Utility class for analyzing modification patterns in open search results. More...

#include <OpenMS/ANALYSIS/ID/OpenSearchModificationAnalysis.h>

Classes
struct	FuzzyDoubleComparator
	Comparator for approximate comparison of double values. More...

struct	ModificationPattern
	Stores details of a modification pattern found in the data. More...

struct	ModificationSummary
	Data structure for modification summary output. More...

Public Types
using	DeltaMassHistogram = std::map< double, double, FuzzyDoubleComparator >
	Type definitions for delta mass analysis. More...

using	DeltaMassToChargeCount = std::map< double, int, FuzzyDoubleComparator >

Public Member Functions
	OpenSearchModificationAnalysis ()=default
	Default constructor. More...

	~OpenSearchModificationAnalysis ()=default
	Destructor. More...

std::pair< DeltaMassHistogram, DeltaMassToChargeCount >	analyzeDeltaMassPatterns (const PeptideIdentificationList &peptide_ids, bool use_smoothing=false, bool debug=false) const
	Analyze delta mass patterns from peptide identifications. More...

std::vector< ModificationSummary >	mapDeltaMassesToModifications (const DeltaMassHistogram &delta_mass_histogram, const DeltaMassToChargeCount &charge_histogram, PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true, const String &output_file="") const
	Map delta masses to known modifications and annotate peptides. More...

std::vector< ModificationSummary >	analyzeModifications (PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true, bool use_smoothing=false, const String &output_file="") const
	Complete analysis workflow: analyze patterns and map to modifications. More...

Private Member Functions
void	writeModificationSummary_ (const std::vector< ModificationSummary > &modifications, const String &output_file) const
	Write modification summary table to file. More...

Static Private Member Functions
static double	gaussian_ (double x, double sigma)
	Gaussian function for smoothing. More...

static DeltaMassHistogram	smoothDeltaMassHistogram_ (const DeltaMassHistogram &histogram, double sigma=0.001)
	Smooth delta mass histogram using Gaussian kernel density estimation. More...

static DeltaMassHistogram	findPeaksInHistogram_ (const DeltaMassHistogram &histogram, double count_threshold=0.0, double snr=2.0)
	Find peaks in delta mass histogram based on count threshold and signal-to-noise ratio. More...

Detailed Description

Utility class for analyzing modification patterns in open search results.

This class provides functionality to analyze delta mass patterns from open search peptide identifications, identify common modifications, and map them to known modifications from the ModificationsDB. Originally extracted from SageAdapter.

Class Documentation

◆ OpenMS::OpenSearchModificationAnalysis::ModificationPattern

struct OpenMS::OpenSearchModificationAnalysis::ModificationPattern

Stores details of a modification pattern found in the data.

Collaboration diagram for OpenSearchModificationAnalysis::ModificationPattern:

[legend]

Class Members
double	count	Number of peptides with this modification.
vector< double >	masses	Masses associated with the modification.
int	num_charge_states	Number of different charge states observed.

◆ OpenMS::OpenSearchModificationAnalysis::ModificationSummary

struct OpenMS::OpenSearchModificationAnalysis::ModificationSummary

Data structure for modification summary output.

Collaboration diagram for OpenSearchModificationAnalysis::ModificationSummary:

[legend]

Class Members
int	count	Modification rate (number of occurrences)
vector< double >	masses	Masses associated with the modification.
String	name	Modification name.
int	num_charge_states	Number of charge states.

Member Typedef Documentation

◆ DeltaMassHistogram

using DeltaMassHistogram = std::map<double, double, FuzzyDoubleComparator>

Type definitions for delta mass analysis.

◆ DeltaMassToChargeCount

using DeltaMassToChargeCount = std::map<double, int, FuzzyDoubleComparator>

Constructor & Destructor Documentation

◆ OpenSearchModificationAnalysis()

OpenSearchModificationAnalysis ( )

default

Default constructor.

◆ ~OpenSearchModificationAnalysis()

~OpenSearchModificationAnalysis ( )

default

Destructor.

