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:

Classes
struct	DesignCell
	Experimental-design coordinates of one (basename, label) cell. More...

struct	FileLabelHash

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.

typedef std::map< UInt, std::map< UInt, double > >	FractionGroupAbundances
	Mapping: experimental-design fraction group -> label/channel -> abundance.

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

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

Public Member Functions
	PeptideAndProteinQuant ()
	Constructor.

	~PeptideAndProteinQuant () override
	Destructor.

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

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

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

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

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

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

const Statistics &	getStatistics ()
	Get summary statistics.

const PeptideQuant &	getPeptideResults ()
	Get peptide abundance data.

const ProteinQuant &	getProteinResults ()
	Get protein abundance data.

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

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::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 std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

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

Private Types
typedef std::unordered_map< std::string, std::vector< const PeptideQuant::value_type * > >	UnmodifiedToEntriesIndex

typedef std::map< UInt, std::map< Int, std::map< UInt, double > > >	FractionGroupFractionAbundances
	Mapping: fraction group -> fraction -> label/channel -> abundance.

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.

void	quantifyFeature_ (const FeatureHandle &feature, size_t fraction, const std::string &filename, const PeptideHit &hit, UInt channel_or_label)
	Gather quantitative information from a feature.

bool	getBestCharge_ (const std::map< Int, std::map< std::string, std::map< Int, std::map< UInt, double > > > > &peptide_abundances, Int &best_charge) const
	Select one charge state globally for a modified peptide.

void	collapseFractions_ (const FractionGroupFractionAbundances &fraction_abundances, FractionGroupAbundances &assay_abundances) const
	Combine the fractions of every fraction group into assay abundances.

template<typename T >
void	orderBest_ (const std::map< T, FractionGroupAbundances > &abundances, std::vector< T > &result)
	Order keys according to how many assays they quantify, breaking ties by total abundance.

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

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

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

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

void	calculateFractionGroupLevelProteinAbundances_ (const std::string &protein_accession, const std::vector< std::string > &selected_peptides, const std::string &aggregate_method, Size top_n, bool include_all)
	Calculate protein abundances at experimental-design fraction-group/label grain.

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

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

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

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

void	buildSampleIDLookup_ ()
	(Re)build design-cell lookups from `experimental_design_`.

const DesignCell &	getDesignCellFromFilenameAndChannel_ (const std::string &filename, UInt channel_or_label) const
	Map (filename, channel) to its experimental-design cell.

Size	getSampleIDFromFilenameAndChannel_ (const std::string &filename, UInt channel_or_label) const
	Map (filename, channel) to a sample using the precomputed design-cell lookup.

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

Static Private Member Functions
static Int	selectBestFraction_ (const std::map< Int, std::map< UInt, double > > &fraction_abundances)
	Select the fraction to keep for one fraction group, see 'fractions:aggregate' 'best'.

static Size	countQuantifiedAssays_ (const FractionGroupAbundances &abundances)
	Number of assays in which `abundances` is actually quantified.

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

PeptideQuant	pep_quant_
	Peptide quantification data.

std::map< AASequence, Int >	best_charge_by_peptidoform_

ProteinQuant	prot_quant_
	Protein quantification data.

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

std::unordered_map< std::pair< std::string, UInt >, DesignCell, FileLabelHash >	design_cell_lookup_

std::set< std::pair< UInt, UInt > >	quantification_fraction_group_labels_

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

Protected Member Functions inherited from DefaultParamHandler
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< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::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

