Completes peptide multiplets and resolves quant/ID conflicts within them. More...

#include <OpenMS/FEATUREFINDER/MultiplexResolverAlgorithm.h>

Inheritance diagram for MultiplexResolverAlgorithm:

Classes
struct	OwnerCheckCounts_
	What the owner-aware blacklist check found in resolve(), for its log. More...

Public Member Functions
	MultiplexResolverAlgorithm ()
	Constructor; registers the `algorithm` and `labels` parameter sections.

void	resolve (const ConsensusMap &map_in, ConsensusMap &map_out, ConsensusMap &map_conflicts, const MSExperiment &blacklist=MSExperiment()) const
	Split the annotated multiplets of `map_in` into resolved and conflicting ones.

std::vector< bool >	checkIdentifications (const ConsensusFeature &consensus) const
	Which peptide identifications of `consensus` agree with its detected mass shifts?

std::vector< double >	expectedChannelMZs (const AASequence &sequence, int charge, Size &position) const
	Where the peptide of `sequence` appears in every channel.

std::vector< double >	expectedChannelMZs (const AASequence &sequence, int charge, Size &position, std::vector< MultiplexDeltaMasses::LabelSet > &label_sets) const
	As expectedChannelMZs() above, and the labels of the peptide in every channel.

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.

Protected Member Functions
MultiplexDeltaMassesGenerator	createGenerator_ () const
	The generator of the theoretical mass-shift patterns, as configured in the sections `algorithm` and `labels`.

bool	matchDeltaMasses_ (const ConsensusFeature &consensus, double detected_delta_mass_at_label_set, const std::vector< MultiplexDeltaMasses::DeltaMass > &pattern, double theoretical_delta_mass_at_label_set, std::vector< bool > &delta_mass_matched) const
	Check whether all delta masses of the detected pattern match one of the theoretical pattern.

int	findMatchingPattern_ (const ConsensusFeature &consensus, double detected_delta_mass_at_label_set, const AASequence &sequence, const MultiplexDeltaMasses::LabelSet &label_set, const std::vector< MultiplexDeltaMasses > &theoretical_patterns, const std::vector< std::vector< std::string > > &samples, std::vector< bool > &delta_mass_matched, int &index_label_set) const
	Find the theoretical delta mass pattern matching the detected one.

bool	isBlacklisted_ (const MSExperiment &blacklist, double rt, double mz, size_t charge, const ConsensusFeature &consensus) const
	Is one of the first three isotopes of a (dummy) feature at this position blacklisted? (anonymous blacklist: the first peak at or above each position)

bool	isReservedByOther_ (const MSExperiment &blacklist, double rt, double mz, size_t charge, const ConsensusFeature &consensus, const OwnerPeptides &peptides, OwnerCheckCounts_ &counts) const
	Is a peak reserved by another multiplet within the m/z tolerance of one of the first three isotopes at this position?

ConsensusFeature	completeConsensus_ (const ConsensusFeature &consensus, const std::vector< MultiplexDeltaMasses::DeltaMass > &pattern, const std::vector< bool > &delta_mass_matched, int index_label_set, const MSExperiment &blacklist, const OwnerPeptides peptides=nullptr, OwnerCheckCounts_ counts=nullptr) const
	Complete an incomplete multiplet with dummy features.

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.

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

Static Protected Member Functions
static double	deltaMassFromMapIndex_ (const ConsensusFeature::HandleSetType &feature_handles, unsigned idx)
	Relative delta mass between the first feature handle and the handle with map index `idx` (NaN if absent)

static double	matchLabelSet_ (const std::vector< MultiplexDeltaMasses::DeltaMass > &pattern, const MultiplexDeltaMasses::LabelSet &label_set, int &index_label_set)
	Mass shift of the theoretical pattern whose label set equals `label_set`.

static bool	matchesResidues_ (const std::vector< MultiplexDeltaMasses::DeltaMass > &pattern, const AASequence &sequence, const std::vector< std::vector< std::string > > &samples)
	Does every channel of `pattern` label exactly the residues `sequence` has?

static double	findNewMZ_ (double mz, int charge, const std::vector< MultiplexDeltaMasses::DeltaMass > &pattern, const std::vector< bool > &delta_mass_matched)
	m/z of the lightest peptide of the complete multiplet, given the incomplete one at `mz`

Protected Attributes
double	mass_tolerance_ = 0.1
	Mass tolerance in Da for matching detected to theoretical mass shifts.

double	mz_tolerance_ = 10.0
	m/z tolerance in ppm for the blacklist check

double	rt_tolerance_ = 5.0
	RT tolerance in seconds for the blacklist check.

bool	use_blacklist_owners_ = false
	Use the owners of blacklisted peaks, if recorded ('algorithm:use_blacklist_owners')

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;.

