Class representing a single peptide fragment. More...

#include <ms_fragment.hpp>

Public Types
enum	LABEL_FORMAT { LABEL_FORMAT_TRADITIONAL = 0 , LABEL_FORMAT_PEPTIDE_VIEW = 1 }
	Format of fragment labels returned by getLabel(). More...

Public Member Functions
	ms_fragment ()
	Default constructor (don't use it).

	ms_fragment (const char *seriesName, const double massValue, const double nlValue, const int col, const int chargeState=1, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for regular series ions.

	ms_fragment (const char residueName, const double massValue, const double nlValue, const int col=-1, const int chargeState=1, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for immonium ion.

	ms_fragment (const double massValue, const double nlValue, const int chargeState, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for precursor neutral loss peak.

	ms_fragment (const int seriesID, const double massValue, const double nlValue, const char *peptideStr, const int startPos, const int endPos, const int chargeState=1, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for internal series ions only.

	ms_fragment (const int seriesID, const double massValue, const double nlValue, const int col, const int chargeState=1, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for regular series ions.

	ms_fragment (const ms_fragment &src)
	Copying constructor.

	ms_fragment (const ms_peptide::PSM psmComponent, const char *seriesName, const double massValue, const double nlValue, const int col, const int chargeState, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for regular series ions of a crosslinked peptide.

	ms_fragment (const ms_peptide::PSM psmComponent, const char residueName, const double massValue, const double nlValue, const int col, const int chargeState, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for immonium ion of a crosslinked peptide.

	ms_fragment (const ms_peptide::PSM psmComponent, const int seriesID, const double massValue, const double nlValue, const char *peptideStr, const int startPos, const int endPos, const int chargeState, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for internal series ions of a crosslinked peptide.

	ms_fragment (const ms_peptide::PSM psmComponent, const int seriesID, const double massValue, const double nlValue, const int col, const int chargeState, const double matchedExptMass=0, const double matchedExptIntensity=0)
	A constructor for regular series ions of a crosslinked peptide.

void	clearMatchedIon ()
	Sets the fragment to be 'unmatched'.

void	copyFrom (const ms_fragment *src)
	Copies the whole content of another instance.

int	getAllMatchedIons (std::vector< double > &masses, std::vector< double > &intensities) const
	Returns the list of all experimental data that matched the calculated fragment mass.

int	getCharge () const
	Returns the charge state (1, 2, 3 etc.) for the ion.

int	getColumn () const
	Returns the 1-based position index in case of a regular series.

int	getEnd () const
	Returns the 1-based last position in case of an internal fragment.

std::string	getLabel (const LABEL_FORMAT fmt=LABEL_FORMAT_TRADITIONAL) const
	Returns a symbolic label like "a*(6)++".

double	getMass () const
	Returns the ion mass (m/z) value.

double	getMatchedIonIntensity () const
	Returns the intensity of an experimental peak that matched the calculated mass value.

double	getMatchedIonMass () const
	Returns the m/z value of an experimental peak that matched the calculated mass value.

double	getNeutralLoss () const
	Returns the neutral loss (m/z) values applied to the fragment.

std::string	getPeptideSubstring () const
	Returns the peptide substring for internal fragments, residue name for immonium.

std::string	getSeriesName () const
	Returns the ion series name.

int	getStart () const
	Returns the 1-based start position within the peptide sequence.

bool	isCTerminal () const
	Returns TRUE for `y, v, w, x, z` series, and FALSE for other series, internal ions and immonium ions.

bool	isFromAlpha () const
	Returns TRUE if this fragment comes from the alpha peptide of a crosslinked match.

bool	isFromBeta () const
	Returns TRUE if this fragment comes from the beta peptide of a crosslinked match.

bool	isImmonium () const
	Returns TRUE for immonium ions.

bool	isInternal () const
	Returns TRUE for internal fragments `ya` and `yb`.

bool	isNTerminal () const
	Returns TRUE for `a, b, c, d` series, and FALSE for other series, internal ions and immonium ions.

bool	isPrecursorNL () const
	Returns TRUE for precursor neutral loss peaks.

bool	isRegular () const
	Returns TRUE for `a, b, c, d, y, v, w, x, z` series and their derivatives.

ms_fragment &	operator= (const ms_fragment &right)
	Assignment operator for C++ programs.

void	setMatchedIon (const double mass, const double intensity)

Detailed Description

Class representing a single peptide fragment.

