The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code. More...

#include <OpenMS/ANALYSIS/XLMS/OPXLHelper.h>

Classes
struct	PeptideIDScoreComparator
	A comparator for PeptideIdentifications that compares the scores in the first PeptideHit. More...

Static Public Member Functions
static std::vector< OPXLDataStructs::XLPrecursor >	enumerateCrossLinksAndMasses (const std::vector< OPXLDataStructs::AASeqWithMass > &peptides, double cross_link_mass_light, const DoubleList &cross_link_mass_mono_link, const StringList &cross_link_residue1, const StringList &cross_link_residue2, const std::vector< double > &spectrum_precursors, std::vector< int > &precursor_correction_positions, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm)
	Enumerates precursor masses for all candidates in an XL-MS search. More...

static std::vector< OPXLDataStructs::AASeqWithMass >	digestDatabase (std::vector< FASTAFile::FASTAEntry > fasta_db, EnzymaticDigestion digestor, Size min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide)
	Digests a database with the given EnzymaticDigestion settings and precomputes masses for all peptides. More...

static std::vector< OPXLDataStructs::ProteinProteinCrossLink >	buildCandidates (const std::vector< OPXLDataStructs::XLPrecursor > &candidates, const std::vector< int > &precursor_corrections, const std::vector< int > &precursor_correction_positions, const std::vector< OPXLDataStructs::AASeqWithMass > &peptide_masses, const StringList &cross_link_residue1, const StringList &cross_link_residue2, double cross_link_mass, const DoubleList &cross_link_mass_mono_link, const std::vector< double > &spectrum_precursor_vector, const std::vector< double > &allowed_error_vector, String cross_link_name)
	Builds specific cross-link candidates with all possible combinations of linked positions from peptide pairs. Used to build candidates for the precursor mass window of a single MS2 spectrum. More...

static void	buildFragmentAnnotations (std::vector< PeptideHit::PeakAnnotation > &frag_annotations, const std::vector< std::pair< Size, Size > > &matching, const PeakSpectrum &theoretical_spectrum, const PeakSpectrum &experiment_spectrum)
	Fills up the given FragmentAnnotation vector with annotations from a theoretical spectrum. More...

static void	buildPeptideIDs (std::vector< PeptideIdentification > &peptide_ids, const std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > &top_csms_spectrum, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, Size all_top_csms_current_index, const PeakMap &spectra, Size scan_index, Size scan_index_heavy)
	Builds PeptideIdentifications and PeptideHits. More...

static void	addProteinPositionMetaValues (std::vector< PeptideIdentification > &peptide_ids)
	adds MetaValues for cross-link positions to PeptideHits More...

static void	addXLTargetDecoyMV (std::vector< PeptideIdentification > &peptide_ids)
	adds xl_target_decoy MetaValue that combines alpha and beta target_decoy info More...

static void	addBetaAccessions (std::vector< PeptideIdentification > &peptide_ids)
	adds accessions_beta MetaValue to alpha peptides for TOPPView visualization and CSV table output More...

static void	removeBetaPeptideHits (std::vector< PeptideIdentification > &peptide_ids)
	removes beta peptides from cross-link IDs, since all info is already contained in the alpha peptide hits More...

static void	addPercolatorFeatureList (ProteinIdentification &prot_id)
	adds the list of features that percolator should use for OpenPepXL More...

static void	computeDeltaScores (std::vector< PeptideIdentification > &peptide_ids)
	sorts PeptideHits for each PeptideIdentification by score and adds the delta score as a MetaValue More...

static std::vector< PeptideIdentification >	combineTopRanksFromPairs (std::vector< PeptideIdentification > &peptide_ids, Size number_top_hits)
	combines all hits to spectrum pairs with the same light spectrum into one ranked list More...

static std::vector< OPXLDataStructs::ProteinProteinCrossLink >	collectPrecursorCandidates (const IntList &precursor_correction_steps, double precursor_mass, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, const std::vector< OPXLDataStructs::AASeqWithMass > &filtered_peptide_masses, double cross_link_mass, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, String cross_link_name, bool use_sequence_tags=false, const std::vector< std::string > &tags=std::vector< std::string >())
	Searches for cross-link candidates for a MS/MS spectrum. More...

static double	computePrecursorError (OPXLDataStructs::CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge)
	Computes the mass error of a precursor mass to a hit. More...

static void	isoPeakMeans (OPXLDataStructs::CrossLinkSpectrumMatch &csm, DataArrays::IntegerDataArray &num_iso_peaks_array, std::vector< std::pair< Size, Size > > &matched_spec_linear_alpha, std::vector< std::pair< Size, Size > > &matched_spec_linear_beta, std::vector< std::pair< Size, Size > > &matched_spec_xlinks_alpha, std::vector< std::pair< Size, Size > > &matched_spec_xlinks_beta)
	Computes the mass error of a precursor mass to a hit. More...

static void	filterPrecursorsByTags (std::vector< OPXLDataStructs::XLPrecursor > &candidates, std::vector< int > &precursor_correction_positions, const std::vector< std::string > &tags)
	Filters the list of candidates for cases that include at least one of the tags in at least one of the two sequences. More...