Owners of blacklisted peaks
FeatureFinderMultiplexAlgorithm records which feature reserved each blacklisted peak, as two integer data arrays aligned with the peaks of each blacklist spectrum: `owner_unique_id_high` and `owner_unique_id_low`, the upper and lower 32 bits of the feature's unique id (an integer data array holds 32-bit values). 0 in both means that no reported feature owns the peak (the multiplets it was reserved for were dropped after it was reserved). The arrays survive mzML files (as non-standard data arrays).
enum class	OwnerRelation { ORPHAN , OWN , SAME_PEPTIDE , UNIDENTIFIED , OTHER_PEPTIDE }
	How the owner of a blacklisted peak relates to a multiplet. More...

using	OwnerPeptides = std::unordered_map< UInt64, std::string >
	Peptide (as compared by classifyBlacklistOwner()) of each detected channel of the identified multiplets of a map, by unique id.

OwnerPeptides	ownerPeptides (const ConsensusMap &multiplets) const
	The peptide of every detected channel (feature handle with a unique id) of the identified multiplets in `multiplets`.

std::string	peptideKey (const PeptideHit &hit, int charge) const
	The peptide of `hit` at charge `charge`, as ownerPeptides() names it (the sequence without the labels, and the charge)

static bool	hasBlacklistOwners (const MSExperiment &blacklist)

static UInt64	blacklistOwner (const MSSpectrum &spectrum, Size peak_index)
	The unique id of the feature that reserved peak `peak_index` of `spectrum` (UniqueIdInterface::INVALID if none, or if not recorded)

static void	setBlacklistOwners (MSSpectrum &spectrum, const std::vector< UInt64 > &owners)
	Record `owners` (one unique id per peak, INVALID if none) as the owners of the peaks of `spectrum`.

static OwnerRelation	classifyBlacklistOwner (UInt64 owner, const ConsensusFeature &consensus, const OwnerPeptides &peptides)
	How the feature `owner`, which reserved a blacklisted peak, relates to the multiplet `consensus`.

static OwnerRelation	classifyBlacklistOwner (UInt64 owner, const std::string &peptide, const OwnerPeptides &peptides)
	How the feature `owner`, which reserved a blacklisted peak, relates to the peptide `peptide` (of an identification without a multiplet)

static bool	isForeign (OwnerRelation relation)
	Does a peak reserved by an owner of this relation belong to another multiplet? (UNIDENTIFIED, SAME_PEPTIDE, OTHER_PEPTIDE)

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.

Detailed Description

Completes peptide multiplets and resolves quant/ID conflicts within them.

Tools such as FeatureFinderMultiplexAlgorithm detect peptide feature multiplets (pairs, triplets, ...) in MS1-labeled data (SILAC, Dimethyl, ...). Once the multiplets carry peptide sequences (e.g. via IDMapper), this class consolidates quantitative and sequence information in two steps:

Multiplets whose observed mass shifts contradict the labels found in the annotated sequence are moved to a conflict map. Example: a sequence carrying a single Arg10 label mapped to the light feature of a SILAC triplet - either the feature detection or the sequence is wrong.
Incomplete multiplets (e.g. only the heavy partner of a pair was detected) are completed with dummy features. A dummy feature gets intensity 0 when nothing was blacklisted around its position during feature detection (the peptide is absent), and NaN (not quantifiable) when the region was blacklisted, i.e. another feature overlaps with it.

With algorithm:use_blacklist_owners, and a blacklist that records who reserved each peak (hasBlacklistOwners(), as FeatureFinderMultiplexAlgorithm writes it), only peaks reserved by another multiplet make a channel not quantifiable (isForeign()): peaks of the multiplet's own channels (their isotopes) and of no reported feature (a pattern the detection dropped later) do not. A dummy feature of intensity 0 then means that no other multiplet occupies its position, not that the peptide is absent, so the caller has to measure it (MS1LabeledWorkflow re-quantifies such channels). All blacklisted peaks within the m/z tolerance count, on either side of the expected positions, and channels that MS1LabeledWorkflow added for an identification (intensity 0, no unique id) are checked like dummy features. Otherwise (the default) the owners are ignored: a dummy feature is not quantifiable if the first blacklisted peak at or above one of its expected positions is within the tolerance, and added channels are not checked.