Examples: tools_aahelper.cpp.

Member Enumeration Documentation

◆ LABEL_FORMAT

enum LABEL_FORMAT

Format of fragment labels returned by getLabel().

The traditional label format was introduced in Parser 2.2. It has three parts, in this order: fragment ID, charge state and neutral loss. NL is separated from charge state by a space. If NL is zero, there is no space. Fragment ID depends on the series:

Regular ion series: series name followed by column in parentheses, e.g. "a(1)" or "y(15)"
Immoniums: amino acid residue, e.g. "R" or "K"
Internal series: peptide substring, e.g. "LVIK" or "LV"
Precursor NL peaks: "M"

Examples of labels in traditional format: "b(3)++ -64", "LVIK -16", "a(1)++", "y(15)"

The Peptide View label format was introduced in Mascot 2.1. The format contains the same three parts as the traditional format, but the order is different: fragment ID, neutral loss, charge state. There is no space between the elements. Peptide View format supports negative doubly charged ions.

Examples of labels in Peptide View format: "b(3)-64++", "LVIK-16", "a(1)++", "y(15)", "b(3)-64--"

Enumerator
LABEL_FORMAT_TRADITIONAL	Format introduced in Parser 2.2.
LABEL_FORMAT_PEPTIDE_VIEW	Format used by Peptide View since Mascot 2.1.

Constructor & Destructor Documentation

◆ ms_fragment() [1/11]

ms_fragment ( )

Default constructor (don't use it).

Initialises all values to defaults.

◆ ms_fragment() [2/11]

ms_fragment ( const ms_fragment & src )

Copying constructor.

Note: This constructor can only be used from C++. Use copyFrom() from other programming languages.

Parameters

src	is the original fragment to base the new one on.

◆ ms_fragment() [3/11]

ms_fragment	(	const int	seriesID,
		const double	massValue,
		const double	nlValue,
		const int	col,
		const int	chargeState = `1`,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for regular series ions.

Parameters

seriesID	ion series number. It must be one of the values in matrix_science::ms_fragmentationrules::FRAG_SERIES_TYPE.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [4/11]

ms_fragment	(	const ms_peptide::PSM	psmComponent,
		const int	seriesID,
		const double	massValue,
		const double	nlValue,
		const int	col,
		const int	chargeState,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for regular series ions of a crosslinked peptide.

Parameters

psmComponent	One of the values for ms_peptide::PSM. If ms_peptide::PSM_COMPLETE, the object is the same as if it had been constructed with ms_fragment(const int, const double, const double, const int, const int, const double, const double).
seriesID	ion series number. It must be one of the values in matrix_science::ms_fragmentationrules::FRAG_SERIES_TYPE.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [5/11]

ms_fragment	(	const char *	seriesName,
		const double	massValue,
		const double	nlValue,
		const int	col,
		const int	chargeState = `1`,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for regular series ions.

Parameters

seriesName	ion series name.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [6/11]

ms_fragment	(	const ms_peptide::PSM	psmComponent,
		const char *	seriesName,
		const double	massValue,
		const double	nlValue,
		const int	col,
		const int	chargeState,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for regular series ions of a crosslinked peptide.

