A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses. More...

#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>

Inheritance diagram for InternalCalibration:

Collaboration diagram for InternalCalibration:

Classes
struct	CalibrantStats_
	statistics when adding peptide calibrants More...

struct	LockMass
	helper class, describing a lock mass More...

Public Member Functions
	InternalCalibration ()
	Default constructor. More...

	~InternalCalibration () override
	Destructor. More...

Size	fillCalibrants (const PeakMap &exp, const std::vector< InternalCalibration::LockMass > &ref_masses, double tol_ppm, bool lock_require_mono, bool lock_require_iso, CalibrationData &failed_lock_masses, bool verbose=true)
	Extract calibrants from Raw data (mzML) More...

Size	fillCalibrants (const FeatureMap &fm, double tol_ppm)
	Extract calibrants from identifications. More...

Size	fillCalibrants (const std::vector< PeptideIdentification > &pep_ids, double tol_ppm)
	Extract calibrants from identifications. More...

const CalibrationData &	getCalibrationPoints () const
	Get container of calibration points. More...

bool	calibrate (PeakMap &exp, const IntList &target_mslvl, MZTrafoModel::MODELTYPE model_type, double rt_chunk, bool use_RANSAC, double post_ppm_median, double post_ppm_MAD, const String &file_models="", const String &file_models_plot="", const String &file_residuals="", const String &file_residuals_plot="", const String &rscript_executable="Rscript")
	Apply calibration to data. More...

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

virtual	~ProgressLogger ()
	Destructor. More...

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

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

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

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

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

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

void	endProgress (UInt64 bytes_processed=0) const

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

Static Public Member Functions
static void	applyTransformation (std::vector< Precursor > &pcs, const MZTrafoModel &trafo)
	Transform a precursor's m/z. More...

static void	applyTransformation (PeakMap::SpectrumType &spec, const IntList &target_mslvl, const MZTrafoModel &trafo)
	Transform a spectrum (data+precursor) More...

static void	applyTransformation (PeakMap &exp, const IntList &target_mslvl, const MZTrafoModel &trafo)
	Transform spectra from a whole map (data+precursor) More...

Protected Member Functions
void	fillID_ (const PeptideIdentification &pep_id, const double tol_ppm, CalibrantStats_ &stats)
	Add(no prior clear) calibrants to internal list. More...

void	fillIDs_ (const std::vector< PeptideIdentification > &pep_ids, const double tol_ppm, CalibrantStats_ &stats)
	calls fillID_ on all PeptideIDs More...

bool	isDecalibrated_ (const PeptideIdentification &pep_id, const double mz_obs, const double tol_ppm, CalibrantStats_ &stats, double &mz_ref)
	determine if sequence is within tol_ppm and update stats; fills mz_ref with the theoretical m/z of the sequence More...

Static Protected Member Functions
static void	applyTransformation_ (PeakMap::SpectrumType &spec, const MZTrafoModel &trafo)
	Calibrate m/z of a spectrum, ignoring precursors! More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Private Attributes
CalibrationData	cal_data_

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

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference masses.

...

Constructor & Destructor Documentation

◆ InternalCalibration()

InternalCalibration ( )

Default constructor.

◆ ~InternalCalibration()

~InternalCalibration ( )

inlineoverride

Destructor.

Member Function Documentation

◆ applyTransformation() [1/3]

static void applyTransformation	(	PeakMap &	exp,
		const IntList &	target_mslvl,
		const MZTrafoModel &	trafo
	)

static

Transform spectra from a whole map (data+precursor)

All data peaks and precursor information (if present) are calibrated in m/z.

Only spectra whose MS-level is contained in 'target_mslvl' are calibrated. In addition, if a fragmentation spectrum's precursor information originates from an MS level in 'target_mslvl', the precursor (not the spectrum itself) is also subjected to calibration. E.g., If we only have MS and MS/MS spectra: for 'target_mslvl' = {1} then all MS1 spectra and MS2 precursors are calibrated. If 'target_mslvl' = {2}, only MS2 spectra (not their precursors) are calibrated. If 'target_mslvl' = {1,2} all spectra and precursors are calibrated.