Only the first peptide identification of a consensus feature is taken into account, so the map should have been reduced to one identification per feature (IDConflictResolverAlgorithm::resolve()) first. checkIdentifications() tells beforehand which of several identifications agree with a multiplet, so that the reduction can prefer one of those over a better-scoring one that would make the multiplet a conflict. Multiplets without sequence annotation are written to the conflict map unchanged.

The identifications must carry the map index of the feature handle they were mapped to in the meta value map_index (IDMapper with annotate_ids_with_subelements). When a multiplet is completed, the new map index of the identified feature is recorded in the meta value map_index of the first peptide hit.

Parameters: section algorithm holds the label specification and tolerances, section labels the mass shift of every known label (see MultiplexDeltaMassesGenerator).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
algorithm:labels	string	[][Lys8,Arg10]		Labels used for labelling the samples. [...] specifies the labels for a single sample. For example [][Lys8,Arg10] ... SILAC [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC [Dimethyl0][Dimethyl6] ... Dimethyl [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL
algorithm:max_nr_labelled_aas	int	0	min: 0	Maximum number of labelled amino acids per peptide, minus one. The algorithm searches for peptides with up to (this value + 1) labelled amino acids. For SILAC with trypsin digestion, this parameter corresponds to the maximum number of missed cleavages.
algorithm:mass_tolerance	float	0.1		Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern.
algorithm:mz_tolerance	float	10.0	min: 0.0	m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted.
algorithm:rt_tolerance	float	5.0	min: 0.0	Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted.
algorithm:use_blacklist_owners	string	false	true, false	For a blacklist that records which feature reserved each peak (FeatureFinderMultiplex -out_blacklist). true: a missing channel is not quantifiable (NaN) only if a peak reserved by another multiplet lies at its expected position, and channels added for an identification (intensity 0, no feature id) are checked the same way. Peaks of the multiplet's own channels (their isotopes) or of no reported feature (a pattern the detection dropped; FeatureFinderMultiplex records only the first and the last pattern that reserved a peak) leave it at 0, which then means 'not occupied', not 'absent': use this only if such channels are measured afterwards (as MS1LabeledWorkflow re-quantifies them). false: the owners are ignored, every blacklisted peak counts.
labels:Arg6	float	6.0201290268	min: 0.0	Label:13C(6) \| C(-6) 13C(6) \| unimod @#188
labels:Arg10	float	10.008268599999999	min: 0.0	Label:13C(6)15N(4) \| C(-6) 13C(6) N(-4) 15N(4) \| unimod @#267
labels:Lys4	float	4.0251069836	min: 0.0	Label:2H(4) \| H(-4) 2H(4) \| unimod @#481
labels:Lys6	float	6.0201290268	min: 0.0	Label:13C(6) \| C(-6) 13C(6) \| unimod @#188
labels:Lys8	float	8.0141988132	min: 0.0	Label:13C(6)15N(2) \| C(-6) 13C(6) N(-2) 15N(2) \| unimod @#259
labels:Leu3	float	3.01883	min: 0.0	Label:2H(3) \| H(-3) 2H(3) \| unimod @#262
labels:Dimethyl0	float	28.031300000000002	min: 0.0	Dimethyl \| H(4) C(2) \| unimod @#36
labels:Dimethyl4	float	32.056407	min: 0.0	Dimethyl:2H(4) \| 2H(4) C(2) \| unimod @#199
labels:Dimethyl6	float	34.063116999999998	min: 0.0	Dimethyl:2H(4)13C(2) \| 2H(4) 13C(2) \| unimod @#510
labels:Dimethyl8	float	36.075670000000002	min: 0.0	Dimethyl:2H(6)13C(2) \| H(-2) 2H(6) 13C(2) \| unimod @#330
labels:ICPL0	float	105.021463999999995	min: 0.0	ICPL \| H(3) C(6) N O \| unimod @#365
labels:ICPL4	float	109.046571	min: 0.0	ICPL:2H(4) \| H(-1) 2H(4) C(6) N O \| unimod @#687
labels:ICPL6	float	111.041593000000006	min: 0.0	ICPL:13C(6) \| H(3) 13C(6) N O \| unimod @#364
labels:ICPL10	float	115.066699999999997	min: 0.0	ICPL:13C(6)2H(4) \| H(-1) 2H(4) 13C(6) N O \| unimod @#866

Note:

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

Class Documentation

◆ OpenMS::MultiplexResolverAlgorithm::OwnerCheckCounts_

struct OpenMS::MultiplexResolverAlgorithm::OwnerCheckCounts_

What the owner-aware blacklist check found in resolve(), for its log.