Detailed Description

The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code.

Member Function Documentation

◆ addBetaAccessions()

static void addBetaAccessions ( std::vector< PeptideIdentification > & peptide_ids )

static

adds accessions_beta MetaValue to alpha peptides for TOPPView visualization and CSV table output

Parameters

peptide_ids The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins

◆ addPercolatorFeatureList()

static void addPercolatorFeatureList ( ProteinIdentification & prot_id )

static

adds the list of features that percolator should use for OpenPepXL

Parameters

search_params The search parameters of OpenPepXL

◆ addProteinPositionMetaValues()

static void addProteinPositionMetaValues ( std::vector< PeptideIdentification > & peptide_ids )

static

adds MetaValues for cross-link positions to PeptideHits

Parameters

peptide_ids The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins

◆ addXLTargetDecoyMV()

static void addXLTargetDecoyMV ( std::vector< PeptideIdentification > & peptide_ids )

static

adds xl_target_decoy MetaValue that combines alpha and beta target_decoy info

Parameters

peptide_ids The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins

◆ buildCandidates()

static std::vector<OPXLDataStructs::ProteinProteinCrossLink> buildCandidates	(	const std::vector< OPXLDataStructs::XLPrecursor > &	candidates,
		const std::vector< int > &	precursor_corrections,
		const std::vector< int > &	precursor_correction_positions,
		const std::vector< OPXLDataStructs::AASeqWithMass > &	peptide_masses,
		const StringList &	cross_link_residue1,
		const StringList &	cross_link_residue2,
		double	cross_link_mass,
		const DoubleList &	cross_link_mass_mono_link,
		const std::vector< double > &	spectrum_precursor_vector,
		const std::vector< double > &	allowed_error_vector,
		String	cross_link_name
	)

static

Builds specific cross-link candidates with all possible combinations of linked positions from peptide pairs. Used to build candidates for the precursor mass window of a single MS2 spectrum.

Parameters

candidates	The XLPrecursors containing indices of two peptides
peptide_masses	The digested peptide database, that the indices in the XLPrecursors refer to
cross_link_residue1	A list of residues, to which the first side of the linker can react
cross_link_residue2	A list of residues, to which the second side of the linker can react
cross_link_mass	mass of the cross-linker, only the light one if a labeled linker is used
cross_link_mass_mono_link	A list of possible masses for the cross-link, if it is attached to a peptide on one side
precursor_mass	The precursor mass of the experimental spectrum (used to filter out certain candidates, e.g. mono- and loop-links have a different mass)
allowed_error	The maximal precursor mass error in Da
cross_link_name	The name of the cross-linker
n_term_linker	True, if the cross-linker can react with the N-terminal of a protein
c_term_linker	True, if the cross-linker can react with the C-terminal of a protein

Returns: A vector of ProteinProteinCrossLink candidates containing all necessary information to generate theoretical spectra

◆ buildFragmentAnnotations()

static void buildFragmentAnnotations	(	std::vector< PeptideHit::PeakAnnotation > &	frag_annotations,
		const std::vector< std::pair< Size, Size > > &	matching,
		const PeakSpectrum &	theoretical_spectrum,
		const PeakSpectrum &	experiment_spectrum
	)

static

Fills up the given FragmentAnnotation vector with annotations from a theoretical spectrum.

This function takes an alignment of a theoretical spectrum with meta information and an experimental spectrum and builds annotations taking the MZ and intensity values from the experimental spectrum and the ion names and charges from the theoretical spectrum to annotate matched experimental peaks.

Parameters

frag_annotations	The vector to fill. Does not have to be empty, as annotations from several alignments can just be added on to the same vector.
matching	The alignment between the two spectra
theoretical_spectrum	The theoretical spectrum with meta information
experiment_spectrum	The experimental spectrum

◆ buildPeptideIDs()

static void buildPeptideIDs	(	std::vector< PeptideIdentification > &	peptide_ids,
		const std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > &	top_csms_spectrum,
		std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &	all_top_csms,
		Size	all_top_csms_current_index,
		const PeakMap &	spectra,
		Size	scan_index,
		Size	scan_index_heavy
	)

static

Builds PeptideIdentifications and PeptideHits.