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	string	false	true, false	Distinguish between fraction and charge states in detailed peptide output. For protein quantification, select one charge per modified peptide globally: maximize the number of (fraction group, label) assays with a positive abundance, then break ties by total abundance; retain that charge's values in every assay. By default, protein abundances are summed over all charge states. How the retained values of several fractions are combined is governed by 'fractions:aggregate', not by this flag.
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)
fractions:aggregate	string	sum	sum, best	How the fractions of one fraction group are combined into that group's (fraction group, label) assay values. - sum - add up every fraction, i.e. treat them as the parts of one separated sample that they are. - best - keep a single fraction per peptide and fraction group and discard the others. The fraction is chosen ONCE per peptide, ranked by the number of labels in which it has a positive abundance and then by the total of those abundances (an exact tie keeps the lowest fraction number), and ALL of its labels are then taken from it. The choice is deliberately not made per label: taking one channel from one fraction and another channel from a different fraction would mix physical aliquots and destroy the reporter-ion ratios that isobaric quantification consists of. Only the assay values are affected. Per-(file, channel) quantities are per fraction by definition and always report every file.
consensus:normalize	string	false	true, false	Scale peptide abundances so that the median of each (fraction group, label) assay matches the overall median. Abundances of zero count as 'not detected' and are left out of the medians; an assay without any positive abundance takes no part in the normalization.
consensus:fix_peptides	string	false	true, false	Use the same peptides for protein quantification across all (fraction group, label) assays. With 'N 0',all peptides that occur in every assay are considered. Otherwise ('N'), the N peptides that occur in the most assays (independently of each other) are selected, breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!). A peptide counts as occurring in an assay only where its abundance is positive: an abundance stored as zero means 'not detected' (e.g. an isobaric reporter below 'min_reporter_intensity'), not a measurement of absence.

Note:

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

Class Documentation

◆ OpenMS::PeptideAndProteinQuant::DesignCell

struct OpenMS::PeptideAndProteinQuant::DesignCell

Experimental-design coordinates of one (basename, label) cell.

Class Members
UInt	fraction_group = 0
Size	sample = 0

Member Typedef Documentation

◆ FractionGroupAbundances

typedef std::map<UInt, std::map<UInt, double> > FractionGroupAbundances

Mapping: experimental-design fraction group -> label/channel -> abundance.

◆ FractionGroupFractionAbundances

typedef std::map<UInt, std::map<Int, std::map<UInt, double> > > FractionGroupFractionAbundances

private

Mapping: fraction group -> fraction -> label/channel -> abundance.

◆ PeptideQuant

typedef std::map<AASequence, PeptideData> PeptideQuant

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

◆ ProteinQuant

typedef std::map<std::string, ProteinData> ProteinQuant

Mapping: protein accession -> protein data.

◆ SampleAbundances

typedef std::map<UInt64, double> SampleAbundances

Mapping: sample ID -> abundance.

◆ UnmodifiedToEntriesIndex

typedef std::unordered_map<std::string, std::vector<const PeptideQuant::value_type*> > UnmodifiedToEntriesIndex

private

Index: unmodified peptide sequence -> all pep_quant_ entries (modified peptidoforms) sharing that unmodified sequence. Built once per quantifyProteins() call so that channel-level aggregation does not rescan pep_quant_ (calling AASequence::toUnmodifiedString() on every entry) for every (protein, peptide) pair. Only looked up by key (never range-iterated); the per-bucket vector preserves pep_quant_ (AASequence-sorted) order, so an unordered map keeps output identical.

Constructor & Destructor Documentation

◆ PeptideAndProteinQuant()

PeptideAndProteinQuant ( )

Constructor.

◆ ~PeptideAndProteinQuant()

~PeptideAndProteinQuant ( )

inlineoverride

Destructor.

Member Function Documentation

◆ aggregateAbundances_()

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

private

Aggregate abundances using the specified mathematical method.

Parameters

[in]	abundances	Vector of abundance values to aggregate
[in]	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.

◆ buildSampleIDLookup_()

void buildSampleIDLookup_ ( )

private

(Re)build design-cell lookups from experimental_design_.

Maps each (basename without extension, channel/label) of the MS file section to its sample and fraction group. Conflicting duplicate cells and fraction-group labels that resolve to different samples are rejected. Called whenever the experimental design is (re)set.

Exceptions

Exception::MissingInformation if a cell refers outside the sample section, duplicate cells conflict, one run belongs to several fraction groups, or one fraction-group label resolves to several samples

◆ calculateFileAndChannelLevelProteinAbundances_()

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

private

Calculate detailed protein abundances at channel level using selected peptides.