Class Members
Size	added = 0	channels added for an identification checked
Size	added_vetoed = 0	added channels found not quantifiable
Size	anonymous = 0	dummy features the check without owners finds blacklisted
Size	dummies = 0	dummy features checked
Size	dummies_vetoed = 0	dummy features found not quantifiable
Size	orphan = 0	... with a peak of no reported feature
Size	other_peptide = 0	not quantifiable: a peak reserved by another identified peptide
Size	own = 0	... of these, with a peak of the multiplet's own channels
Size	same_peptide = 0	not quantifiable: a peak reserved by another multiplet of the same peptide (no other peptide)
Size	unidentified = 0	not quantifiable: peaks reserved by unidentified multiplets only
Size	usable = 0	reserved peaks, but none foreign

Member Typedef Documentation

◆ OwnerPeptides

using OwnerPeptides = std::unordered_map<UInt64, std::string>

Peptide (as compared by classifyBlacklistOwner()) of each detected channel of the identified multiplets of a map, by unique id.

Member Enumeration Documentation

◆ OwnerRelation

enum class OwnerRelation

strong

How the owner of a blacklisted peak relates to a multiplet.

Enumerator
ORPHAN	no reported feature owns the peak
OWN	a detected channel of the multiplet itself
SAME_PEPTIDE	a channel of another multiplet identified as the same peptide (and charge)
UNIDENTIFIED	a channel of an unidentified multiplet (or of none in the map)
OTHER_PEPTIDE	a channel of a multiplet identified as another peptide

Constructor & Destructor Documentation

◆ MultiplexResolverAlgorithm()

MultiplexResolverAlgorithm ( )

Constructor; registers the algorithm and labels parameter sections.

Member Function Documentation

◆ blacklistOwner()

static UInt64 blacklistOwner	(	const MSSpectrum &	spectrum,
		Size	peak_index
	)

static

The unique id of the feature that reserved peak peak_index of spectrum (UniqueIdInterface::INVALID if none, or if not recorded)

◆ checkIdentifications()

std::vector< bool > checkIdentifications ( const ConsensusFeature & consensus ) const

Which peptide identifications of consensus agree with its detected mass shifts?

This is the check resolve() applies to the (first) identification of a multiplet, for every identification: the label set of its first peptide hit has to occur in a theoretical pattern whose mass shifts explain every detected feature, relative to the feature named by the identification's map_index. Use it to choose, among several identifications mapped onto one multiplet, one that does not turn the multiplet into a conflict.

Returns: One flag per peptide identification of consensus, in order. Identifications without hits, without map_index, or whose map_index names no feature handle are not consistent.

◆ classifyBlacklistOwner() [1/2]

static OwnerRelation classifyBlacklistOwner	(	UInt64	owner,
		const ConsensusFeature &	consensus,
		const OwnerPeptides &	peptides
	)

static

How the feature owner, which reserved a blacklisted peak, relates to the multiplet consensus.

Parameters

[in]	owner	Unique id of the owner (blacklistOwner())
[in]	consensus	The multiplet; its detected channels carry the unique ids of their features
[in]	peptides	ownerPeptides() of the map the multiplets were detected in (incl. `consensus`)

◆ classifyBlacklistOwner() [2/2]

static OwnerRelation classifyBlacklistOwner	(	UInt64	owner,
		const std::string &	peptide,
		const OwnerPeptides &	peptides
	)

static

How the feature owner, which reserved a blacklisted peak, relates to the peptide peptide (of an identification without a multiplet)

As above, for a peptide that has no multiplet of its own (never OWN).

