This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMDecoy.h>

Inheritance diagram for MRMDecoy:

Collaboration diagram for MRMDecoy:

Public Types
typedef std::vector< size_t >	IndexType

typedef std::vector< OpenMS::TargetedExperiment::Protein >	ProteinVectorType

typedef std::vector< OpenMS::TargetedExperiment::Peptide >	PeptideVectorType

typedef std::vector< OpenMS::ReactionMonitoringTransition >	TransitionVectorType

typedef std::map< String, std::vector< const ReactionMonitoringTransition * > >	PeptideTransitionMapType

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	MRMDecoy ()

void	generateDecoys (const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const
	Generate decoys from a TargetedExperiment. More...

void	switchKR (OpenMS::TargetedExperiment::Peptide &peptide) const
	Switch the final Amino Acid of a tryptic peptide. E.g. If the last Amino Acid is "K" switch to "R" (and vice versa). More...

float	AASequenceIdentity (const String &sequence, const String &decoy) const
	Compute relative identity (relative number of matches of amino acids at the same position) between two sequences. More...

OpenMS::TargetedExperiment::Peptide	shufflePeptide (OpenMS::TargetedExperiment::Peptide peptide, const double identity_threshold, int seed=-1, const int max_attempts=100) const
	Shuffle a peptide (with its modifications) 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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Member Functions
static OpenMS::TargetedExperiment::Peptide	reversePeptide (const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())
	Reverse a peptide sequence (with its modifications) More...

static IndexType	findFixedResidues (const std::string &sequence, bool keepN, bool keepC, const OpenMS::String &keep_const_pattern)
	Find all residues in a sequence that should not be reversed / shuffled. More...

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. More...

Protected Member Functions
bool	hasCNterminalMods_ (const OpenMS::TargetedExperiment::Peptide &peptide, bool checkCterminalAA) const
	Check if a peptide has C or N terminal modifications. More...

IndexType	findFixedResidues_ (const std::string &sequence) const
	Find all K, R, P sites in a sequence to be set as fixed. More...

IndexType	findFixedAndTermResidues_ (const std::string &sequence) const
	Find all K, R, P and C-/N-terminal sites in a sequence to be set as fixed. More...

OpenMS::TargetedExperiment::Peptide	pseudoreversePeptide_ (const OpenMS::TargetedExperiment::Peptide &peptide) const
	Pseudo-reverse a peptide sequence (with its modifications) More...

OpenMS::TargetedExperiment::Peptide	reversePeptide_ (const OpenMS::TargetedExperiment::Peptide &peptide) const
	Reverse a peptide sequence (with its modifications) More...

String	getModifiedPeptideSequence_ (const OpenMS::TargetedExperiment::Peptide &pep) const
	Convert a peptide to a string which contains the peptide sequence and modifications. More...

void	updateMembers_ () override
	Synchronize members with param class. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
String	keep_const_pattern_

bool	keepN_

bool	keepC_

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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.

There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.

Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.

First, the algorithm goes through all peptides and applies the decoy method to the target peptide sequence (pseudo-reverse, reverse or shuffle) in order to produce the decoy sequence. Then, for each peptide, the fragment ions in the target library are matched to their most likely origin (e.g. the ions are annotated with their ion series (a,b,y) and the fragment number and optionally a neutral loss (10 different neutral losses are currently implemented)). For each fragment ion from the target peptide, an equivalent ion is created for the decoy peptide with the same intensity (e.g. if the target peptide sequence has a b5 ion with a normalized intensity of 200, an equivalent b5 ion for the decoy sequence is created and assigned the intensity 200). Optionally, the m/z values are corrected to reflect the theoretical value rather than the experimental value in the library.

Member Typedef Documentation

◆ IndexType

typedef std::vector<size_t> IndexType

◆ PeptideTransitionMapType

typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType

◆ PeptideVectorType

typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType

◆ ProteinVectorType

typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType

◆ TransitionVectorType

typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType

Constructor & Destructor Documentation

◆ MRMDecoy()

MRMDecoy ( )

Member Function Documentation

◆ AASequenceIdentity()

float AASequenceIdentity	(	const String &	sequence,
		const String &	decoy
	)		const

Compute relative identity (relative number of matches of amino acids at the same position) between two sequences.

◆ findFixedAndTermResidues_()

IndexType findFixedAndTermResidues_ ( const std::string & sequence ) const

protected

Find all K, R, P and C-/N-terminal sites in a sequence to be set as fixed.

This method was adapted from the SpectraST decoy generator

◆ findFixedResidues()

static IndexType findFixedResidues	(	const std::string &	sequence,
		bool	keepN,
		bool	keepC,
		const OpenMS::String &	keep_const_pattern
	)

static

Find all residues in a sequence that should not be reversed / shuffled.