Parameters

[in]	protein_accession	The protein accession
[in]	selected_peptides	Vector of peptide sequences to use for quantification
[in]	aggregate_method	Method to aggregate peptide abundances
[in]	top_n	Maximum number of peptides to use per file/channel cell
[in]	include_all	Whether to include proteins with insufficient peptides
[in]	accession_to_leader	Map for resolving protein group leaders
[in]	unmod_to_entries	Precomputed index from unmodified peptide sequence to the `pep_quant_` entries sharing it (avoids rescanning `pep_quant_`)

◆ calculateFractionGroupLevelProteinAbundances_()

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

private

Calculate protein abundances at experimental-design fraction-group/label grain.

Parameters

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

◆ collapseFractions_()

void collapseFractions_	(	const FractionGroupFractionAbundances &	fraction_abundances,
		FractionGroupAbundances &	assay_abundances
	)		const

private

Combine the fractions of every fraction group into assay abundances.

Applies 'fractions:aggregate': 'sum' adds all fractions up, 'best' keeps the single fraction chosen by selectBestFraction_() and discards the others. Either way every label observed in any fraction of a group becomes a cell of that group's assays, so that the two settings produce the same set of keys and a label seen only in a discarded fraction reports "not detected" rather than disappearing.

Parameters

[in]	fraction_abundances	Mapping fraction group -> fraction -> label -> abundance
[out]	assay_abundances	Mapping fraction group -> label -> abundance

◆ 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.

◆ countQuantifiedAssays_()

static Size countQuantifiedAssays_ ( const FractionGroupAbundances & abundances )

staticprivate

Number of assays in which abundances is actually quantified.

Counts the entries with a positive abundance, not the entries. A zero is not a measurement of "no protein": IsobaricChannelExtractor stores a reporter it could not find - or one below 'min_reporter_intensity' - as 0.0, and quantifyFeature_ records that handle like any other, so the assay key exists with value 0. Counting those keys would report a peptide with signal in 2 of 10 TMT channels as quantified in all 10.

This is the rule normalizePeptides_() already applies to its medians and getBestCharge_() to its charge prevalence; it belongs to every count of "in how many assays".

◆ getAccession_()

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

private

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

Parameters

[in]	pep_accessions	Protein accessions of a peptide
[in]	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.

◆ getBestCharge_()

bool getBestCharge_	(	const std::map< Int, std::map< std::string, std::map< Int, std::map< UInt, double > > > > &	peptide_abundances,
		Int &	best_charge
	)		const

private

Select one charge state globally for a modified peptide.

Positive observations are collapsed to (fraction group, label) assays through the experimental design. The charge quantified in the most distinct assays wins; ties are resolved by its summed abundance across all assays. If both criteria tie, the lower charge wins deterministically.

Parameters

[in]	peptide_abundances	Mapping fraction -> filename -> charge -> channel -> abundance
[out]	best_charge	Selected charge state

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

◆ getDesignCellFromFilenameAndChannel_()

const DesignCell & getDesignCellFromFilenameAndChannel_	(	const std::string &	filename,
		UInt	channel_or_label
	)		const

private

Map (filename, channel) to its experimental-design cell.

Parameters

[in]	filename	The base filename (without path/extension)
[in]	channel_or_label	The channel/label identifier

Returns: The design coordinates corresponding to the filename and channel

Exceptions

Exception::MissingInformation if the (filename, channel) pair is not in the experimental design

◆ getPeptideResults()

const PeptideQuant & getPeptideResults ( )

Get peptide abundance data.

◆ getProteinResults()

const ProteinQuant & getProteinResults ( )

Get protein abundance data.

◆ getSampleIDFromFilenameAndChannel_()

Size getSampleIDFromFilenameAndChannel_	(	const std::string &	filename,
		UInt	channel_or_label
	)		const

private

Map (filename, channel) to a sample using the precomputed design-cell lookup.

Parameters

[in]	filename	The base filename without path or extension
[in]	channel_or_label	The channel or label identifier

Returns: The sample corresponding to the filename and channel

Exceptions

Exception::MissingInformation if the (filename, channel) pair is not in the experimental design

◆ getStatistics()

const Statistics & getStatistics ( )

Get summary statistics.

◆ mapAccessionToLeader()

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

◆ normalizePeptides_()

void normalizePeptides_ ( )

private

Normalize peptide abundances across assays by multiplicative scaling to equal medians.

