generates complete list of all possible mass shifts due to isotopic labelling More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexDeltaMassesGenerator.h>

Inheritance diagram for MultiplexDeltaMassesGenerator:

Collaboration diagram for MultiplexDeltaMassesGenerator:

Classes
struct	Label
	complete label information More...

Public Member Functions
	MultiplexDeltaMassesGenerator ()
	constructor More...

	MultiplexDeltaMassesGenerator (String labels, int missed_cleavages, std::map< String, double > label_mass_shift)
	constructor More...

void	generateKnockoutDeltaMasses ()
	generate all mass shifts that can occur due to the absence of one or multiple peptides (e.g. for a triplet experiment generate the doublets and singlets that might be present) More...

void	printSamplesLabelsList (std::ostream &stream) const
	write the list of labels for each of the sample More...

void	printDeltaMassesList (std::ostream &stream) const
	write the list of all mass patterns More...

std::vector< MultiplexDeltaMasses >	getDeltaMassesList ()
	returns the list of mass shift patterns More...

const std::vector< MultiplexDeltaMasses > &	getDeltaMassesList () const
	returns the list of mass shift patterns More...

std::vector< std::vector< String > >	getSamplesLabelsList ()
	returns the list of samples with their corresponding labels More...

const std::vector< std::vector< String > > &	getSamplesLabelsList () const
	returns the list of samples with their corresponding labels More...

String	getLabelShort (String label)
	returns the short label string More...

String	getLabelLong (String label)
	returns the long label string More...

MultiplexDeltaMasses::LabelSet	extractLabelSet (AASequence sequence)
	extract the label set from the sequence More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Private Member Functions
void	fillLabelMasterList_ ()
	fill label master list More...

Private Attributes
String	labels_
	isotopic labels More...

std::vector< String >	labels_list_
	flat list of all occurring isotopic labels More...

std::vector< std::vector< String > >	samples_labels_
	list of samples with their corresponding labels More...

int	missed_cleavages_
	maximum number of missed cleavages More...

std::vector< MultiplexDeltaMasses >	delta_masses_list_
	list of all possible mass shift patterns More...

std::vector< Label >	label_master_list_
	master list of all labels More...

std::map< String, double >	label_delta_mass_
	mapping from single label to delta mass e.g. "Arg10" -> 10.0082686 More...

std::map< String, String >	label_short_long_
	mapping from a short label (as in the user params) to a long label (as in PSI-MS name) e.g. "Arg10" -> "Label:13C(6)15N(4)" More...

std::map< String, String >	label_long_short_
	mapping from a long label (as in PSI-MS name) to a short label (as in the user params) e.g. "Label:13C(6)15N(4)" -> "Arg10" More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

generates complete list of all possible mass shifts due to isotopic labelling

Isotopic labelling results in the shift of peptide masses.

For example in a Lys8/Arg10 SILAC labelled sample, some peptides (the ones with one Arg in their sequence) will show a relative mass shift between light and heavy partners of 10 Da. This class constructs the complete list of all possible mass shifts that arise from isotopic labelling.

Constructor & Destructor Documentation

◆ MultiplexDeltaMassesGenerator() [1/2]

MultiplexDeltaMassesGenerator ( )

constructor

◆ MultiplexDeltaMassesGenerator() [2/2]

MultiplexDeltaMassesGenerator	(	String	labels,
		int	missed_cleavages,
		std::map< String, double >	label_mass_shift
	)

constructor

Parameters

labels	string describing the labels used in each sample. [...] specifies the labels for a single sample. For example For example, [][Lys8,Arg10] describes a standard SILAC experiment. In the "light" sample, none of the amino acids are labelled []. In the "heavy" sample, lysines and arginines are isotopically labelled [Lys8,Arg10].
missed_cleavages	maximum number of missed cleavages due to incomplete digestion
label_mass_shift	name of labels (e.g. Lys8) and their corresponding mass shifts (e.g. 8.0141988132)

Member Function Documentation

◆ extractLabelSet()

MultiplexDeltaMasses::LabelSet extractLabelSet ( AASequence sequence )

extract the label set from the sequence

Parameters

sequence amino acid sequence

For example, the sequence VLSEEEIDDNFK(Label:13C(6)15N(2))AQR(Label:13C(6)15N(4)) contains a set of two labels, Lys8 and Arg10.

