Parser and writer for mzPAF (Peak Annotation Format) notation. More...

#include <OpenMS/CHEMISTRY/MzPAF.h>

Static Public Member Functions
static MzPAFAnnotation	parse (const std::string &input)
	Parse an mzPAF string into a single annotation.

static MzPAFPeakAnnotations	parseMultiple (const std::string &input)
	Parse an mzPAF string with potentially multiple annotations.

static std::optional< MzPAFAnnotation >	tryParse (const std::string &input)
	Try to parse an mzPAF string (non-throwing)

static std::optional< MzPAFPeakAnnotations >	tryParseMultiple (const std::string &input)
	Try to parse multiple annotations (non-throwing)

static std::string	toString (const MzPAFAnnotation &ann)
	Convert an annotation to mzPAF string.

static std::string	toString (const MzPAFPeakAnnotations &anns)
	Convert multiple annotations to mzPAF string.

static PeptideHit::PeakAnnotation	toPeakAnnotation (const MzPAFAnnotation &mzpaf, double mz, double intensity)
	Create a PeptideHit::PeakAnnotation from mzPAF data.

static MzPAFPeakAnnotations	fromPeakAnnotation (const PeptideHit::PeakAnnotation &peak_annotation)
	Parse mzPAF annotations from a PeptideHit::PeakAnnotation.

static bool	isMzPAFFormat (const std::string &annotation)
	Check if a string appears to be in mzPAF format.

static std::optional< double >	calculateTheoreticalMZ (const MzPAFAnnotation &ann, const AASequence &sequence)
	Calculate theoretical m/z for an annotation.

static bool	isPeptideFragmentIon (MzPAFIonSeries series)
	Check if ion series is a peptide fragment ion (a, b, c, d, v, w, x, y, z)

static char	ionSeriesToChar (MzPAFIonSeries series)
	Get the ion series character for an annotation.

static bool	charToIonSeries (char c, MzPAFIonSeries &series)
	Parse ion series from character.

Private Member Functions
	MzPAF ()=delete

Detailed Description

Parser and writer for mzPAF (Peak Annotation Format) notation.

mzPAF is the HUPO-PSI standard string notation for fragment ion peak annotations, used in mzSpecLib and other spectral library formats.

This class provides static methods for:

Parsing mzPAF strings into MzPAFAnnotation structures
Converting MzPAFAnnotation structures back to mzPAF strings
Integration with OpenMS PeptideHit::PeakAnnotation
Validation and format detection

Usage example:

// Parse a single annotation
MzPAFAnnotation ann = MzPAF::parse("y4^2-H2O/0.001*0.75");
 
// Parse multiple annotations (comma-separated)
MzPAFPeakAnnotations anns = MzPAF::parseMultiple("b2,y4^2");
 
// Convert back to string
std::string s = MzPAF::toString(ann);
 
// Check if a string is mzPAF format
if (MzPAF::isMzPAFFormat("y4^2")) { ... }

See also: MzPAFAnnotation, MzPAFPeakAnnotations

Constructor & Destructor Documentation

◆ MzPAF()

MzPAF ( )

privatedelete

Member Function Documentation

◆ calculateTheoreticalMZ()

static std::optional< double > calculateTheoreticalMZ	(	const MzPAFAnnotation &	ann,
		const AASequence &	sequence
	)

static

Calculate theoretical m/z for an annotation.

Calculates the theoretical m/z value for the annotated ion based on the sequence.

Note: Satellite ions (d, v, w, including their subtypes) are parsed and serialized, but their residue-dependent side-chain losses are not yet supported here; these ions return std::nullopt.

Parameters

[in]	ann	The annotation
[in]	sequence	The peptide sequence

Returns: Theoretical m/z, or std::nullopt if calculation not possible

◆ charToIonSeries()

static bool charToIonSeries	(	char	c,
		MzPAFIonSeries &	series
	)

static

Parse ion series from character.

Parameters

[in]	c	The character to parse
[out]	series	Output ion series if successful

Returns: True if parsing successful

◆ fromPeakAnnotation()

static MzPAFPeakAnnotations fromPeakAnnotation ( const PeptideHit::PeakAnnotation & peak_annotation )

static

Parse mzPAF annotations from a PeptideHit::PeakAnnotation.

Attempts to parse the annotation string from a PeakAnnotation as mzPAF.