◆ orderBest_()

template<typename T >

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

inlineprivate

Order keys according to how many assays they 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

[in] proteins Protein identification information containing sequences

◆ quantifyFeature_()

void quantifyFeature_	(	const FeatureHandle &	feature,
		size_t	fraction,
		const std::string &	filename,
		const PeptideHit &	hit,
		UInt	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) Channel identifiers originate from consensus map headers/experimental designs and are therefore non-negative. 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

[in] 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.

◆ selectBestFraction_()

static Int selectBestFraction_ ( const std::map< Int, std::map< UInt, double > > & fraction_abundances )

staticprivate

Select the fraction to keep for one fraction group, see 'fractions:aggregate' 'best'.

Ranked by the number of labels with a positive abundance, then by the total of those abundances. An exact tie keeps the lowest fraction number. The choice is made for the fraction group as a whole and never per label: taking one channel from one fraction and another channel from a different fraction would mix physical aliquots and destroy the reporter-ion ratios that isobaric quantification consists of.

Parameters

[in] fraction_abundances Mapping fraction -> label -> abundance of one fraction group

Returns: Key of the winning fraction

Exceptions

Exception::InvalidValue if fraction_abundances is empty

◆ selectPeptidesForQuantification_()

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

private

Select peptides for protein quantification based on filtering criteria.

Parameters

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

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

[in] proteins Protein identification information

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Clear all data when parameters are set.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ best_charge_by_peptidoform_

std::map<AASequence, Int> best_charge_by_peptidoform_

private

Charge selected per modified peptide when best_charge is enabled. Kept separately so detailed peptide output can retain all observed charge states.

◆ design_cell_lookup_

std::unordered_map<std::pair<std::string, UInt>, DesignCell, FileLabelHash> design_cell_lookup_

private

Precomputed lookup (basename without extension, channel/label) -> design coordinates, built once from experimental_design_ to avoid linear scans of the MS file section for every peptide/channel during aggregation. Pure lookup (never iterated), so an unordered map is used for O(1) access without affecting output.

◆ 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.

◆ quantification_fraction_group_labels_

std::set<std::pair<UInt, UInt> > quantification_fraction_group_labels_

private

Fraction-group/label cells represented by the current quantification input. For a ConsensusMap this is the intersection of its column headers with the design, so design files that were not part of the map do not create invented zero-valued QPX quantities.

◆ stats_

Statistics stats_

private

Processing statistics for output in the end.

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::PeptideAndProteinQuant::DesignCell

Member Typedef Documentation

◆ FractionGroupAbundances

◆ FractionGroupFractionAbundances

◆ PeptideQuant

◆ ProteinQuant

◆ SampleAbundances

◆ UnmodifiedToEntriesIndex

Constructor & Destructor Documentation

◆ PeptideAndProteinQuant()

◆ ~PeptideAndProteinQuant()

Member Function Documentation

◆ aggregateAbundances_()

◆ annotateQuantificationsToProteins()

◆ buildSampleIDLookup_()

◆ calculateFileAndChannelLevelProteinAbundances_()

◆ calculateFractionGroupLevelProteinAbundances_()

◆ collapseFractions_()

◆ countPeptides_()

◆ countQuantifiedAssays_()

◆ getAccession_()

◆ getAnnotation_()

◆ getBestCharge_()

◆ getDesignCellFromFilenameAndChannel_()

◆ getPeptideResults()

◆ getProteinResults()

◆ getSampleIDFromFilenameAndChannel_()

◆ getStatistics()

◆ mapAccessionToLeader()

◆ normalizePeptides_()

◆ orderBest_()

◆ performIbaqNormalization_()

◆ quantifyFeature_()

◆ quantifyPeptides()

◆ quantifyProteins()

◆ readQuantData() [1/3]

◆ readQuantData() [2/3]

◆ readQuantData() [3/3]

◆ selectBestFraction_()

◆ selectPeptidesForQuantification_()

◆ transferPeptideDataToProteins_()

◆ updateMembers_()

Member Data Documentation

◆ best_charge_by_peptidoform_

◆ design_cell_lookup_

◆ experimental_design_

◆ pep_quant_

◆ prot_quant_

◆ quantification_fraction_group_labels_

◆ stats_