Parameters

peptide_ids	The vector of PeptideIdentifications for the whole experiment. The created PepIds will be pushed on this one.
top_csms_spectrum	All CrossLinkSpectrumMatches from the current spectrum to be written out
all_top_csms	A vector of all CrossLinkSpectrumMatches of the experiment, that is also extended in this function
all_top_csms_current_index	The index of the current spectrum in all_top_csms (some spectra have no matches, so this is not equal to the spectrum index)
spectra	The searched spectra as a PeakMap
scan_index	The index of the current spectrum
scan_index_heavy	The index of the heavy spectrum in a spectrum pair with labeled linkers

◆ collectPrecursorCandidates()

static std::vector<OPXLDataStructs::ProteinProteinCrossLink> collectPrecursorCandidates	(	const IntList &	precursor_correction_steps,
		double	precursor_mass,
		double	precursor_mass_tolerance,
		bool	precursor_mass_tolerance_unit_ppm,
		const std::vector< OPXLDataStructs::AASeqWithMass > &	filtered_peptide_masses,
		double	cross_link_mass,
		DoubleList	cross_link_mass_mono_link,
		StringList	cross_link_residue1,
		StringList	cross_link_residue2,
		String	cross_link_name,
		bool	use_sequence_tags = `false`,
		const std::vector< std::string > &	tags = `std::vector< std::string >()`
	)

static

Searches for cross-link candidates for a MS/MS spectrum.

This function uses enumerateCrossLinksAndMasses and buildCandidates to search for peptide pairs fitting to the given precursor mass_light and all considered precursor corrections.

Parameters

precursor_correction_steps	An IntList of integers as indices of isotopic peaks around the experimental precursor
precursor_mass	The decharged precursor mass
precursor_mass_tolerance	The precursor tolerance
precursor_mass_tolerance_unit_ppm	The unit of the precursor tolerance. "ppm" if true, "Da" if false
filtered_peptide_masses	A vector of AASeqWithMass containing the sorted (ascending) peptide database with precomputed peptide masses
cross_link_mass	The mass of the cross-linker (light mass, if labeled)
cross_link_mass_mono_link	A list of possible mono-link masses
cross_link_residue1	A list of one-letter-code residues, that the first side of the cross-linker can attach to
cross_link_residue2	A list of one-letter-code residues, that the second side of the cross-linker can attach to
cross_link_name	The name of the cross-linker, e.g. "DSS" or "BS3"
use_sequence_tags	Whether to use sequence tags to filter out candidates
tags	The list of sequence tags that are used to filter candidate sequences. Only applied if use_sequence_tags = true

◆ combineTopRanksFromPairs()

static std::vector< PeptideIdentification > combineTopRanksFromPairs	(	std::vector< PeptideIdentification > &	peptide_ids,
		Size	number_top_hits
	)

static

combines all hits to spectrum pairs with the same light spectrum into one ranked list

This function is a post-processing step for OpenPepXL with labeled linkers. This function collects PeptideIdentifications from all spectrum pairs with the same light spectrum, then resorts them by the score, makes them unique in case of equal candidates and reduces their number down to the chosen number of reported top hits.

Parameters

peptide_ids	PeptideIdentifications from a Cross-Linking MS search with labeled linkers
number_top_hits	The chosen number of reported top hits

◆ computeDeltaScores()

static void computeDeltaScores ( std::vector< PeptideIdentification > & peptide_ids )

static

sorts PeptideHits for each PeptideIdentification by score and adds the delta score as a MetaValue

Parameters

peptide_ids The vector of peptide_ids containing XL-MS search results without beta PeptideHits

◆ computePrecursorError()

static double computePrecursorError	(	OPXLDataStructs::CrossLinkSpectrumMatch	csm,
		double	precursor_mz,
		int	precursor_charge
	)

static

Computes the mass error of a precursor mass to a hit.

Parameters

csm	The cross-link spectrum match containing the hit
precursor_mz	The precursor mz of the MS/MS spectrum
precursor_charge	The charge of the precursor

◆ digestDatabase()

static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase	(	std::vector< FASTAFile::FASTAEntry >	fasta_db,
		EnzymaticDigestion	digestor,
		Size	min_peptide_length,
		StringList	cross_link_residue1,
		StringList	cross_link_residue2,
		const ModifiedPeptideGenerator::MapToResidueType &	fixed_modifications,
		const ModifiedPeptideGenerator::MapToResidueType &	variable_modifications,
		Size	max_variable_mods_per_peptide
	)

static

Digests a database with the given EnzymaticDigestion settings and precomputes masses for all peptides.

Also keeps track of the peptides at protein terminals and builds peptide candidates with all possible modification patterns according to the parameters.