Parameters

psmComponent	One of the values for ms_peptide::PSM. If ms_peptide::PSM_COMPLETE, the object is the same as if it had been constructed with ms_fragment(const char*, const double, const double, const int, const int, const double, const double).
seriesName	ion series name.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [7/11]

ms_fragment	(	const int	seriesID,
		const double	massValue,
		const double	nlValue,
		const char *	peptideStr,
		const int	startPos,
		const int	endPos,
		const int	chargeState = `1`,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for internal series ions only.

Parameters

seriesID	ion series number. It must be one of the values in matrix_science::ms_fragmentationrules::FRAG_SERIES_TYPE.
massValue	ion mass value.
nlValue	neutral loss value.
peptideStr	peptide sequence string.
startPos	first position of the fragment.
endPos	last position of the fragment.
chargeState	for the internals ions series – should be 1 or 2.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [8/11]

ms_fragment	(	const ms_peptide::PSM	psmComponent,
		const int	seriesID,
		const double	massValue,
		const double	nlValue,
		const char *	peptideStr,
		const int	startPos,
		const int	endPos,
		const int	chargeState,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for internal series ions of a crosslinked peptide.

Parameters

psmComponent	One of the values for ms_peptide::PSM. If ms_peptide::PSM_COMPLETE, the object is the same as if it had been constructed with ms_fragment(const int, const double, const double, const char*, const int, const int, const int, const double, const double).
seriesID	ion series number. It must be one of the values in matrix_science::ms_fragmentationrules::FRAG_SERIES_TYPE.
massValue	ion mass value.
nlValue	neutral loss value.
peptideStr	peptide sequence string.
startPos	first position of the fragment.
endPos	last position of the fragment.
chargeState	for the internals ions series – should be 1 or 2.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [9/11]

ms_fragment	(	const char	residueName,
		const double	massValue,
		const double	nlValue,
		const int	col = `-1`,
		const int	chargeState = `1`,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for immonium ion.

This constructor is only used for immonium ions.

Parameters

residueName	amino-acid name.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [10/11]

ms_fragment	(	const ms_peptide::PSM	psmComponent,
		const char	residueName,
		const double	massValue,
		const double	nlValue,
		const int	col,
		const int	chargeState,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for immonium ion of a crosslinked peptide.

This constructor is only used for immonium ions.

Parameters

psmComponent	One of the values for ms_peptide::PSM. If ms_peptide::PSM_COMPLETE, the object is the same as if it had been constructed with ms_fragment(const char, const double, const double, const int, const int, const double, const double).
residueName	amino-acid name.
massValue	ion mass value.
nlValue	neutral loss value.
col	position index for the ion.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

◆ ms_fragment() [11/11]

ms_fragment	(	const double	massValue,
		const double	nlValue,
		const int	chargeState,
		const double	matchedExptMass = `0`,
		const double	matchedExptIntensity = `0`
	)

A constructor for precursor neutral loss peak.

This constructor is only used for precursor neutral loss peaks. Normally massValue = (mrCalc - nlValue + protonMass * chargeState) / chargeState, where mrCalc is the relative precursor mass.

Parameters

massValue	ion mass value.
nlValue	neutral loss value.
chargeState	charge state (1, 2, 3 etc.) of the ion.
matchedExptMass	is the m/z value of an experimental peak that matches this calculated fragment ion.
matchedExptIntensity	is the intensity of an experimental peak that matches this calculated fragment ion.

Member Function Documentation

◆ copyFrom()

void copyFrom ( const ms_fragment * src )

Copies the whole content of another instance.

Copy everything from src onto this fragment object.

Parameters

src	valid pointer to a ms_fragment object

◆ getAllMatchedIons()

int getAllMatchedIons	(	std::vector< double > &	masses,
		std::vector< double > &	intensities
	)		const

Returns the list of all experimental data that matched the calculated fragment mass.

See ms_fragmentvector::addExperimentalData().

Parameters

masses	is used to return a vector of mass values. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
intensities	is used to return a corresponding vector of intensity values. Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.

Returns: the number of mass/intensity values returned.

