Contaminants Class Reference

QualityControl metric: flag PSMs whose peptide sequences match a user-supplied contaminants FASTA (e.g. cRAP) after digestion. More...

#include <OpenMS/QC/Contaminants.h>

Inheritance diagram for Contaminants:

Collaboration diagram for Contaminants:

Classes
struct	ContaminantsSummary
	Result bundle returned per compute call. More...

Public Member Functions
	Contaminants ()=default
	Default constructor.
virtual	~Contaminants ()=default
	Destructor.
void	compute (FeatureMap &features, const std::vector< FASTAFile::FASTAEntry > &contaminants)
	Annotate the PSMs of features with "is_contaminant" and append a summary to getResults.
const std::string &	getName () const override
	Name of this QC metric ("Contaminants").
const std::vector< Contaminants::ContaminantsSummary > &	getResults ()
	Per-call summaries appended by compute, in call order.
Status	requirements () const override
	Input-data requirements of compute.
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Member Functions
void	compare_ (const std::string &key, PeptideHit &pep_hit, Int64 &total, Int64 &cont, double &sum_total, double &sum_cont, double intensity)
	Increment the contaminant counters and annotate one hit with "is_contaminant".

Private Attributes
const std::string	name_ = "Contaminants"
	Metric name returned by getName.
std::vector< Contaminants::ContaminantsSummary >	results_
	Per-call summaries; compute appends one entry per invocation.
std::unordered_set< std::string >	digested_db_
	Cached digested contaminants database, filled on the first compute call and reused thereafter.

Additional Inherited Members
Public Types inherited from QCBase
enum class	Requires : UInt64 {   NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,   CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...
enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
using	Status = FlagSet< Requires >
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ?
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit

Detailed Description

QualityControl metric: flag PSMs whose peptide sequences match a user-supplied contaminants FASTA (e.g. cRAP) after digestion.

Each call to compute marks the first PeptideHit of every PeptideIdentification in the supplied FeatureMap (both feature-attached and unassigned) with an "is_contaminant" meta value (1 if its unmodified sequence matches an entry in the digested contaminants database, 0 otherwise) and appends a ContaminantsSummary to the internal results list returned by getResults.

Note

The digested contaminants database is cached on the first compute call; subsequent calls reuse the same cache and ignore the contaminants argument's actual contents. The enzyme and missed-cleavage settings used for the initial digestion are also frozen at that point (taken from FeatureMap::getProteinIdentifications()[0].getSearchParameters() of the FeatureMap supplied on the first call).

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Class Documentation

OpenMS::Contaminants::ContaminantsSummary

struct OpenMS::Contaminants::ContaminantsSummary

Result bundle returned per compute call.

All four ratios are unitless and lie in [0, 1] for non-empty denominators; when the corresponding denominator is 0 the ratio evaluates to NaN.

Collaboration diagram for Contaminants::ContaminantsSummary:

Class Members
double	all_contaminants_ratio	#contaminants in all PSMs / #all PSMs.
double	assigned_contaminants_intensity_ratio	Sum of feature intensities of contaminant feature-attached PSMs / sum of feature intensities of all feature-attached PSMs.
double	assigned_contaminants_ratio	#contaminants in feature-attached PSMs / #feature-attached PSMs.
pair< Int64, Int64 >	empty_features	(Number of features without a peptide hit, total number of features).
double	unassigned_contaminants_ratio	#contaminants in unassigned PSMs / #unassigned PSMs.

Constructor & Destructor Documentation

Contaminants()

Contaminants ( )

default

Default constructor.

~Contaminants()

virtual ~Contaminants ( )

virtualdefault

Destructor.

Member Function Documentation

compare_()

void compare_ ( const std::string &  key, PeptideHit &  pep_hit, Int64 &  total, Int64 &  cont, double &  sum_total, double &  sum_cont, double  intensity  )

private

Increment the contaminant counters and annotate one hit with "is_contaminant".

Looks key up in digested_db_ and updates the counters and pep_hit accordingly.

Parameters

[in]	key	Unmodified peptide sequence to look up.
[in,out]	pep_hit	Hit to annotate with "is_contaminant" set to 0 (not found) or 1 (found).
[in,out]	total	Total-PSMs counter; incremented by 1.
[in,out]	cont	Contaminant-PSMs counter; incremented only on a hit.
[in,out]	sum_total	Total-intensity accumulator; incremented by intensity.
[in,out]	sum_cont	Contaminant-intensity accumulator; incremented by intensity only on a hit.
[in]	intensity	Intensity associated with this PSM.

compute()

void compute	(	FeatureMap &	features,
		const std::vector< FASTAFile::FASTAEntry > &	contaminants
	)

Annotate the PSMs of features with "is_contaminant" and append a summary to getResults.

On the first call (when the internal digested-DB cache is empty), the FASTA entries in contaminants are digested using the enzyme and missed-cleavage count from features.getProteinIdentifications()[0].getSearchParameters() and stored in a hash set. Every subsequent call to compute reuses that cache without consulting contaminants again.

The first PeptideHit of every PeptideIdentification in features (both attached to features and in getUnassignedPeptideIdentifications()) is annotated with "is_contaminant" set to 0 or 1. The aggregated ratios and the empty-feature counters are then pushed onto the internal results list (see getResults).

Parameters

[in,out]	features	Source of the PSMs (annotated in place) and – on the first call – of the digestion enzyme used to build the cache.
[in]	contaminants	Contaminants FASTA. Only consulted on the first call; subsequent calls ignore it.

Exceptions

Exception::MissingInformation	when contaminants is empty.
Exception::MissingInformation	when the FeatureMap has no protein identification (only on the first call).
Exception::MissingInformation	when the configured digestion enzyme is "unknown_enzyme" (only on the first call).

Note

When features is empty, a warning is logged and the method still runs (and may produce NaN ratios).

getName()

const std::string & getName ( ) const

overridevirtual

Name of this QC metric ("Contaminants").

Implements QCBase.

getResults()

const std::vector< Contaminants::ContaminantsSummary > & getResults

(

)

Per-call summaries appended by compute, in call order.

requirements()

Status requirements ( ) const

overridevirtual

Input-data requirements of compute.

Returns

Status flags with POSTFDRFEAT and CONTAMINANTS set.

Implements QCBase.

Member Data Documentation

digested_db_

std::unordered_set<std::string> digested_db_

private

Cached digested contaminants database, filled on the first compute call and reused thereafter.

name_

const std::string name_ = "Contaminants"

private

Metric name returned by getName.

results_

std::vector<Contaminants::ContaminantsSummary> results_

private

Per-call summaries; compute appends one entry per invocation.