Parameters

[in] peak_annotation The PeakAnnotation to parse

Returns: Parsed mzPAF annotations, or empty if not valid mzPAF

◆ ionSeriesToChar()

static char ionSeriesToChar ( MzPAFIonSeries series )

static

Get the ion series character for an annotation.

Parameters

[in] series The ion series enum

Returns: The character representation (a, b, c, d, v, w, x, y, z, p, I, m, r, f, _)

Note: The satellite subtype is stored separately in MzPAFAnnotation::satellite_subtype.

◆ isMzPAFFormat()

static bool isMzPAFFormat ( const std::string & annotation )

static

Check if a string appears to be in mzPAF format.

Performs a quick heuristic check to determine if a string looks like mzPAF notation.

Parameters

[in] annotation The string to check

Returns: True if the string appears to be mzPAF format

◆ isPeptideFragmentIon()

static bool isPeptideFragmentIon ( MzPAFIonSeries series )

static

Check if ion series is a peptide fragment ion (a, b, c, d, v, w, x, y, z)

These are exactly the series that mzPAF requires to carry an ordinal.

Parameters

[in] series The ion series to check

Returns: True if it's a peptide fragment ion type

Note: True here does not imply a computable mass. calculateTheoreticalMZ() returns std::nullopt for the satellite series d/v/w, so if (isPeptideFragmentIon(s)) mz = *calculateTheoreticalMZ(...) would dereference an empty optional.

◆ parse()

static MzPAFAnnotation parse ( const std::string & input )

static

Parse an mzPAF string into a single annotation.

Parameters

[in] input The mzPAF string to parse

Returns: The parsed annotation

Exceptions

MzPAFParseError if parsing fails

Note: If the input contains multiple comma-separated annotations, only the first is returned. Use parseMultiple() for multi-annotation strings.

◆ parseMultiple()

static MzPAFPeakAnnotations parseMultiple ( const std::string & input )

static

Parse an mzPAF string with potentially multiple annotations.

Parameters

[in] input The mzPAF string to parse (may contain comma-separated annotations)

Returns: All parsed annotations

Exceptions

MzPAFParseError if parsing fails

◆ toPeakAnnotation()

static PeptideHit::PeakAnnotation toPeakAnnotation	(	const MzPAFAnnotation &	mzpaf,
		double	mz,
		double	intensity
	)

static

Create a PeptideHit::PeakAnnotation from mzPAF data.

Converts an MzPAFAnnotation to the OpenMS PeakAnnotation format used in PeptideHit.

Parameters

[in]	mzpaf	The mzPAF annotation
[in]	mz	The observed m/z value
[in]	intensity	The peak intensity

Returns: A PeptideHit::PeakAnnotation

◆ toString() [1/2]

static std::string toString ( const MzPAFAnnotation & ann )

static

Convert an annotation to mzPAF string.

Parameters

[in] ann The annotation to convert

Returns: The mzPAF string representation

Note: This function is total and never throws. An annotation carrying a satellite subtype that mzPAF does not allow – anything other than 'a'/'b', or a subtype on a series other than d/w – is written without it, mirroring how an UNKNOWN series is written as '?'. Use isValid() to reject such an annotation.

◆ toString() [2/2]

static std::string toString ( const MzPAFPeakAnnotations & anns )

static

Convert multiple annotations to mzPAF string.

Parameters

[in] anns The annotations to convert

Returns: The mzPAF string representation (comma-separated)

◆ tryParse()

static std::optional< MzPAFAnnotation > tryParse ( const std::string & input )

static

Try to parse an mzPAF string (non-throwing)

Parameters

[in] input The mzPAF string to parse

Returns: The parsed annotation, or std::nullopt on failure

◆ tryParseMultiple()

static std::optional< MzPAFPeakAnnotations > tryParseMultiple ( const std::string & input )

static

Try to parse multiple annotations (non-throwing)

Parameters

[in] input The mzPAF string to parse

Returns: The parsed annotations, or empty on failure

Static Public Member Functions

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MzPAF()

Member Function Documentation

◆ calculateTheoreticalMZ()

◆ charToIonSeries()

◆ fromPeakAnnotation()

◆ ionSeriesToChar()

◆ isMzPAFFormat()

◆ isPeptideFragmentIon()

◆ parse()

◆ parseMultiple()

◆ toPeakAnnotation()

◆ toString() [1/2]

◆ toString() [2/2]

◆ tryParse()

◆ tryParseMultiple()