Helper class for peptide and protein quantification based on feature data annotated with IDs. More...

#include <OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h>

Inheritance diagram for PeptideAndProteinQuant:

Collaboration diagram for PeptideAndProteinQuant:

Classes
struct	PeptideData
	Quantitative and associated data for a peptide. More...

struct	ProteinData
	Quantitative and associated data for a protein. More...

struct	Statistics
	Statistics for processing summary. More...

Public Types
typedef std::map< UInt64, double >	SampleAbundances
	Mapping: sample ID -> abundance. More...

typedef std::map< AASequence, PeptideData >	PeptideQuant
	Mapping: peptide sequence (modified) -> peptide data. More...

typedef std::map< String, ProteinData >	ProteinQuant
	Mapping: protein accession -> protein data. More...

Public Member Functions
	PeptideAndProteinQuant ()
	Constructor. More...

	~PeptideAndProteinQuant () override
	Destructor. More...

void	readQuantData (FeatureMap &features, const ExperimentalDesign &ed)
	Read quantitative data from a feature map. More...

void	readQuantData (ConsensusMap &consensus, const ExperimentalDesign &ed)
	Read quantitative data from a consensus map. More...

void	readQuantData (std::vector< ProteinIdentification > &proteins, PeptideIdentificationList &peptides, const ExperimentalDesign &ed)
	Read quantitative data from identification results (for quantification via spectral counting). More...

void	quantifyPeptides (const PeptideIdentificationList &peptides=PeptideIdentificationList())
	Compute peptide abundances. More...

void	quantifyProteins (const ProteinIdentification &proteins=ProteinIdentification())
	Compute protein abundances. More...

std::map< OpenMS::String, OpenMS::String >	mapAccessionToLeader (const OpenMS::ProteinIdentification &proteins) const

const Statistics &	getStatistics ()
	Get summary statistics. More...

const PeptideQuant &	getPeptideResults ()
	Get peptide abundance data. More...

const ProteinQuant &	getProteinResults ()
	Get protein abundance data. More...

void	annotateQuantificationsToProteins (const ProteinQuant &protein_quants, ProteinIdentification &proteins, bool remove_unquantified=true)
	Annotate protein quant results as meta data to protein ids. 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...

Private Member Functions
PeptideHit	getAnnotation_ (PeptideIdentificationList &peptides)
	Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications. More...

void	quantifyFeature_ (const FeatureHandle &feature, size_t fraction, const String &filename, const PeptideHit &hit, Int channel_or_label)
	Gather quantitative information from a feature. More...

bool	getBest_ (const std::map< Int, std::map< String, std::map< Int, std::map< Int, double >>>> &peptide_abundances, std::tuple< size_t, String, size_t, Int > &best)
	Determine fraction, filename, charge state, and channel of a peptide with the highest number of abundances. More...

template<typename T >
void	orderBest_ (const std::map< T, SampleAbundances > &abundances, std::vector< T > &result)
	Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance. More...

void	normalizePeptides_ ()
	Normalize peptide abundances across samples by (multiplicative) scaling to equal medians. More...

void	transferPeptideDataToProteins_ (const ProteinIdentification &proteins)
	Transfer peptide-level quantitative data to protein-level data structures. More...

std::vector< String >	selectPeptidesForQuantification_ (const String &protein_accession, Size top_n, bool fix_peptides)
	Select peptides for protein quantification based on filtering criteria. More...

double	aggregateAbundances_ (const std::vector< double > &abundances, const String &method) const
	Aggregate abundances using the specified mathematical method. More...

void	calculateProteinAbundances_ (const String &protein_accession, const std::vector< String > &selected_peptides, const String &aggregate_method, Size top_n, bool include_all)
	Calculate protein abundances for a single protein using selected peptides. More...

void	calculateFileAndChannelLevelProteinAbundances_ (const String &protein_accession, const std::vector< String > &selected_peptides, const String &aggregate_method, Size top_n, bool include_all, const std::map< String, String > &accession_to_leader)
	Calculate detailed protein abundances at channel level using selected peptides. More...

void	performIbaqNormalization_ (const ProteinIdentification &proteins)
	Perform iBAQ normalization on protein abundances. More...

