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

#include <OpenMS/FEATUREFINDER/MultiplexDeltaMassesGenerator.h>

Inheritance diagram for MultiplexDeltaMassesGenerator:

Collaboration diagram for MultiplexDeltaMassesGenerator:

Classes
struct	Label
	complete label information More...

Public Member Functions
	MultiplexDeltaMassesGenerator ()
	constructor

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

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)

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

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

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

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

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

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

String	getLabelShort (const String &label)
	returns the short label string

String	getLabelLong (const String &label)
	returns the long label string

MultiplexDeltaMasses::LabelSet	extractLabelSet (const AASequence &sequence)
	extract the label set from the sequence

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

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

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

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

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

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

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

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

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

Private Member Functions
void	fillLabelMasterList_ ()
	fill label master list

Private Attributes
String	labels_
	isotopic labels

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

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

int	missed_cleavages_
	maximum number of missed cleavages

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

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

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

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)"

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"

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

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.

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

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

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

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

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

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

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

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

[in]	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].
[in]	missed_cleavages	maximum number of missed cleavages due to incomplete digestion
[in]	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 ( const AASequence & sequence )

extract the label set from the sequence

Parameters

[in] 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

◆ getDeltaMassesList() [2/2]

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

returns the list of mass shift patterns

◆ getLabelLong()

String getLabelLong ( const String & label )

returns the long label string

Parameters

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

◆ getLabelShort()

String getLabelShort ( const String & label )

returns the short label string

Parameters

[in] 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

[out] 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

Parameters

[out] stream output stream

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_