OPXLDataStructs.h File Reference

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CONCEPT/HashUtils.h>
#include <functional>

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Classes
class	OPXLDataStructs
struct	OPXLDataStructs::ProteinProteinCrossLink
	The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL. More...
struct	OPXLDataStructs::CrossLinkSpectrumMatch
	The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL. More...
struct	OPXLDataStructs::CLSMScoreComparator
	Comparator to sort CrossLinkSpectrumMatches by the main score. More...
struct	OPXLDataStructs::XLPrecursor
	The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL. More...
struct	OPXLDataStructs::XLPrecursorComparator
	The XLPrecursorComparator is a comparator for XLPrecursors, that allows direct comparison of the XLPrecursor precursor mass with double numbers. More...
struct	OPXLDataStructs::AASeqWithMass
	The AASeqWithMass struct represents a normal peptide with its precomputed mass. More...
struct	OPXLDataStructs::AASeqWithMassComparator
	The AASeqWithMassComparator is a comparator for AASeqWithMass objects. More...
struct	OPXLDataStructs::PreprocessedPairSpectra
	The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spectra to each other. More...
struct	hash< OpenMS::OPXLDataStructs::ProteinProteinCrossLink >
	std::hash specialization for ProteinProteinCrossLink More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.
namespace	std
	STL namespace.

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Class Documentation

OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch

struct OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch

The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum in OpenPepXL.

This struct contains a ProteinProteinCrossLink and indices to one or two spectra. It also contains the results of a match between the ProteinProteinCrossLink and these spectra as scores and peak annotations. Used as a temporary container to collect results efficiently, since only a few top matches will be kept for each experimental spectrum for output.

Collaboration diagram for OPXLDataStructs::CrossLinkSpectrumMatch:

Class Members
ProteinProteinCrossLink	cross_link	structure of the cross-link
vector< PeakAnnotation >	frag_annotations
double	int_sum = 0
double	intsum_alpha = 0
double	intsum_beta = 0
double	log_occupancy = 0
double	log_occupancy_alpha = 0
double	log_occupancy_beta = 0
double	match_odds = 0
double	match_odds_alpha = 0
double	match_odds_beta = 0
Size	matched_linear_alpha = 0
Size	matched_linear_beta = 0
Size	matched_xlink_alpha = 0
Size	matched_xlink_beta = 0
double	num_iso_peaks_mean = 0
double	num_iso_peaks_mean_linear_alpha = 0
double	num_iso_peaks_mean_linear_beta = 0
double	num_iso_peaks_mean_xlinks_alpha = 0
double	num_iso_peaks_mean_xlinks_beta = 0
Size	peptide_id_index = 0
double	percTIC = 0
double	ppm_error_abs_sum = 0
double	ppm_error_abs_sum_alpha = 0
double	ppm_error_abs_sum_beta = 0
double	ppm_error_abs_sum_linear = 0
double	ppm_error_abs_sum_linear_alpha = 0
double	ppm_error_abs_sum_linear_beta = 0
double	ppm_error_abs_sum_xlinks = 0
double	ppm_error_abs_sum_xlinks_alpha = 0
double	ppm_error_abs_sum_xlinks_beta = 0
double	pre_score = 0
int	precursor_correction = 0
double	precursor_error_ppm = 0
Size	precursor_residual_peak_count = 0
double	precursor_signal_proportion = 0
double	precursor_target_intensity = 0
Size	precursor_target_peak_count = 0
double	precursor_total_intensity = 0
Size	rank = 0	rank among the matches to the same spectrum
Size	scan_index_heavy = 0
Size	scan_index_light = 0	reference to pair of spectra
double	score = 0	final score
double	total_current = 0
double	wTIC = 0
double	wTICold = 0
double	xcorrc_max = 0
double	xcorrx_max = 0
double	xquest_score = 0	counts, scores and other data for xQuest-like output

OpenMS::OPXLDataStructs::XLPrecursor

struct OpenMS::OPXLDataStructs::XLPrecursor

The XLPrecursor struct represents a cross-link candidate in the process of filtering candidates by precursor masses in OpenPepXL.

Since the precursor mass does not change depending on the exact linked residues, one XLPrecursor can represent several ProteinProteinCrossLinks in the process of filtering by precursor mass. The precursor mass is the sum of the masses of the two peptides and the cross-linker. This struct also contains the indices of the two peptides in a vector, so that the two peptides can be identified again. This precursor mass is enumerated for all peptide pairs in the protein database given as input to OpenPepXL and is one of the major contributors to the memory usage of the tool because of the squared complexity of this enumeration. Therefore this should be kept as compact as possible.

Collaboration diagram for OPXLDataStructs::XLPrecursor:

Class Members
unsigned int	alpha_index = 0
String	alpha_seq
unsigned int	beta_index = 0
String	beta_seq
float	precursor_mass {}

OpenMS::OPXLDataStructs::AASeqWithMass

struct OpenMS::OPXLDataStructs::AASeqWithMass

The AASeqWithMass struct represents a normal peptide with its precomputed mass.

This struct stores information about a peptide as an AASequence and a PeptidePosition. It is used to enumerate pairs of peptides in OpenPepXL. Since the mass of every peptide is used many times, it is precomputed once and also stored in this struct. A vector of these structs is used to represent the digested protein database in OpenPepXL. An instance of this struct is created only once for each peptide in the digested database, so it does not contribute to memory usage as much as XLPrecursor does.

Collaboration diagram for OPXLDataStructs::AASeqWithMass:

Class Members
double	peptide_mass = 0
AASequence	peptide_seq
PeptidePosition	position = PeptidePosition::INTERNAL
String	unmodified_seq