String	getAccession_ (const std::set< String > &pep_accessions, const std::map< String, String > &accession_to_leader) const
	Get the "canonical" protein accession from the list of protein accessions of a peptide. More...

void	countPeptides_ (PeptideIdentificationList &peptides)
	Count the number of identifications (best hits only) of each peptide sequence. More...

size_t	getSampleIDFromFilenameAndChannel_ (const String &filename, Int channel_or_label, const ExperimentalDesign &ed) const
	Map (filename, channel) to sample using ExperimentalDesign. More...

void	updateMembers_ () override
	Clear all data when parameters are set. More...

Private Attributes
Statistics	stats_
	Processing statistics for output in the end. More...

PeptideQuant	pep_quant_
	Peptide quantification data. More...

ProteinQuant	prot_quant_
	Protein quantification data. More...

ExperimentalDesign	experimental_design_
	Experimental design for filename/channel to sample mapping. More...

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. More...

Protected Member Functions inherited from DefaultParamHandler
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

Helper class for peptide and protein quantification based on feature data annotated with IDs.

This class is used by ProteinQuantifier. See there for further documentation.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
method	string	top	top, iBAQ	- top - quantify based on three most abundant peptides (number can be changed in 'top'). - iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!
best_charge_and_fraction	string	false	true, false	Distinguish between fraction and charge states of a peptide. For peptides, abundances will be reported separately for each fraction and charge; for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions). By default, abundances are summed over all charge states.
top:N	int	3	min: 0	Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)
top:aggregate	string	median	median, mean, weighted_mean, sum	Aggregation method used to compute protein abundances from peptide abundances
top:include_all	string	false	true, false	Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)
consensus:normalize	string	false	true, false	Scale peptide abundances so that medians of all samples are equal
consensus:fix_peptides	string	false	true, false	Use the same peptides for protein quantification across all samples. With 'N 0',all peptides that occur in every sample are considered. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected, breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!).

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

◆ PeptideQuant

typedef std::map<AASequence, PeptideData> PeptideQuant

Mapping: peptide sequence (modified) -> peptide data.

◆ ProteinQuant

typedef std::map<String, ProteinData> ProteinQuant

Mapping: protein accession -> protein data.

◆ SampleAbundances

typedef std::map<UInt64, double> SampleAbundances

Mapping: sample ID -> abundance.

Constructor & Destructor Documentation

◆ PeptideAndProteinQuant()

PeptideAndProteinQuant ( )

Constructor.

◆ ~PeptideAndProteinQuant()

~PeptideAndProteinQuant ( )

inlineoverride

Destructor.

Member Function Documentation

◆ aggregateAbundances_()

double aggregateAbundances_	(	const std::vector< double > &	abundances,
		const String &	method
	)		const

private

Aggregate abundances using the specified mathematical method.

Parameters

abundances	Vector of abundance values to aggregate
method	Aggregation method ("median", "mean", "weighted_mean", "sum")

Returns: Aggregated abundance value

◆ annotateQuantificationsToProteins()

void annotateQuantificationsToProteins	(	const ProteinQuant &	protein_quants,
		ProteinIdentification &	proteins,
		bool	remove_unquantified = `true`
	)

Annotate protein quant results as meta data to protein ids.

◆ calculateFileAndChannelLevelProteinAbundances_()

void calculateFileAndChannelLevelProteinAbundances_	(	const String &	protein_accession,
		const std::vector< String > &	selected_peptides,
		const String &	aggregate_method,
		Size	top_n,
		bool	include_all,
		const std::map< String, String > &	accession_to_leader
	)

private

Calculate detailed protein abundances at channel level using selected peptides.

Parameters

protein_accession	The protein accession
selected_peptides	Vector of peptide sequences to use for quantification
aggregate_method	Method to aggregate peptide abundances
top_n	Maximum number of peptides to use per sample
include_all	Whether to include proteins with insufficient peptides
accession_to_leader	Map for resolving protein group leaders

◆ calculateProteinAbundances_()

void calculateProteinAbundances_	(	const String &	protein_accession,
		const std::vector< String > &	selected_peptides,
		const String &	aggregate_method,
		Size	top_n,
		bool	include_all
	)

private

Calculate protein abundances for a single protein using selected peptides.