Parameters

exp	Uncalibrated peak map
target_mslvl	List (can be unsorted) of MS levels to calibrate
trafo	The calibration function to apply

◆ applyTransformation() [2/3]

static void applyTransformation	(	PeakMap::SpectrumType &	spec,
		const IntList &	target_mslvl,
		const MZTrafoModel &	trafo
	)

static

Transform a spectrum (data+precursor)

See applyTransformation(MSExperiment, ...) for details.

Parameters

spec	Uncalibrated MSSpectrum
target_mslvl	List (can be unsorted) of MS levels to calibrate
trafo	The calibration function to apply

◆ applyTransformation() [3/3]

static void applyTransformation	(	std::vector< Precursor > &	pcs,
		const MZTrafoModel &	trafo
	)

static

Transform a precursor's m/z.

Calibrate m/z of precursors.

Parameters

pcs	Uncalibrated Precursors
trafo	The calibration function to apply

◆ applyTransformation_()

static void applyTransformation_	(	PeakMap::SpectrumType &	spec,
		const MZTrafoModel &	trafo
	)

staticprotected

Calibrate m/z of a spectrum, ignoring precursors!

This method is not exposed as public, because its easy to be misused on spectra while forgetting about the precursors of high-level spectra.

◆ calibrate()

bool calibrate	(	PeakMap &	exp,
		const IntList &	target_mslvl,
		MZTrafoModel::MODELTYPE	model_type,
		double	rt_chunk,
		bool	use_RANSAC,
		double	post_ppm_median,
		double	post_ppm_MAD,
		const String &	file_models = `""`,
		const String &	file_models_plot = `""`,
		const String &	file_residuals = `""`,
		const String &	file_residuals_plot = `""`,
		const String &	rscript_executable = `"Rscript"`
	)

Apply calibration to data.

For each spectrum, a calibration model will be computed and applied. Make sure to call fillCalibrants() before, so a model can be created.

The MSExperiment will be sorted by RT and m/z if unsorted.

Parameters

exp	MSExperiment holding the Raw data to calibrate
target_mslvl	MS-levels where calibration should be applied to
model_type	Linear or quadratic model; select based on your instrument
rt_chunk	RT-window size (one-sided) of calibration points to collect around each spectrum. Set to negative values, to build one global model instead.
use_RANSAC	Remove outliers before fitting a model?!
post_ppm_median	The median ppm error of the calibrants must be at least this good after calibration; otherwise this method returns false(fail)
post_ppm_MAD	The median absolute deviation of the calibrants must be at least this good after calibration; otherwise this method returns false(fail)
file_models	Output CSV filename, where model parameters are written to (pass empty string to skip)
file_models_plot	Output PNG image model parameters (pass empty string to skip)
file_residuals	Output CSV filename, where ppm errors of calibrants before and after model fitting parameters are written to (pass empty string to skip)
file_residuals_plot	Output PNG image of the ppm errors of calibrants (pass empty string to skip)
rscript_executable	Full path to the Rscript executable

Returns: true upon successful calibration

◆ fillCalibrants() [1/3]

Size fillCalibrants	(	const FeatureMap &	fm,
		double	tol_ppm
	)

Extract calibrants from identifications.

Extracts only the first hit from the first peptide identification of each feature. Hits are sorted beforehand. Ambiguities should be resolved before, e.g. using IDFilter. RT and m/z are taken from the features, not from the identifications (for an exception see below)!

Unassigned peptide identifications are also taken into account! RT and m/z are naturally taken from the IDs, since to feature is assigned. If you do not want these IDs, remove them from the feature map before calling this function.

A filtering step is done in the m/z dimension using tol_ppm. Since precursor masses could be annotated wrongly (e.g. isotope peak instead of mono), larger outliers are removed before accepting an ID as calibrant.

Parameters

fm	FeatureMap with peptide identifications
tol_ppm	Only accept ID's whose theoretical mass deviates at most this much from annotated

Returns: Number of calibration masses found

◆ fillCalibrants() [2/3]

Size fillCalibrants	(	const PeakMap &	exp,
		const std::vector< InternalCalibration::LockMass > &	ref_masses,
		double	tol_ppm,
		bool	lock_require_mono,
		bool	lock_require_iso,
		CalibrationData &	failed_lock_masses,
		bool	verbose = `true`
	)

Extract calibrants from Raw data (mzML)

Lock masses are searched in each spectrum and added to the internal calibrant database.