◆ getEnd()

int getEnd ( ) const

Returns the 1-based last position in case of an internal fragment.

This will be -1 for a 'regular' series, immonium ions and precursor NL ions.

Returns: end of the series

Examples: tools_aahelper.cpp.

◆ getLabel()

std::string getLabel ( const LABEL_FORMAT fmt = LABEL_FORMAT_TRADITIONAL ) const

Returns a symbolic label like "a*(6)++".

Parameters

fmt	Output format of the label. Default is ms_fragment::LABEL_FORMAT_TRADITIONAL.

Returns: Formatted label; see ms_fragment::LABEL_FORMAT for examples.

Examples: tools_aahelper.cpp.

◆ getMatchedIonIntensity()

double getMatchedIonIntensity ( ) const

Returns the intensity of an experimental peak that matched the calculated mass value.

See ms_fragmentvector::addExperimentalData().

Returns: the intensity of the most intense experimental m/z value that matched the peak. This value will be zero if no peak matched.

◆ getMatchedIonMass()

double getMatchedIonMass ( ) const

Returns the m/z value of an experimental peak that matched the calculated mass value.

See ms_fragmentvector::addExperimentalData().

Returns: the mass of the most intense experimental m/z value that matched the peak. This value will be zero if no peak matched.

◆ getSeriesName()

std::string getSeriesName ( ) const

Returns the ion series name.

The ions series name will be one of:

a
a*
a0
b
b*
b0
c
x
y
y*
y0
z
z+1
d
v
w
z+2
ya
yb
immonium
precursor

Returns: name of the series

Examples: tools_aahelper.cpp.

◆ getStart()

int getStart ( ) const

Returns the 1-based start position within the peptide sequence.

Returns: 1-based position in case of an internal fragment, which will also be valid for a 'regular' series. Returns 0 if this is a precursor NL peak.

Examples: tools_aahelper.cpp.

◆ isFromAlpha()

bool isFromAlpha ( ) const

Returns TRUE if this fragment comes from the alpha peptide of a crosslinked match.

Returns: False if the fragment is from the beta peptide or from a linear (non-crosslinked) peptide. True otherwise.

◆ isFromBeta()

bool isFromBeta ( ) const

Returns TRUE if this fragment comes from the beta peptide of a crosslinked match.

Returns: False if the fragment is from the alpha peptide or from a linear (non-crosslinked) peptide. True otherwise.

◆ operator=()

ms_fragment & operator= ( const ms_fragment & right )

Assignment operator for C++ programs.

Parameters

right is the original fragment to copy to the new one.

Returns: reference to the current object

◆ setMatchedIon()

void setMatchedIon	(	const double	mass,
		const double	intensity
	)

Sets the mass and intensity of experimental data that matched the calculated mass value.

See ms_fragmentvector::addExperimentalData().

These values will be zero if no peak matched.

Parameters

mass	is the experimental m/z value that matched the peak.
intensity	is the experimental intensity value that matched the peak.

The documentation for this class was generated from the following files:

ms_fragment.hpp
ms_fragment.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ LABEL_FORMAT

Constructor & Destructor Documentation

◆ ms_fragment() [1/11]

◆ ms_fragment() [2/11]

◆ ms_fragment() [3/11]

◆ ms_fragment() [4/11]

◆ ms_fragment() [5/11]

◆ ms_fragment() [6/11]

◆ ms_fragment() [7/11]

◆ ms_fragment() [8/11]

◆ ms_fragment() [9/11]

◆ ms_fragment() [10/11]

◆ ms_fragment() [11/11]

Member Function Documentation

◆ copyFrom()

◆ getAllMatchedIons()

◆ getEnd()

◆ getLabel()

◆ getMatchedIonIntensity()

◆ getMatchedIonMass()

◆ getSeriesName()

◆ getStart()

◆ isFromAlpha()

◆ isFromBeta()

◆ operator=()

◆ setMatchedIon()