Parameters

protein_accession	The protein accession
selected_peptides	Vector of peptide sequences to use for quantification
aggregate_method	Method to aggregate peptide abundances
top_n	Maximum number of peptides to use per sample
include_all	Whether to include proteins with insufficient peptides

◆ countPeptides_()

void countPeptides_ ( PeptideIdentificationList & peptides )

private

Count the number of identifications (best hits only) of each peptide sequence.

The peptide hits in peptides are sorted by score in the process.

◆ getAccession_()

String getAccession_	(	const std::set< String > &	pep_accessions,
		const std::map< String, String > &	accession_to_leader
	)		const

private

Get the "canonical" protein accession from the list of protein accessions of a peptide.

Parameters

pep_accessions	Protein accessions of a peptide
accession_to_leader	Captures information about indistinguishable proteins (maps accession to accession of group leader)

If there is no information about indistinguishable proteins (from protXML) available, a canonical accession exists only for proteotypic peptides - it's the single accession for the respective peptide.

Otherwise, a peptide has a canonical accession if it maps only to proteins of one indistinguishable group. In this case, the canonical accession is that of the group leader.

If there is no canonical accession, the empty string is returned.

◆ getAnnotation_()

PeptideHit getAnnotation_ ( PeptideIdentificationList & peptides )

private

Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications.

Only the best-scoring peptide hit of each ID in peptides is taken into account. The hits of each ID must already be sorted! If there's more than one ID and the best hits are not identical by sequence, or if there's no peptide ID, an empty peptide hit (for "ambiguous/no annotation") is returned. Protein accessions from identical peptide hits are accumulated.

◆ getBest_()

bool getBest_	(	const std::map< Int, std::map< String, std::map< Int, std::map< Int, double >>>> &	peptide_abundances,
		std::tuple< size_t, String, size_t, Int > &	best
	)

private

Determine fraction, filename, charge state, and channel of a peptide with the highest number of abundances.

Parameters

peptide_abundances	Const input map fraction -> filename -> charge -> channel -> abundance
best	Will additionally return the best fraction, filename, charge state, and channel

Returns: true if at least one abundance was found, false otherwise

◆ getPeptideResults()

const PeptideQuant& getPeptideResults ( )

Get peptide abundance data.

◆ getProteinResults()

const ProteinQuant& getProteinResults ( )

Get protein abundance data.

◆ getSampleIDFromFilenameAndChannel_()

size_t getSampleIDFromFilenameAndChannel_	(	const String &	filename,
		Int	channel_or_label,
		const ExperimentalDesign &	ed
	)		const

private

Map (filename, channel) to sample using ExperimentalDesign.

Parameters

filename	The base filename (without path/extension)
channel_or_label	The channel/label identifier
ed	The experimental design containing the mapping information

Returns: The sample ID corresponding to the filename and channel

◆ getStatistics()

const Statistics& getStatistics ( )

Get summary statistics.

◆ mapAccessionToLeader()

std::map<OpenMS::String, OpenMS::String> mapAccessionToLeader ( const OpenMS::ProteinIdentification & proteins ) const

◆ normalizePeptides_()

void normalizePeptides_ ( )

private

Normalize peptide abundances across samples by (multiplicative) scaling to equal medians.

◆ orderBest_()

void orderBest_	(	const std::map< T, SampleAbundances > &	abundances,
		std::vector< T > &	result
	)

inlineprivate

Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance.

The keys of abundances are stored ordered in result, best first.

◆ performIbaqNormalization_()

void performIbaqNormalization_ ( const ProteinIdentification & proteins )

private

Perform iBAQ normalization on protein abundances.

Parameters

proteins Protein identification information containing sequences

◆ quantifyFeature_()

void quantifyFeature_	(	const FeatureHandle &	feature,
		size_t	fraction,
		const String &	filename,
		const PeptideHit &	hit,
		Int	channel_or_label
	)

private

Gather quantitative information from a feature.

Store quantitative information from feature in member pep_quant_, based on the peptide annotation in hit. fraction, use 0 for first fraction (or if no fractionation was performed) filename, the base filename (without path/extension) from which the feature originates channel_or_label, the channel/label identifier (e.g., TMT channel, typically 1 for LFQ) If hit is empty ("ambiguous/no annotation"), nothing is stored.