Filters can be used to exclude spurious peaks, i.e. require the calibrant peak to be monoisotopic or to have a +1 isotope (should not be used for very low abundant calibrants). If a calibrant is not found, it is added to a 'failed_lock_masses' database which is returned and not stored internally. The intensity of the peaks describe the reason for failed detection: 0.0 - peak not found with the given ppm tolerance; 1.0 - peak is not monoisotopic (can only occur if 'lock_require_mono' is true) 2.0 - peak has no +1 isotope (can only occur if 'lock_require_iso' is true)

Parameters

exp	Peak map containing the lock masses
ref_masses	List of lock masses
tol_ppm	Search window for lock masses in 'exp'
lock_require_mono	Require that a lock mass is the monoisotopic peak (i.e. not an isotope peak) – lock mass is rejected otherwise
lock_require_iso	Require that a lock mass has isotope peaks to its right – lock mass is rejected otherwise
failed_lock_masses	Set of calibration masses which were not found, i.e. their expected m/z and RT positions;
verbose	Print information on 'lock_require_XXX' matches during search

Returns: Number of calibration masses found

◆ fillCalibrants() [3/3]

Size fillCalibrants	(	const std::vector< PeptideIdentification > &	pep_ids,
		double	tol_ppm
	)

Extract calibrants from identifications.

Extracts only the first hit from each peptide identification. Hits are sorted beforehand. Ambiguities should be resolved before, e.g. using IDFilter.

A filtering step is done in the m/z dimension using tol_ppm. Since precursor masses could be annotated wrongly (e.g. isotope peak instead of mono), larger outliers are removed before accepting an ID as calibrant.

Parameters

pep_ids	Peptide ids (e.g. from an idXML file)
tol_ppm	Only accept ID's whose theoretical mass deviates at most this much from annotated

Returns: Number of calibration masses found

◆ fillID_()

void fillID_	(	const PeptideIdentification &	pep_id,
		const double	tol_ppm,
		CalibrantStats_ &	stats
	)

protected

Add(no prior clear) calibrants to internal list.

Extracts only the first hit from each peptide identification. Hits are sorted beforehand. Ambiguities should be resolved before, e.g. using IDFilter.

A filtering step is done in the m/z dimension using tol_ppm. Since precursor masses could be annotated wrongly (e.g. isotope peak instead of mono), larger outliers are removed before accepting an ID as calibrant.

Parameters

pep_id	A single PeptideID (e.g. from an idXML file); only the top peptide hit is used
tol_ppm	Only accept ID's whose theoretical mass deviates at most this much from annotated
stats	Update stats, if calibrant cannot be used (no RT, no MZ, no sequence, out-of tolerance)

◆ fillIDs_()

void fillIDs_	(	const std::vector< PeptideIdentification > &	pep_ids,
		const double	tol_ppm,
		CalibrantStats_ &	stats
	)

protected

calls fillID_ on all PeptideIDs

◆ getCalibrationPoints()

const CalibrationData& getCalibrationPoints ( ) const

Get container of calibration points.

Filled using fillCalibrants() methods.

Returns: Container of calibration points

◆ isDecalibrated_()

bool isDecalibrated_	(	const PeptideIdentification &	pep_id,
		const double	mz_obs,
		const double	tol_ppm,
		CalibrantStats_ &	stats,
		double &	mz_ref
	)

protected

determine if sequence is within tol_ppm and update stats; fills mz_ref with the theoretical m/z of the sequence

Member Data Documentation

◆ cal_data_

CalibrationData cal_data_

private

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ InternalCalibration()

◆ ~InternalCalibration()

Member Function Documentation

◆ applyTransformation() [1/3]

◆ applyTransformation() [2/3]

◆ applyTransformation() [3/3]

◆ applyTransformation_()

◆ calibrate()

◆ fillCalibrants() [1/3]

◆ fillCalibrants() [2/3]

◆ fillCalibrants() [3/3]

◆ fillID_()

◆ fillIDs_()

◆ getCalibrationPoints()

◆ isDecalibrated_()

Member Data Documentation

◆ cal_data_