◆ fillLabelMasterList_()

void fillLabelMasterList_ ( )

private

fill label master list

◆ generateKnockoutDeltaMasses()

void generateKnockoutDeltaMasses ( )

generate all mass shifts that can occur due to the absence of one or multiple peptides (e.g. for a triplet experiment generate the doublets and singlets that might be present)

◆ getDeltaMassesList() [1/2]

std::vector<MultiplexDeltaMasses> getDeltaMassesList ( )

returns the list of mass shift patterns

Parameters

stream output stream

◆ getDeltaMassesList() [2/2]

const std::vector<MultiplexDeltaMasses>& getDeltaMassesList ( ) const

returns the list of mass shift patterns

◆ getLabelLong()

String getLabelLong ( String label )

returns the long label string

Parameters

label short label, as it appears in the "labels" parameter, e.g. "Arg10"

◆ getLabelShort()

String getLabelShort ( String label )

returns the short label string

Parameters

label long label, UniMod name as it appears in peptide sequences, e.g. "Label:13C(6)15N(4)"

◆ getSamplesLabelsList() [1/2]

std::vector<std::vector<String> > getSamplesLabelsList ( )

returns the list of samples with their corresponding labels

For example in a standard SILAC experiment: sample 1: no_label sample 2: Lys8 Arg10

◆ getSamplesLabelsList() [2/2]

const std::vector<std::vector<String> >& getSamplesLabelsList ( ) const

returns the list of samples with their corresponding labels

For example in a standard SILAC experiment: sample 1: no_label sample 2: Lys8 Arg10

◆ printDeltaMassesList()

void printDeltaMassesList ( std::ostream & stream ) const

write the list of all mass patterns

For example in a standard SILAC experiment allowing for one missed cleavage, five mass shift patterns are possible. mass shift 1: 0 (no_label) 8.0142 (Lys8) mass shift 2: 0 (no_label) 10.0083 (Arg10) mass shift 3: 0 (no_label) 16.0284 (Lys8,Lys8) mass shift 4: 0 (no_label) 18.0225 (Arg10,Lys8) mass shift 5: 0 (no_label) 20.0165 (Arg10,Arg10)

Parameters

stream output stream

◆ printSamplesLabelsList()

void printSamplesLabelsList ( std::ostream & stream ) const

write the list of labels for each of the sample

For example in a standard SILAC experiment, sample 1 (light) is unlabelled and sample 2 (heavy) contains Lys8 and Arg 10 labels. sample 1: no_label sample 2: Lys8 Arg10

Member Data Documentation

◆ delta_masses_list_

std::vector<MultiplexDeltaMasses> delta_masses_list_

private

list of all possible mass shift patterns

◆ label_delta_mass_

std::map<String, double> label_delta_mass_

private

mapping from single label to delta mass e.g. "Arg10" -> 10.0082686

◆ label_long_short_

std::map<String, String> label_long_short_

private

mapping from a long label (as in PSI-MS name) to a short label (as in the user params) e.g. "Label:13C(6)15N(4)" -> "Arg10"

◆ label_master_list_

std::vector<Label> label_master_list_

private

master list of all labels

◆ label_short_long_

std::map<String, String> label_short_long_

private

mapping from a short label (as in the user params) to a long label (as in PSI-MS name) e.g. "Arg10" -> "Label:13C(6)15N(4)"

◆ labels_

String labels_

private

isotopic labels

◆ labels_list_

std::vector<String> labels_list_

private

flat list of all occurring isotopic labels

◆ missed_cleavages_

int missed_cleavages_

private

maximum number of missed cleavages

◆ samples_labels_

std::vector<std::vector<String> > samples_labels_

private

list of samples with their corresponding labels

Classes

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MultiplexDeltaMassesGenerator() [1/2]

◆ MultiplexDeltaMassesGenerator() [2/2]

Member Function Documentation

◆ extractLabelSet()

◆ fillLabelMasterList_()

◆ generateKnockoutDeltaMasses()

◆ getDeltaMassesList() [1/2]

◆ getDeltaMassesList() [2/2]

◆ getLabelLong()

◆ getLabelShort()

◆ getSamplesLabelsList() [1/2]

◆ getSamplesLabelsList() [2/2]

◆ printDeltaMassesList()

◆ printSamplesLabelsList()

Member Data Documentation

◆ delta_masses_list_

◆ label_delta_mass_

◆ label_long_short_

◆ label_master_list_

◆ label_short_long_

◆ labels_

◆ labels_list_

◆ missed_cleavages_

◆ samples_labels_