Parameters

[in]	owner	Unique id of the owner (blacklistOwner())
[in]	peptide	The peptide, as peptideKey() names it
[in]	peptides	ownerPeptides() of the map the multiplets were detected in

◆ completeConsensus_()

ConsensusFeature completeConsensus_	(	const ConsensusFeature &	consensus,
		const std::vector< MultiplexDeltaMasses::DeltaMass > &	pattern,
		const std::vector< bool > &	delta_mass_matched,
		int	index_label_set,
		const MSExperiment &	blacklist,
		const OwnerPeptides *	peptides = `nullptr`,
		OwnerCheckCounts_ *	counts = `nullptr`
	)		const

protected

Complete an incomplete multiplet with dummy features.

Parameters

[in]	consensus	Possibly incomplete multiplet
[in]	pattern	Matching theoretical pattern
[in]	delta_mass_matched	Which delta masses of the pattern were matched
[in]	index_label_set	Index within the pattern at which the label set was matched
[in]	blacklist	Blacklisted spectral peaks (may be empty)
[in]	peptides	If not null, the owners of the blacklisted peaks are used and these are the ownerPeptides() of the map: owner-aware check of dummy features and of channels added for an identification
[in,out]	counts	Counts of the owner-aware check (used only with `peptides`)

Returns: The complete multiplet

◆ createGenerator_()

MultiplexDeltaMassesGenerator createGenerator_ ( ) const

protected

The generator of the theoretical mass-shift patterns, as configured in the sections algorithm and labels.

◆ deltaMassFromMapIndex_()

static double deltaMassFromMapIndex_	(	const ConsensusFeature::HandleSetType &	feature_handles,
		unsigned	idx
	)

staticprotected

Relative delta mass between the first feature handle and the handle with map index idx (NaN if absent)

◆ expectedChannelMZs() [1/2]

std::vector< double > expectedChannelMZs	(	const AASequence &	sequence,
		int	charge,
		Size &	position
	)		const

Where the peptide of sequence appears in every channel.

The theoretical pattern of the peptide is the one whose label set at some position equals the labels of sequence and whose channels label exactly the residues it has (see matchesResidues_()). Its mass shifts, relative to the position of sequence, give the m/z of the peptide at charge charge in every channel.

Parameters

[in]	sequence	Identified peptidoform, with its labels
[in]	charge	Charge state (non-zero)
[out]	position	Position (channel) of `sequence` itself within the returned m/z values

Returns: The m/z per channel (pattern position), empty if no theoretical pattern fits sequence

◆ expectedChannelMZs() [2/2]

std::vector< double > expectedChannelMZs	(	const AASequence &	sequence,
		int	charge,
		Size &	position,
		std::vector< MultiplexDeltaMasses::LabelSet > &	label_sets
	)		const

As expectedChannelMZs() above, and the labels of the peptide in every channel.

Parameters

[in]	sequence	Identified peptidoform, with its labels
[in]	charge	Charge state (non-zero)
[out]	position	Position (channel) of `sequence` itself within the returned m/z values
[out]	label_sets	The label set per channel (pattern position) of the theoretical pattern, e.g. {Lys4, Lys4} for a peptide with two lysines in the Lys4 channel; empty if no theoretical pattern fits `sequence`

Returns: The m/z per channel (pattern position), empty if no theoretical pattern fits sequence

◆ findMatchingPattern_()

int findMatchingPattern_	(	const ConsensusFeature &	consensus,
		double	detected_delta_mass_at_label_set,
		const AASequence &	sequence,
		const MultiplexDeltaMasses::LabelSet &	label_set,
		const std::vector< MultiplexDeltaMasses > &	theoretical_patterns,
		const std::vector< std::vector< std::string > > &	samples,
		std::vector< bool > &	delta_mass_matched,
		int &	index_label_set
	)		const

protected

Find the theoretical delta mass pattern matching the detected one.

Parameters

[in]	consensus	Detected pattern
[in]	detected_delta_mass_at_label_set	Detected mass shift of the identified feature (relative to the first feature)
[in]	sequence	Sequence annotated to the detected pattern
[in]	label_set	Label set extracted from `sequence`
[in]	theoretical_patterns	All theoretical patterns
[in]	samples	Labels of every sample (MultiplexDeltaMassesGenerator::getSamplesLabelsList())
[out]	delta_mass_matched	Which delta masses of the matching pattern were matched
[out]	index_label_set	Index within the matching pattern at which the label set was matched

Returns: Index of the matching pattern, or -1

◆ findNewMZ_()

static double findNewMZ_	(	double	mz,
		int	charge,
		const std::vector< MultiplexDeltaMasses::DeltaMass > &	pattern,
		const std::vector< bool > &	delta_mass_matched
	)

staticprotected

m/z of the lightest peptide of the complete multiplet, given the incomplete one at mz

◆ hasBlacklistOwners()

static bool hasBlacklistOwners ( const MSExperiment & blacklist )

static

Does every spectrum of blacklist that has peaks record their owners (and is there a peak)?