Parameters

fasta_db	The protein database
digestor	The object containing the digestion settings, e.g. the enzyme
min_peptide_length	The minimal peptide length for the digestion
cross_link_residue1	A list of residues, to which the first side of the linker can react
cross_link_residue2	A list of residues, to which the second side of the linker can react
fixed_modifications	The list of fixed modifications
variable_modifications	The list of variable modifications
max_variable_mods_per_peptide	The maximal number of variable modifications per peptide
count_proteins	A variable to keep track of the number of proteins in the database. Should be an externally declared variable and = 0 when calling this function.
count_peptides	A variable to keep track of the number of peptides after digestion. Should be an externally declared variable and = 0 when calling this function.
n_term_linker	True, if the cross-linker can react with the N-terminal of a protein
c_term_linker	True, if the cross-linker can react with the C-terminal of a protein

Returns: A vector of AASeqWithMass containing the peptides, their masses and information about terminal peptides

◆ enumerateCrossLinksAndMasses()

static std::vector<OPXLDataStructs::XLPrecursor> enumerateCrossLinksAndMasses	(	const std::vector< OPXLDataStructs::AASeqWithMass > &	peptides,
		double	cross_link_mass_light,
		const DoubleList &	cross_link_mass_mono_link,
		const StringList &	cross_link_residue1,
		const StringList &	cross_link_residue2,
		const std::vector< double > &	spectrum_precursors,
		std::vector< int > &	precursor_correction_positions,
		double	precursor_mass_tolerance,
		bool	precursor_mass_tolerance_unit_ppm
	)

static

Enumerates precursor masses for all candidates in an XL-MS search.

Assumes the list of peptides and the list of spectrum precursor masses are sorted by mass in ascending order, and the list of mono-link masses is sorted in descending order.

Parameters

peptides	The peptides with precomputed masses from the digestDatabase function
cross_link_mass_light	Mass of the cross-linker, only the light one if a labeled linker is used
cross_link_mass_mono_link	A list of possible masses for the cross-link, if it is attached to a peptide on one side
cross_link_residue1	A list of residues, to which the first side of the linker can react
cross_link_residue2	A list of residues, to which the second side of the linker can react
spectrum_precursors	A vector of all MS2 precursor masses of the searched spectra. Used to filter out candidates.
precursor_correction_positions	A vector of the position of the used precursor correction
precursor_mass_tolerance	The precursor mass tolerance
precursor_mass_tolerance_unit_ppm	The unit of the precursor mass tolerance ("Da" or "ppm")

Returns: A vector of XLPrecursors containing all possible candidate cross-links

◆ filterPrecursorsByTags()

static void filterPrecursorsByTags	(	std::vector< OPXLDataStructs::XLPrecursor > &	candidates,
		std::vector< int > &	precursor_correction_positions,
		const std::vector< std::string > &	tags
	)

static

Filters the list of candidates for cases that include at least one of the tags in at least one of the two sequences.

Parameters

candidates	The list of XLPrecursors as enumerated by e.g. enumerateCrossLinksAndMasses
tags	The list of tags for the current spectrum produced by the Tagger

◆ isoPeakMeans()

static void isoPeakMeans	(	OPXLDataStructs::CrossLinkSpectrumMatch &	csm,
		DataArrays::IntegerDataArray &	num_iso_peaks_array,
		std::vector< std::pair< Size, Size > > &	matched_spec_linear_alpha,
		std::vector< std::pair< Size, Size > > &	matched_spec_linear_beta,
		std::vector< std::pair< Size, Size > > &	matched_spec_xlinks_alpha,
		std::vector< std::pair< Size, Size > > &	matched_spec_xlinks_beta
	)

static

Computes the mass error of a precursor mass to a hit.

Parameters

csm	The cross-link spectrum match containing the hit
precursor_mz	The precursor mz of the MS/MS spectrum
precursor_charge	The charge of the precursor

◆ removeBetaPeptideHits()

static void removeBetaPeptideHits ( std::vector< PeptideIdentification > & peptide_ids )

static

removes beta peptides from cross-link IDs, since all info is already contained in the alpha peptide hits

Parameters

peptide_ids The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits

Classes

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ addBetaAccessions()

◆ addPercolatorFeatureList()

◆ addProteinPositionMetaValues()

◆ addXLTargetDecoyMV()

◆ buildCandidates()

◆ buildFragmentAnnotations()

◆ buildPeptideIDs()

◆ collectPrecursorCandidates()

◆ combineTopRanksFromPairs()

◆ computeDeltaScores()

◆ computePrecursorError()

◆ digestDatabase()

◆ enumerateCrossLinksAndMasses()

◆ filterPrecursorsByTags()

◆ isoPeakMeans()

◆ removeBetaPeptideHits()