Member Function Documentation

◆ analyzeDeltaMassPatterns()

std::pair<DeltaMassHistogram, DeltaMassToChargeCount> analyzeDeltaMassPatterns	(	const PeptideIdentificationList &	peptide_ids,
		bool	use_smoothing = `false`,
		bool	debug = `false`
	)		const

Analyze delta mass patterns from peptide identifications.

Parameters

peptide_ids	List of peptide identifications containing delta mass information
use_smoothing	Whether to apply smoothing to the delta mass histogram
debug	Enable debug output

Returns: Pair containing delta mass histogram and charge state counts

◆ analyzeModifications()

std::vector<ModificationSummary> analyzeModifications	(	PeptideIdentificationList &	peptide_ids,
		double	precursor_mass_tolerance = `5.0`,
		bool	precursor_mass_tolerance_unit_ppm = `true`,
		bool	use_smoothing = `false`,
		const String &	output_file = `""`
	)		const

Complete analysis workflow: analyze patterns and map to modifications.

Parameters

peptide_ids	List of peptide identifications (modified in-place)
precursor_mass_tolerance	Mass tolerance for mapping
precursor_mass_tolerance_unit_ppm	Whether tolerance is in ppm (true) or Da (false)
use_smoothing	Whether to apply smoothing to delta mass histogram
output_file	Optional file path for writing modification summary table

Returns: List of modification summaries found

◆ findPeaksInHistogram_()

static DeltaMassHistogram findPeaksInHistogram_	(	const DeltaMassHistogram &	histogram,
		double	count_threshold = `0.0`,
		double	snr = `2.0`
	)

staticprivate

Find peaks in delta mass histogram based on count threshold and signal-to-noise ratio.

◆ gaussian_()

static double gaussian_	(	double	x,
		double	sigma
	)

staticprivate

Gaussian function for smoothing.

◆ mapDeltaMassesToModifications()

std::vector<ModificationSummary> mapDeltaMassesToModifications	(	const DeltaMassHistogram &	delta_mass_histogram,
		const DeltaMassToChargeCount &	charge_histogram,
		PeptideIdentificationList &	peptide_ids,
		double	precursor_mass_tolerance = `5.0`,
		bool	precursor_mass_tolerance_unit_ppm = `true`,
		const String &	output_file = `""`
	)		const

Map delta masses to known modifications and annotate peptides.

Parameters

delta_mass_histogram	Histogram of delta masses
charge_histogram	Charge state counts for each delta mass
peptide_ids	List of peptide identifications to annotate (modified in-place)
precursor_mass_tolerance	Mass tolerance for mapping
precursor_mass_tolerance_unit_ppm	Whether tolerance is in ppm (true) or Da (false)
output_file	Optional file path for writing modification summary table

Returns: List of modification summaries found

◆ smoothDeltaMassHistogram_()

static DeltaMassHistogram smoothDeltaMassHistogram_	(	const DeltaMassHistogram &	histogram,
		double	sigma = `0.001`
	)

staticprivate

Smooth delta mass histogram using Gaussian kernel density estimation.

◆ writeModificationSummary_()

void writeModificationSummary_	(	const std::vector< ModificationSummary > &	modifications,
		const String &	output_file
	)		const

private

Write modification summary table to file.

Classes

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Detailed Description

Class Documentation

◆ OpenMS::OpenSearchModificationAnalysis::ModificationPattern

◆ OpenMS::OpenSearchModificationAnalysis::ModificationSummary

Member Typedef Documentation

◆ DeltaMassHistogram

◆ DeltaMassToChargeCount

Constructor & Destructor Documentation

◆ OpenSearchModificationAnalysis()

◆ ~OpenSearchModificationAnalysis()

Member Function Documentation

◆ analyzeDeltaMassPatterns()

◆ analyzeModifications()

◆ findPeaksInHistogram_()

◆ gaussian_()

◆ mapDeltaMassesToModifications()

◆ smoothDeltaMassHistogram_()

◆ writeModificationSummary_()