◆ quantifyPeptides()

void quantifyPeptides ( const PeptideIdentificationList & peptides = PeptideIdentificationList() )

Compute peptide abundances.

Based on quantitative data for individual charge states (in member pep_quant_), overall abundances for peptides are computed (and stored again in pep_quant_).

Quantitative data must first be read via readQuantData().

Optional (peptide-level) protein inference information (e.g. from Fido or ProteinProphet) can be supplied via peptides. In that case, peptide-to-protein associations - the basis for protein-level quantification - will also be read from peptides!

◆ quantifyProteins()

void quantifyProteins ( const ProteinIdentification & proteins = ProteinIdentification() )

Compute protein abundances.

Peptide abundances must be computed first with quantifyPeptides(). Optional protein inference information (e.g. BasicProteinInference or Epifany) can be supplied via proteins.

Parameters

proteins Optional protein inference information

◆ readQuantData() [1/3]

void readQuantData	(	ConsensusMap &	consensus,
		const ExperimentalDesign &	ed
	)

Read quantitative data from a consensus map.

Parameters should be set before using this method, as setting parameters will clear all results.

◆ readQuantData() [2/3]

void readQuantData	(	FeatureMap &	features,
		const ExperimentalDesign &	ed
	)

Read quantitative data from a feature map.

Parameters should be set before using this method, as setting parameters will clear all results.

◆ readQuantData() [3/3]

void readQuantData	(	std::vector< ProteinIdentification > &	proteins,
		PeptideIdentificationList &	peptides,
		const ExperimentalDesign &	ed
	)

Read quantitative data from identification results (for quantification via spectral counting).

Parameters should be set before using this method, as setting parameters will clear all results.

◆ selectPeptidesForQuantification_()

std::vector<String> selectPeptidesForQuantification_	(	const String &	protein_accession,
		Size	top_n,
		bool	fix_peptides
	)

private

Select peptides for protein quantification based on filtering criteria.

Parameters

protein_accession	The protein accession to select peptides for
top_n	Maximum number of peptides to select (0 = no limit)
fix_peptides	Whether to use consistent peptides across samples

Returns: Vector of selected peptide sequences

◆ transferPeptideDataToProteins_()

void transferPeptideDataToProteins_ ( const ProteinIdentification & proteins )

private

Transfer peptide-level quantitative data to protein-level data structures.

This method populates prot_quant_ with peptide abundance and PSM count data.

Parameters

proteins Protein identification information

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Clear all data when parameters are set.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ experimental_design_

ExperimentalDesign experimental_design_

private

Experimental design for filename/channel to sample mapping.

◆ pep_quant_

PeptideQuant pep_quant_

private

Peptide quantification data.

◆ prot_quant_

ProteinQuant prot_quant_

private

Protein quantification data.

◆ stats_

Statistics stats_

private

Processing statistics for output in the end.

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PeptideQuant

◆ ProteinQuant

◆ SampleAbundances

Constructor & Destructor Documentation

◆ PeptideAndProteinQuant()

◆ ~PeptideAndProteinQuant()

Member Function Documentation

◆ aggregateAbundances_()

◆ annotateQuantificationsToProteins()

◆ calculateFileAndChannelLevelProteinAbundances_()

◆ calculateProteinAbundances_()

◆ countPeptides_()

◆ getAccession_()

◆ getAnnotation_()

◆ getBest_()

◆ getPeptideResults()

◆ getProteinResults()

◆ getSampleIDFromFilenameAndChannel_()

◆ getStatistics()

◆ mapAccessionToLeader()

◆ normalizePeptides_()

◆ orderBest_()

◆ performIbaqNormalization_()

◆ quantifyFeature_()

◆ quantifyPeptides()

◆ quantifyProteins()

◆ readQuantData() [1/3]

◆ readQuantData() [2/3]

◆ readQuantData() [3/3]

◆ selectPeptidesForQuantification_()

◆ transferPeptideDataToProteins_()

◆ updateMembers_()

Member Data Documentation

◆ experimental_design_

◆ pep_quant_

◆ prot_quant_

◆ stats_