_ion_data)

Bases: object

Parameters:

fragment_ion_data (dict[IonType, FragmentIonInfo])

get(key, default=None)

Get fragment ion or None if not found

Return type:

FragmentIonInfo | None

Parameters:

• key (str | IonType)

• default (FragmentIonInfo | None)

query_id(ion_id)

Query by fragment ion ID (e.g., ‘a’, ‘b’, ‘y’, ‘z’)

Return type:

FragmentIonInfo | None

Parameters:

ion_id (str)

query_ion_type(ion_type)

Query by IonType enum

Return type:

FragmentIonInfo | None

Parameters:

ion_type (IonType)

query_name(name)

Query by fragment ion name (e.g., ‘A-Ion’, ‘Y-Ion’)

Return type:

FragmentIonInfo | None

Parameters:

name (str)

class tacular.ion_types.IonType(*values)

Bases: StrEnum

Fragment ion types following ProForma notation

A = 'a'

AX = 'ax'

AY = 'ay'

AZ = 'az'

B = 'b'

BX = 'bx'

BY = 'by'

BZ = 'bz'

C = 'c'

CX = 'cx'

CY = 'cy'

CZ = 'cz'

C_MINUS_H = 'c-H'

D = 'd'

DA = 'da'

DA_ISOLEUCINE = 'da-isoleucine'

DA_THREONINE = 'da-threonine'

DB = 'db'

DB_ISOLEUCINE = 'db-isoleucine'

DB_THREONINE = 'db-threonine'

D_VALINE = 'd-valine'

IMMONIUM = 'i'

NEUTRAL = 'n'

PRECURSOR = 'p'

V = 'v'

W = 'w'

WA = 'wa'

WA_ISOLEUCINE = 'wa-isoleucine'

WA_THREONINE = 'wa-threonine'

WB = 'wb'

WB_ISOLEUCINE = 'wb-isoleucine'

WB_THREONINE = 'wb-threonine'

W_VALINE = 'w-valine'

X = 'x'

Y = 'y'

Z = 'z'

Z_PLUS_H = 'z+H'

Z_RADICAL = 'z.'

class tacular.ion_types.IonTypeProperty(*values)

Bases: Flag

Flag enum for ion type properties.

AA_SPECIFIC_BWD = 32

AA_SPECIFIC_FWD = 16

BACKWARD = 2

FORWARD = 1

INTACT = 8

INTERNAL = 4

NONE = 0