Tagger Class Reference

Calculate sequence tags from m/z values. More...

#include <OpenMS/CHEMISTRY/Tagger.h>

Collaboration diagram for Tagger:

Public Member Functions
	Tagger (size_t min_tag_length, double ppm, size_t max_tag_length=65535, size_t min_charge=1, size_t max_charge=1, const StringList &fixed_mods=StringList(), const StringList &var_mods=StringList())
	Constructor for Tagger. More...
void	getTag (const std::vector< double > &mzs, std::vector< std::string > &tags) const
	Generate tags from mass vector mzs. More...
void	getTag (const MSSpectrum &spec, std::vector< std::string > &tags) const
	Generate tags from an MSSpectrum. More...
void	setMaxCharge (size_t max_charge)
	Change the maximal charge considered by the tagger. More...

Private Member Functions
char	getAAByMass_ (double m) const
	get a residue one letter code by matching the mass m to the map of residues mass2aa_, returns ' ' if there is no match More...
void	getTag_ (std::string &tag, const std::vector< double > &mzs, const size_t i, std::vector< std::string > &tags, const size_t charge) const
	start searching for tags starting from peak i of the mz vector mzs More...

Private Attributes
double	min_gap_
	will be set to smallest residue mass in ResidueDB More...
double	max_gap_
	will be set to highest residue mass in ResidueDB More...
double	ppm_
	tolerance More...
size_t	min_tag_length_
	minimum tag length More...
size_t	max_tag_length_
	maximum tag length More...
size_t	min_charge_
	minimal fragment charge More...
size_t	max_charge_
	maximal fragment charge More...
std::map< double, char >	mass2aa_
	mapping of residue masses to their one letter codes More...

Detailed Description

Calculate sequence tags from m/z values.

Current restrictions and potential extensions:

• first prefix/suffix ion don't give rise to first character in tags (as currently ion types are not specified)
• gaps are not supported
• I/L are treated redundantly, all possible combinations are written out

Constructor & Destructor Documentation

Tagger()

Tagger	(	size_t	min_tag_length,
		double	ppm,
		size_t	max_tag_length = 65535,
		size_t	min_charge = 1,
		size_t	max_charge = 1,
		const StringList &	fixed_mods = StringList(),
		const StringList &	var_mods = StringList()
	)

Constructor for Tagger.

The parameter max_charge_ should be >= min_charge_. Also max_tag_length should be >= min_tag_length.

Parameters

min_tag_length	the minimal sequence tag length.
ppm	the tolerance for matching residue masses to peak delta masses.
max_tag_length	the maximal sequence tag length.
min_charge	minimal fragment charge considered for each sequence tag.
max_charge	maximal fragment charge considered for each sequence tag.
fixed_mods	a list of modification names. The modified residues replace the unmodified versions.
var_mods	a list of modification names. The modified residues are added as additional entries to the list of residues.

Member Function Documentation

getAAByMass_()

char getAAByMass_ ( double  m ) const

private

get a residue one letter code by matching the mass m to the map of residues mass2aa_, returns ' ' if there is no match

getTag() [1/2]

void getTag	(	const MSSpectrum &	spec,
		std::vector< std::string > &	tags
	)		const

Generate tags from an MSSpectrum.

The parameter tags is filled with one string per sequence tag. It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor.

Parameters

spec	a centroided fragment spectrum.
tags	the vector of tags, that is filled with this function.

getTag() [2/2]

void getTag	(	const std::vector< double > &	mzs,
		std::vector< std::string > &	tags
	)		const

Generate tags from mass vector mzs.

The parameter tags is filled with one string per sequence tag. It uses the standard residues from ResidueDB including the fixed and variable modifications given to the constructor.

Parameters

mzs	a vector of mz values, containing the mz values from a centroided fragment spectrum.
tags	the vector of tags, that is filled with this function.

getTag_()

void getTag_ ( std::string &  tag, const std::vector< double > &  mzs, const size_t  i, std::vector< std::string > &  tags, const size_t  charge  ) const

private

start searching for tags starting from peak i of the mz vector mzs

setMaxCharge()

void setMaxCharge

(

size_t

max_charge

)

Change the maximal charge considered by the tagger.

Allows to change the maximal considered charge e.g. based on a spectra precursor charge without calling the constructor multiple times.

Parameters

max_charge

the new maximal charge.

Member Data Documentation

mass2aa_

std::map<double, char> mass2aa_

private

mapping of residue masses to their one letter codes

max_charge_

size_t max_charge_

private

maximal fragment charge

max_gap_

double max_gap_

private

will be set to highest residue mass in ResidueDB

max_tag_length_

size_t max_tag_length_

private

maximum tag length

min_charge_

size_t min_charge_

private

minimal fragment charge

min_gap_

double min_gap_

private

will be set to smallest residue mass in ResidueDB

min_tag_length_

size_t min_tag_length_

private

minimum tag length

ppm_

double ppm_

private

tolerance