Parameters

sequence	The amino acid sequence
keepN	Whether to keep N terminus constant
keepC	Whether to keep C terminus constant
keep_const_pattern	A string containing the AA to not change (e.g. 'KRP')

◆ findFixedResidues_()

IndexType findFixedResidues_ ( const std::string & sequence ) const

protected

Find all K, R, P sites in a sequence to be set as fixed.

This method was adapted from the SpectraST decoy generator

◆ generateDecoys()

void generateDecoys	(	const OpenMS::TargetedExperiment &	exp,
		OpenMS::TargetedExperiment &	dec,
		const String &	method,
		const double	aim_decoy_fraction,
		const bool	switchKR,
		const String &	decoy_tag,
		const int	max_attempts,
		const double	identity_threshold,
		const double	precursor_mz_shift,
		const double	product_mz_shift,
		const double	product_mz_threshold,
		const std::vector< String > &	fragment_types,
		const std::vector< size_t > &	fragment_charges,
		const bool	enable_specific_losses,
		const bool	enable_unspecific_losses,
		const int	round_decPow = `-4`
	)		const

Generate decoys from a TargetedExperiment.

Will generate decoy peptides for each target peptide provided in exp and write them into the decoy experiment.

Valid methods: shuffle, reverse, pseudo-reverse

If theoretical is true, the target transitions will be returned but their masses will be adjusted to match the theoretical value of the fragment ion that is the most likely explanation for the product.

mz_threshold is used for the matching of theoretical ion series to the observed one

To generate decoys with different precursor mass, use the "switchKR" flag which switches terminal K/R (switches K to R and R to K). This generates different precursor m/z and ensures that the y ion series has a different mass. For a description of the procedure, see (supplemental material)

Bruderer et al. Mol Cell Proteomics. 2017. 10.1074/mcp.RA117.000314.

◆ getModifiedPeptideSequence_()

String getModifiedPeptideSequence_ ( const OpenMS::TargetedExperiment::Peptide & pep ) const

protected

Convert a peptide to a string which contains the peptide sequence and modifications.

◆ hasCNterminalMods_()

bool hasCNterminalMods_	(	const OpenMS::TargetedExperiment::Peptide &	peptide,
		bool	checkCterminalAA
	)		const

protected

Check if a peptide has C or N terminal modifications.

◆ pseudoreversePeptide_()

OpenMS::TargetedExperiment::Peptide pseudoreversePeptide_ ( const OpenMS::TargetedExperiment::Peptide & peptide ) const

protected

Pseudo-reverse a peptide sequence (with its modifications)

Note: Pseudo reverses a peptide sequence, leaving the C terminus (the last AA constant)

◆ reversePeptide()

static OpenMS::TargetedExperiment::Peptide reversePeptide	(	const OpenMS::TargetedExperiment::Peptide &	peptide,
		const bool	keepN,
		const bool	keepC,
		const String &	const_pattern = `String()`
	)

static

Reverse a peptide sequence (with its modifications)

Parameters

peptide	The peptide sequence and modifications
keepN	Whether to keep N terminus in place
keepC	Whether to keep C terminus in place
const_pattern	A list of AA to leave in place

◆ reversePeptide_()

OpenMS::TargetedExperiment::Peptide reversePeptide_ ( const OpenMS::TargetedExperiment::Peptide & peptide ) const

protected

Reverse a peptide sequence (with its modifications)

Note: Does not keep N / C terminus in place.

◆ shufflePeptide()

OpenMS::TargetedExperiment::Peptide shufflePeptide	(	OpenMS::TargetedExperiment::Peptide	peptide,
		const double	identity_threshold,
		int	seed = `-1`,
		const int	max_attempts = `100`
	)		const

Shuffle a peptide (with its modifications) sequence.

This function will shuffle the given peptide sequences and its modifications such that the resulting relative sequence identity is below identity_threshold.

◆ switchKR()

void switchKR ( OpenMS::TargetedExperiment::Peptide & peptide ) const

Switch the final Amino Acid of a tryptic peptide. E.g. If the last Amino Acid is "K" switch to "R" (and vice versa).

Note: If the last Amino Acid is neither "K" or "R", the last Amino Acid is changed to a random Amino Acid .

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ keep_const_pattern_

String keep_const_pattern_

protected

◆ keepC_

bool keepC_

protected

◆ keepN_

bool keepN_

protected

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ IndexType

◆ PeptideTransitionMapType

◆ PeptideVectorType

◆ ProteinVectorType

◆ TransitionVectorType

Constructor & Destructor Documentation

◆ MRMDecoy()

Member Function Documentation

◆ AASequenceIdentity()

◆ findFixedAndTermResidues_()

◆ findFixedResidues()

◆ findFixedResidues_()

◆ generateDecoys()

◆ getModifiedPeptideSequence_()

◆ hasCNterminalMods_()

◆ pseudoreversePeptide_()

◆ reversePeptide()

◆ reversePeptide_()

◆ shufflePeptide()

◆ switchKR()

◆ updateMembers_()

Member Data Documentation

◆ keep_const_pattern_

◆ keepC_

◆ keepN_