◆ isBlacklisted_()

bool isBlacklisted_	(	const MSExperiment &	blacklist,
		double	rt,
		double	mz,
		size_t	charge,
		const ConsensusFeature &	consensus
	)		const

protected

Is one of the first three isotopes of a (dummy) feature at this position blacklisted? (anonymous blacklist: the first peak at or above each position)

◆ isForeign()

static bool isForeign ( OwnerRelation relation )

static

Does a peak reserved by an owner of this relation belong to another multiplet? (UNIDENTIFIED, SAME_PEPTIDE, OTHER_PEPTIDE)

Such a peak makes a missing channel at its position not quantifiable, and a channel must not use it. Another multiplet of the same peptide (e.g. its missing channel, detected on its own) is quantified itself: measuring the channel from its peaks would count them twice.

◆ isReservedByOther_()

bool isReservedByOther_	(	const MSExperiment &	blacklist,
		double	rt,
		double	mz,
		size_t	charge,
		const ConsensusFeature &	consensus,
		const OwnerPeptides &	peptides,
		OwnerCheckCounts_ &	counts
	)		const

protected

Is a peak reserved by another multiplet within the m/z tolerance of one of the first three isotopes at this position?

The owner-aware check of a (dummy or added) channel of consensus: every blacklisted peak in the RT and m/z tolerance counts (both sides), and only foreign owners (isForeign()) make the channel not quantifiable.

◆ matchDeltaMasses_()

bool matchDeltaMasses_	(	const ConsensusFeature &	consensus,
		double	detected_delta_mass_at_label_set,
		const std::vector< MultiplexDeltaMasses::DeltaMass > &	pattern,
		double	theoretical_delta_mass_at_label_set,
		std::vector< bool > &	delta_mass_matched
	)		const

protected

Check whether all delta masses of the detected pattern match one of the theoretical pattern.

Parameters

[in]	consensus	Detected pattern
[in]	detected_delta_mass_at_label_set	Detected mass shift of the identified feature (relative to the first feature)
[in]	pattern	Theoretical pattern
[in]	theoretical_delta_mass_at_label_set	Theoretical mass shift at which the label set was matched
[out]	delta_mass_matched	Which delta masses of the theoretical pattern were matched

Returns: true if every detected delta mass has a theoretical counterpart within the mass tolerance

◆ matchesResidues_()

static bool matchesResidues_	(	const std::vector< MultiplexDeltaMasses::DeltaMass > &	pattern,
		const AASequence &	sequence,
		const std::vector< std::vector< std::string > > &	samples
	)

staticprotected

Does every channel of pattern label exactly the residues sequence has?

Metabolic labels (SILAC Lys/Arg, Leu3) sit on every residue of their kind, so in a pattern that fits the peptide, each channel carries one Lys label per K, one Arg label per R and one Leu label per L, for every residue kind its sample labels - none if the peptide has no residue of that kind. The sample of a channel is the one in samples whose labels include all labels of the channel. E.g. with samples [][Lys8,Arg10], a peptide with one K and one R fits only the pattern whose heavy channel carries Lys8 and Arg10, not the one carrying Lys8 alone. This tells the pattern of an unlabelled identification, whose label set ("no_label") occurs in every pattern. Unlabelled channels impose nothing, and other labels (Dimethyl, ICPL, plain mass shifts) are not counted.

Parameters

[in]	pattern	Theoretical pattern
[in]	sequence	Identified peptidoform
[in]	samples	Labels of every sample (MultiplexDeltaMassesGenerator::getSamplesLabelsList())

◆ matchLabelSet_()

static double matchLabelSet_	(	const std::vector< MultiplexDeltaMasses::DeltaMass > &	pattern,
		const MultiplexDeltaMasses::LabelSet &	label_set,
		int &	index_label_set
	)

staticprotected

Mass shift of the theoretical pattern whose label set equals label_set.

