TheoreticalGlycanSpectrumGenerator Class Reference

Generate positive-mode glycan and singly glycosylated peptide fragments. More...

#include <OpenMS/CHEMISTRY/TheoreticalGlycanSpectrumGenerator.h>

Classes
struct	Fragment
	One interpretation of a fragment, including its charge and attachment. More...
struct	Options
	Generation settings; all size and charge ranges are inclusive. More...
struct	PeptideRetention
	Independent choices of glycan material retained by a backbone ion. More...

Public Types
enum class	IonType {   DIAGNOSTIC , B , C , Y ,   Z , PEPTIDE }
	Glycan series and peptide backbone fragments are kept distinct. More...
enum class	FragmentationMethod { HCD , ETD , ETHCD }
	EThcD combines b/y and c/z ions with intact glycan retention. More...
using	Composition = ProForma::GlycanComposition

Public Member Functions
	TheoreticalGlycanSpectrumGenerator ()
	Construct with default options.
	TheoreticalGlycanSpectrumGenerator (const Options &options)
	Construct with validated options.
void	setOptions (const Options &options)
	Set options; throws InvalidParameter for invalid ranges, loss formulas or rules.
const Options &	getOptions () const
	Return the current options.
std::vector< Fragment >	getFragments (const Composition &composition) const
	Generate diagnostic and bounded composition B/Y (optionally C/Z) ions.
std::vector< Fragment >	getFragments (const GlycanStructure &structure) const
	Generate structural B/Y/C/Z and internal B fragments from a tree.
std::vector< Fragment >	getGlycopeptideFragments (const AASequence &peptide, const Composition &composition, Size attachment_position, FragmentationMethod method) const
	Generate glycan and peptide fragments for one localized glycan.
std::vector< Fragment >	getGlycopeptideFragments (const AASequence &peptide, const GlycanStructure &structure, Size attachment_position, FragmentationMethod method) const
	As above, using topology for glycan fragments.

Static Public Member Functions
static MSSpectrum	toSpectrum (const std::vector< Fragment > &fragments)
	Convert fragment interpretations to a fresh annotated MS2 spectrum.

Private Member Functions
std::vector< Fragment >	generate_ (const Composition &composition, const GlycanStructure *structure, const AASequence *peptide, Size site, FragmentationMethod method) const

Private Attributes
Options	options_

Detailed Description

Generate positive-mode glycan and singly glycosylated peptide fragments.

Composition fragments are explicitly labelled as such: their compositions are possibilities, not claims about topology. Structural fragments are connected subtrees. A B fragment carries a root cleavage and, for internal fragments, additional branch cleavages. Y fragments retain the reducing end. Node indices identify cleaved bonds by their non-reducing-side node (zero is the attachment).

Residue formulas exclude water: B = residue sum, C = B + H2O, Y = reducing end + retained residues, Z = Y - H2O per branch cleavage. Free glycans use H2O as the reducing end; glycopeptides use the peptide. Positive charges add protons. Intensities are uniformly 1, not predicted.

mzPAF does not define glycan series. getAnnotation() therefore uses its named compound syntax, keeping topology/composition and attachment in the name. Resource limits fail explicitly rather than returning a truncated spectrum.

See also

glycan_fragmentation

---

Class Documentation

OpenMS::TheoreticalGlycanSpectrumGenerator::Options

struct OpenMS::TheoreticalGlycanSpectrumGenerator::Options

Generation settings; all size and charge ranges are inclusive.

Class Members
bool	add_b_ions = true
bool	add_c_ions = false
bool	add_diagnostic_ions = true
bool	add_internal_fragments = true
bool	add_y_ions = true
bool	add_z_ions = false
bool	allow_structural = true	False selects the composition fallback even for a tree.
Int	max_charge = 2
Size	max_cleavages = 2	Includes the root cleavage of B/internal fragments.
Size	max_composition_size = 3	Y0 is included separately when Y is enabled.
Size	max_fragments = 10000	Includes charge states, losses and peptide fragments.
Int	max_oxonium_charge = 1
Size	max_states = 100000	Also bounds enumeration work, including rejected candidates.
Int	min_charge = 1
Size	min_composition_size = 1	Retained residues for both composition B and Y.
Int	min_oxonium_charge = 1
vector< EmpiricalFormula >	neutral_losses	Single losses, not a combinatorial loss ladder.
map< char, PeptideRetention >	peptide_retention	Optional overrides for b/y/c/z.
map< string, vector< EmpiricalFormula > >	specific_neutral_losses	Applied only if that residue is retained.

