MzPAFAnnotation Struct Reference

A single mzPAF peak annotation. More...

#include <OpenMS/CHEMISTRY/MzPAF.h>

Collaboration diagram for MzPAFAnnotation:

Public Member Functions
bool	isValid () const
	Check if this annotation has minimal valid data.
bool	operator== (const MzPAFAnnotation &other) const
	Equality comparison.
bool	operator!= (const MzPAFAnnotation &other) const

Public Attributes
std::optional< int >	analyte_index
	Analyte index (0@, 1@, etc.) for multi-analyte spectra.
MzPAFIonSeries	ion_series = MzPAFIonSeries::UNKNOWN
	Ion series type (a, b, c, x, y, z, etc.)
std::optional< int >	ordinal
	Position/ordinal (4 in y4)
std::optional< char >	immonium_residue
	Residue for immonium ions (Y in IY)
std::optional< std::pair< int, int > >	internal_range
	Range for internal fragments (m3:6 -> {3,6})
std::optional< String >	reporter_name
	Name for reporter ions (r[TMT127N])
std::optional< EmpiricalFormula >	formula
	Chemical formula for formula ions (f{C16H22O})
std::optional< String >	named_compound
	Name for named compound ions (_[name])
std::vector< MzPAFNeutralLoss >	neutral_losses
	Neutral losses (-H2O, -NH3, etc.)
std::optional< int >	isotope_offset
	Isotope offset (+1i, +2i for M+1, M+2)
std::optional< EmpiricalFormula >	adduct
	Adduct ion (+Na, +K, etc.)
std::optional< int >	charge
	Charge state (^2, ^3)
std::optional< MzPAFMassDelta >	mass_delta
	Mass delta (/0.001, /-1.4ppm)
std::optional< double >	confidence
	Confidence score (*0.75)
std::optional< String >	embedded_sequence
	Embedded ProForma sequence string ({LC[Carbamidomethyl]})

Detailed Description

A single mzPAF peak annotation.

Represents one annotation for a peak in mzPAF format. mzPAF is the HUPO-PSI standard string notation for fragment ion peak annotations.

Examples:

• y4 - Simple y-ion at position 4
• b2-H2O - b-ion with neutral loss
• y4^2 - Doubly charged y-ion
• y2+2i - Second isotope peak
• y4/0.001 - With mass delta in Da
• y4/-1.4ppm - With mass delta in ppm
• y4*0.75 - With confidence score
• IY - Immonium ion (tyrosine)
• m3:6 - Internal fragment (positions 3-6)
• r[TMT127N] - Reporter ion
• f{C16H22O} - Chemical formula
• 1@y12 - Multi-analyte spectrum (analyte 1)
• 0@b2{LC[Carbamidomethyl]} - Embedded ProForma sequence

Member Function Documentation

isValid()

bool isValid

(

)

const

Check if this annotation has minimal valid data.

operator!=()

bool operator!= ( const MzPAFAnnotation &  other ) const

inline

operator==()

bool operator==

(

const MzPAFAnnotation &

other

)

const

Equality comparison.

Member Data Documentation

adduct

std::optional<EmpiricalFormula> adduct

Adduct ion (+Na, +K, etc.)

analyte_index

std::optional<int> analyte_index

Analyte index (0@, 1@, etc.) for multi-analyte spectra.

charge

std::optional<int> charge

Charge state (^2, ^3)

confidence

std::optional<double> confidence

Confidence score (*0.75)

embedded_sequence

std::optional<String> embedded_sequence

Embedded ProForma sequence string ({LC[Carbamidomethyl]})

formula

std::optional<EmpiricalFormula> formula

Chemical formula for formula ions (f{C16H22O})

immonium_residue

std::optional<char> immonium_residue

Residue for immonium ions (Y in IY)

internal_range

std::optional<std::pair<int, int> > internal_range

Range for internal fragments (m3:6 -> {3,6})

ion_series

MzPAFIonSeries ion_series = MzPAFIonSeries::UNKNOWN

Ion series type (a, b, c, x, y, z, etc.)

isotope_offset

std::optional<int> isotope_offset

Isotope offset (+1i, +2i for M+1, M+2)

mass_delta

std::optional<MzPAFMassDelta> mass_delta

Mass delta (/0.001, /-1.4ppm)

named_compound

std::optional<String> named_compound

Name for named compound ions (_[name])

neutral_losses

std::vector<MzPAFNeutralLoss> neutral_losses

Neutral losses (-H2O, -NH3, etc.)

ordinal

std::optional<int> ordinal

Position/ordinal (4 in y4)

reporter_name

std::optional<String> reporter_name

Name for reporter ions (r[TMT127N])