Parameters

[in]	pattern	Theoretical pattern
[in]	label_set	Label set of the detected pattern
[out]	index_label_set	Index within the pattern at which the label set was matched

Returns: Mass shift at the match, or NaN if no delta mass carries this label set

◆ ownerPeptides()

OwnerPeptides ownerPeptides ( const ConsensusMap & multiplets ) const

The peptide of every detected channel (feature handle with a unique id) of the identified multiplets in multiplets.

A multiplet's peptide is that of its first identification: the sequence without the labels of section algorithm:labels (other modifications kept) and the charge of the multiplet. So the label states of a peptide share it, while another sequence of the same composition or another modification state does not.

◆ peptideKey()

std::string peptideKey	(	const PeptideHit &	hit,
		int	charge
	)		const

The peptide of hit at charge charge, as ownerPeptides() names it (the sequence without the labels, and the charge)

◆ resolve()

void resolve	(	const ConsensusMap &	map_in,
		ConsensusMap &	map_out,
		ConsensusMap &	map_conflicts,
		const MSExperiment &	blacklist = `MSExperiment()`
	)		const

Split the annotated multiplets of map_in into resolved and conflicting ones.

map_out and map_conflicts inherit the meta data of map_in (column headers, protein identifications, unassigned peptide identifications, data processing) and receive the consensus features that could resp. could not be matched to a theoretical mass-shift pattern. Both output maps get fresh unique ids for their features, and the column header sizes of map_out are set to its number of features.

Parameters

[in]	map_in	Multiplets with (at most one) peptide identification each
[out]	map_out	Complete, consistent multiplets; cleared first
[out]	map_conflicts	Multiplets without identification or with conflicting quant/ID information; cleared first
[in]	blacklist	Spectral peaks blacklisted during feature detection (FeatureFinderMultiplexAlgorithm::getBlacklist()). Used to decide whether a dummy feature is absent (intensity 0) or not quantifiable (NaN). May be empty. If its owners are used (`algorithm:use_blacklist_owners` and hasBlacklistOwners()), the feature handles of `map_in` must carry the unique ids of their features, as FeatureFinderMultiplexAlgorithm::getConsensusMap() does.

Exceptions

Exception::MissingInformation	if an identified feature lacks the `map_index` meta value
Exception::InvalidValue	if the `map_index` does not name a feature handle of the consensus feature

◆ setBlacklistOwners()

static void setBlacklistOwners	(	MSSpectrum &	spectrum,
		const std::vector< UInt64 > &	owners
	)

static

Record owners (one unique id per peak, INVALID if none) as the owners of the peaks of spectrum.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ mass_tolerance_

double mass_tolerance_ = 0.1

protected

Mass tolerance in Da for matching detected to theoretical mass shifts.

◆ mz_tolerance_

double mz_tolerance_ = 10.0

protected

m/z tolerance in ppm for the blacklist check

◆ rt_tolerance_

double rt_tolerance_ = 5.0

protected

RT tolerance in seconds for the blacklist check.

◆ use_blacklist_owners_

bool use_blacklist_owners_ = false

protected

Use the owners of blacklisted peaks, if recorded ('algorithm:use_blacklist_owners')

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Owners of blacklisted peaks

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::MultiplexResolverAlgorithm::OwnerCheckCounts_

Member Typedef Documentation

◆ OwnerPeptides

Member Enumeration Documentation

◆ OwnerRelation

Constructor & Destructor Documentation

◆ MultiplexResolverAlgorithm()

Member Function Documentation

◆ blacklistOwner()

◆ checkIdentifications()

◆ classifyBlacklistOwner() [1/2]

◆ classifyBlacklistOwner() [2/2]

◆ completeConsensus_()

◆ createGenerator_()

◆ deltaMassFromMapIndex_()

◆ expectedChannelMZs() [1/2]

◆ expectedChannelMZs() [2/2]

◆ findMatchingPattern_()

◆ findNewMZ_()

◆ hasBlacklistOwners()

◆ isBlacklisted_()

◆ isForeign()

◆ isReservedByOther_()

◆ matchDeltaMasses_()

◆ matchesResidues_()

◆ matchLabelSet_()

◆ ownerPeptides()

◆ peptideKey()

◆ resolve()

◆ setBlacklistOwners()

◆ updateMembers_()

Member Data Documentation

◆ mass_tolerance_

◆ mz_tolerance_

◆ rt_tolerance_

◆ use_blacklist_owners_