This class provides methods for precursor correction. More...

#include <OpenMS/PROCESSING/CALIBRATION/PrecursorCorrection.h>

Collaboration diagram for PrecursorCorrection:

Static Public Member Functions
static void	getPrecursors (const MSExperiment &exp, std::vector< Precursor > &precursors, std::vector< double > &precursors_rt, std::vector< Size > &precursor_scan_index)
	Extract precursors and associated information (precursor retention time and precursor scan index). More...

static void	writeHist (const String &out_csv, const std::vector< double > &delta_mzs, const std::vector< double > &mzs, const std::vector< double > &rts)
	Writer can be used in association with correctToNearestMS1Peak or correctToHighestIntensityMS1Peak. A csv file with additional information (RT, uncorrectedMZ, correctedMZ, deltaMZ). More...

static std::set< Size >	correctToNearestMS1Peak (MSExperiment &exp, double mz_tolerance, bool ppm, std::vector< double > &delta_mzs, std::vector< double > &mzs, std::vector< double > &rts)
	Selection of the peak in closest proximity as corrected precursor mass in a given mass range (e.g. precursor mass +/- 0.2 Da). More...

static std::set< Size >	correctToHighestIntensityMS1Peak (MSExperiment &exp, double mz_tolerance, bool ppm, std::vector< double > &delta_mzs, std::vector< double > &mzs, std::vector< double > &rts)
	Selection of the peak with the highest intensity as corrected precursor mass in a given mass range (e.g. precursor mass +/- 0.2 Da) More...

static std::set< Size >	correctToNearestFeature (const FeatureMap &features, MSExperiment &exp, double rt_tolerance_s=0.0, double mz_tolerance=0.0, bool ppm=true, bool believe_charge=false, bool keep_original=false, bool all_matching_features=false, int max_trace=2, int debug_level=0)
	Reassigns a precursor to the nearest feature in a given rt and mass range. Wrong assignment of the mono-isotopic mass for precursors are assumed: More...

Static Public Attributes
static const std::string	csv_header

Static Protected Member Functions
static bool	overlaps_ (const Feature &feature, const double rt, const double pc_mz, const double rt_tolerance)
	Check if precursor is located in the bounding box of a features convex hull. Here the bounding box of the feature is extended by the retention time tolerance and afterwards the precursor location is validated. More...

static bool	compatible_ (const Feature &feature, double pc_mz, double mz_tolerance, Size max_trace_number=2, int debug_level=0)
	Check precursor and feature compatibility If the precursor mz is in one of the masstraces the feature is compatible. Dependent on 13C mass difference and charge. More...

Detailed Description

This class provides methods for precursor correction.

Supported methods: getPrecursors: Extract precursors and associated information (mz, scan index). writeHist: Write output .csv for validation purposes (corrected, uncorrected). correctToNearestMS1Peak: Correct to the peak in closest proximity in a certain mass range. correctToHighestIntensityMS1Peak: Correct to the peak with the highest intensity in a certain mass range. correctToNearestFeature: Use feature information to re-annotate a precursor (e.g. falsely assigned to non mono-isotopic trace).

Member Function Documentation

◆ compatible_()

static bool compatible_	(	const Feature &	feature,
		double	pc_mz,
		double	mz_tolerance,
		Size	max_trace_number = `2`,
		int	debug_level = `0`
	)

staticprotected

Check precursor and feature compatibility If the precursor mz is in one of the masstraces the feature is compatible. Dependent on 13C mass difference and charge.

Parameters

feature	constant Feature.
pc_mz	double precursor mass to charge.
mz_tolerance	double mass to charge tolerance.
max_trace_number	Size maximum number of mass traces.
debug_level	integer debug level.

Returns: static boolean if the precursor mass to charge is in one of the features masstraces.

◆ correctToHighestIntensityMS1Peak()

static std::set<Size> correctToHighestIntensityMS1Peak	(	MSExperiment &	exp,
		double	mz_tolerance,
		bool	ppm,
		std::vector< double > &	delta_mzs,
		std::vector< double > &	mzs,
		std::vector< double > &	rts
	)

static

Selection of the peak with the highest intensity as corrected precursor mass in a given mass range (e.g. precursor mass +/- 0.2 Da)

For each MS2 spectrum the corresponding MS1 spectrum is determined by using the rt information of the precursor. In the MS1, the peak with the highest intensity in a given mass range to the uncorrected precursor m/z is selected and used as corrected precursor m/z.

Parameters

exp	MSExperiment.
mz_tolerance	double tolerance used for precursor correction in mass range.
ppm	bool enables usage of ppm.
delta_mzs	vector double delta mass to charge.
mzs	vector double mass to charge.
rts	vector double retention time.

Returns: set of Size with corrected precursor information.