OpenMS::TheoreticalGlycanSpectrumGenerator::PeptideRetention

struct OpenMS::TheoreticalGlycanSpectrumGenerator::PeptideRetention

Independent choices of glycan material retained by a backbone ion.

Class Members
bool	intact = false	Include the complete glycan.
bool	stripped = true	Include the peptide with no glycan.
vector< Composition >	stubs	Explicit retained compositions, each a subset of the input.

Member Typedef Documentation

Composition

using Composition = ProForma::GlycanComposition

Member Enumeration Documentation

FragmentationMethod

enum class FragmentationMethod

strong

EThcD combines b/y and c/z ions with intact glycan retention.

Enumerator
HCD
ETD
ETHCD

IonType

enum class IonType

strong

Glycan series and peptide backbone fragments are kept distinct.

Enumerator
DIAGNOSTIC
B
C
Y
Z
PEPTIDE

Constructor & Destructor Documentation

TheoreticalGlycanSpectrumGenerator() [1/2]

TheoreticalGlycanSpectrumGenerator

(

)

Construct with default options.

TheoreticalGlycanSpectrumGenerator() [2/2]

TheoreticalGlycanSpectrumGenerator ( const Options &  options )

explicit

Construct with validated options.

Member Function Documentation

generate_()

std::vector< Fragment > generate_ ( const Composition &  composition, const GlycanStructure *  structure, const AASequence *  peptide, Size  site, FragmentationMethod  method  ) const

private

getFragments() [1/2]

std::vector< Fragment > getFragments

(

const Composition &

composition

)

const

Generate diagnostic and bounded composition B/Y (optionally C/Z) ions.

Parameters

[in]

composition

ProForma composition, with nonnegative counts

Returns

Fragments sorted by m/z; empty input produces no ions

Exceptions

Exception::ElementNotFound	if a named monosaccharide is unknown to MonosaccharideDB
Exception::InvalidParameter	for invalid chemistry or exhausted resource limits

getFragments() [2/2]

std::vector< Fragment > getFragments

(

const GlycanStructure &

structure

)

const

Generate structural B/Y/C/Z and internal B fragments from a tree.

Parameters

[in]

structure

Rooted glycan tree

Returns

Fragments sorted by m/z, including topology-preserving isobaric interpretations

getGlycopeptideFragments() [1/2]

std::vector< Fragment > getGlycopeptideFragments	(	const AASequence &	peptide,
		const Composition &	composition,
		Size	attachment_position,
		FragmentationMethod	method
	)		const

Generate glycan and peptide fragments for one localized glycan.

The peptide must exclude the glycan modification; other peptide modifications are preserved. HCD defaults to b/y ions stripped or with one HexNAc (if present). ETD defaults to c/z ions with the full glycan. EThcD generates b/y/c/z ions with the full glycan; per-series overrides can add stripped/stub ions. Backbone ions named peptide:zN use the radical z+1 form (Residue::Zp1Ion) for both ETD and EThcD; this is distinct from the glycan Z series. Only backbone fragments containing the attachment receive retained glycan mass. Explicit stubs allow, for example, HexNAc+Fuc retention without assuming a core topology from a composition. ETD omits glycan cleavage ions by default.

Parameters

[in]	peptide	Peptide without its glycan modification
[in]	composition	Glycan composition
[in]	attachment_position	Zero-based residue index in the peptide
[in]	method	Fragmentation method

Returns

Fragments sorted by m/z

Exceptions

Exception::ElementNotFound	if a named monosaccharide is unknown to MonosaccharideDB
Exception::InvalidParameter	for an empty glycan, invalid site, or impossible stub

getGlycopeptideFragments() [2/2]

std::vector< Fragment > getGlycopeptideFragments	(	const AASequence &	peptide,
		const GlycanStructure &	structure,
		Size	attachment_position,
		FragmentationMethod	method
	)		const

As above, using topology for glycan fragments.

getOptions()

const Options & getOptions

(

)

const

Return the current options.

setOptions()

void setOptions

(

const Options &

options

)

Set options; throws InvalidParameter for invalid ranges, loss formulas or rules.

toSpectrum()

static MSSpectrum toSpectrum ( const std::vector< Fragment > &  fragments )

static

Convert fragment interpretations to a fresh annotated MS2 spectrum.

Parameters

[in]

fragments

Fragments to convert

Returns

Sorted spectrum with aligned IonNames (mzPAF) and Charges arrays

Member Data Documentation

options_

Options options_

private