OpenMS  3.0.0
OPXLDataStructs.h File Reference
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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...
 

Namespaces

 OpenMS
 Main OpenMS namespace.
 

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:
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Class Members
ProteinProteinCrossLink cross_link structure of the cross-link
vector< PeakAnnotation > frag_annotations
double int_sum
double intsum_alpha
double intsum_beta
double log_occupancy
double log_occupancy_alpha
double log_occupancy_beta
double match_odds
double match_odds_alpha
double match_odds_beta
Size matched_linear_alpha
Size matched_linear_beta
Size matched_xlink_alpha
Size matched_xlink_beta
double num_iso_peaks_mean
double num_iso_peaks_mean_linear_alpha
double num_iso_peaks_mean_linear_beta
double num_iso_peaks_mean_xlinks_alpha
double num_iso_peaks_mean_xlinks_beta
Size peptide_id_index
double percTIC
double ppm_error_abs_sum
double ppm_error_abs_sum_alpha
double ppm_error_abs_sum_beta
double ppm_error_abs_sum_linear
double ppm_error_abs_sum_linear_alpha
double ppm_error_abs_sum_linear_beta
double ppm_error_abs_sum_xlinks
double ppm_error_abs_sum_xlinks_alpha
double ppm_error_abs_sum_xlinks_beta
double pre_score
int precursor_correction
double precursor_error_ppm
Size precursor_residual_peak_count
double precursor_signal_proportion
double precursor_target_intensity
Size precursor_target_peak_count
double precursor_total_intensity
Size rank rank among the matches to the same spectrum
Size scan_index_heavy
Size scan_index_light reference to pair of spectra
double score final score
double total_current
double wTIC
double wTICold
double xcorrc_max
double xcorrx_max
double xquest_score 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:
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Class Members
unsigned int alpha_index
String alpha_seq
unsigned int beta_index
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:
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Class Members
double peptide_mass
AASequence peptide_seq
PeptidePosition position
String unmodified_seq