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OpenMS
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#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>Go to the source code of this file.
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. | |
| 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.
| 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 |
| 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.
| Class Members | ||
|---|---|---|
| unsigned int | alpha_index | |
| String | alpha_seq | |
| unsigned int | beta_index | |
| String | beta_seq | |
| float | precursor_mass | |
| 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.
| Class Members | ||
|---|---|---|
| double | peptide_mass | |
| AASequence | peptide_seq | |
| PeptidePosition | position | |
| String | unmodified_seq | |
1.9.1