MzPAF Class Reference

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

#include <OpenMS/CHEMISTRY/MzPAF.h>

Static Public Member Functions
static MzPAFAnnotation	parse (const String &input)
	Parse an mzPAF string into a single annotation.
static MzPAFPeakAnnotations	parseMultiple (const String &input)
	Parse an mzPAF string with potentially multiple annotations.
static std::optional< MzPAFAnnotation >	tryParse (const String &input)
	Try to parse an mzPAF string (non-throwing)
static std::optional< MzPAFPeakAnnotations >	tryParseMultiple (const String &input)
	Try to parse multiple annotations (non-throwing)
static String	toString (const MzPAFAnnotation &ann)
	Convert an annotation to mzPAF string.
static 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 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	isStandardFragmentIon (MzPAFIonSeries series)
	Check if ion series is a standard fragment ion (a, b, c, 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
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.

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, x, y, z, p, I, m, r, f, _)

isMzPAFFormat()

static bool isMzPAFFormat ( const 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

isStandardFragmentIon()

static bool isStandardFragmentIon ( MzPAFIonSeries  series )

static

Check if ion series is a standard fragment ion (a, b, c, x, y, z)

Parameters

[in]

series

The ion series to check

Returns

True if it's a standard fragment ion type

parse()

static MzPAFAnnotation parse ( const 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 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 String toString ( const MzPAFAnnotation &  ann )

static

Convert an annotation to mzPAF string.

Parameters

[in]

ann

The annotation to convert

Returns

The mzPAF string representation

toString() [2/2]

static 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 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 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