◆ correctToNearestFeature()

static std::set<Size> correctToNearestFeature	(	const FeatureMap &	features,
		MSExperiment &	exp,
		double	rt_tolerance_s = `0.0`,
		double	mz_tolerance = `0.0`,
		bool	ppm = `true`,
		bool	believe_charge = `false`,
		bool	keep_original = `false`,
		bool	all_matching_features = `false`,
		int	max_trace = `2`,
		int	debug_level = `0`
	)

static

Reassigns a precursor to the nearest feature in a given rt and mass range. Wrong assignment of the mono-isotopic mass for precursors are assumed:

if precursor_mz matches the mz of a non-monoisotopic feature mass trace
and in the case that believe_charge is true: if feature_charge matches the precursor_charge In the case of wrong mono-isotopic assignment several options for correction are available: keep_original will create a copy of the precursor and tandem spectrum for the new mono-isotopic mass trace and retain the original one. all_matching_features does this not for only the closest feature but all features in a question.

Parameters

features	constant FeatureMap.
exp	MSExperiment.
rt_tolerance_s	double retention time tolerance in seconds.
mz_tolerance	double tolerance used for precursor correction in mass range.
ppm	bool enables usage of ppm.
believe_charge	bool only add features that match the precursor charge.
keep_original	bool this will create a copy of the precursor and tandem spectrum for the new mono-isotopic trace and retain the original one.
all_matching_features	bool correction is performed for all features in question not only the closest one.
max_trace	integer maximal number of traces used.
debug_level	integer debug level.

Returns: set of Size with corrected precursor information.

◆ correctToNearestMS1Peak()

static std::set<Size> correctToNearestMS1Peak	(	MSExperiment &	exp,
		double	mz_tolerance,
		bool	ppm,
		std::vector< double > &	delta_mzs,
		std::vector< double > &	mzs,
		std::vector< double > &	rts
	)

static

Selection of the peak in closest proximity as corrected precursor mass in a given mass range (e.g. precursor mass +/- 0.2 Da).

For each MS2 spectrum the corresponding MS1 spectrum is determined by using the rt information of the precursor. In the MS1, the peak closest to the uncorrected precursor m/z is selected and used as corrected precursor m/z.

Parameters

exp	MSExperiment.
mz_tolerance	double tolerance used for precursor correction in mass range.
ppm	bool enables usage of ppm.
delta_mzs	vector double delta mass to charge.
mzs	vector double mass to charge.
rts	vector double retention time.

Returns: set of Size with corrected precursor information.

◆ getPrecursors()

static void getPrecursors	(	const MSExperiment &	exp,
		std::vector< Precursor > &	precursors,
		std::vector< double > &	precursors_rt,
		std::vector< Size > &	precursor_scan_index
	)

static

Extract precursors and associated information (precursor retention time and precursor scan index).

Parameters

	exp	Spectra with precursors
[out]	precursors	vector of all precursors in `exp` (can be more than one per MSn spectrum)
[out]	precursors_rt	vector double of precursors retention time (same length as `precursors`)
[out]	precursor_scan_index	Indices into `exp`, which have a precursor

◆ overlaps_()

static bool overlaps_	(	const Feature &	feature,
		const double	rt,
		const double	pc_mz,
		const double	rt_tolerance
	)

staticprotected

Check if precursor is located in the bounding box of a features convex hull. Here the bounding box of the feature is extended by the retention time tolerance and afterwards the precursor location is validated.

Parameters

feature	constant Feature.
rt	constant double retention time.
pc_mz	constant double precursor mass to charge.
rt_tolerance	constant double retention time tolerance in seconds.

Returns: static boolean to check if the precursor is located in the bounding box of a features convex hull.

◆ writeHist()

static void writeHist	(	const String &	out_csv,
		const std::vector< double > &	delta_mzs,
		const std::vector< double > &	mzs,
		const std::vector< double > &	rts
	)

static

Writer can be used in association with correctToNearestMS1Peak or correctToHighestIntensityMS1Peak. A csv file with additional information (RT, uncorrectedMZ, correctedMZ, deltaMZ).

Format: RT uncorrectedMZ correctedMZ deltaMZ 100.1 509.9999 510 0.0001 180.9 610.0001 610 -0.0001 183.92 611.0035 611.0033 -0.0002

Parameters

out_csv	constant String for csv output.
delta_mzs	delta m/z column values.
mzs	m/z column vector (uncorrectedMZ)
rts	retention time column vector

Member Data Documentation

◆ csv_header

const std::string csv_header

static

Static Public Member Functions

Static Public Attributes

Static Protected Member Functions

Detailed Description

Member Function Documentation

◆ compatible_()

◆ correctToHighestIntensityMS1Peak()

◆ correctToNearestFeature()

◆ correctToNearestMS1Peak()

◆ getPrecursors()

◆ overlaps_()

◆ writeHist()

Member Data Documentation

◆ csv_header