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

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

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< ResidueModification >	getModificationsFromStringList (StringList modNames)
	A helper function, that turns a StringList with modification names into a vector of ResidueModifications. 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, std::vector< ResidueModification > fixed_modifications, std::vector< ResidueModification > 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 Private Member Functions
static bool	filter_and_add_candidate (std::vector< OPXLDataStructs::XLPrecursor > &mass_to_candidates, const std::vector< double > &spectrum_precursors, std::vector< int > &precursor_correction_positions, bool precursor_mass_tolerance_unit_ppm, double precursor_mass_tolerance, OPXLDataStructs::XLPrecursor precursor)

Detailed Description

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

Member Function Documentation

◆ 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, 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

◆ 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,
		std::vector< ResidueModification >	fixed_modifications,
		std::vector< ResidueModification >	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.

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

◆ filter_and_add_candidate()

static bool filter_and_add_candidate	(	std::vector< OPXLDataStructs::XLPrecursor > &	mass_to_candidates,
		const std::vector< double > &	spectrum_precursors,
		std::vector< int > &	precursor_correction_positions,
		bool	precursor_mass_tolerance_unit_ppm,
		double	precursor_mass_tolerance,
		OPXLDataStructs::XLPrecursor	precursor
	)

staticprivate

◆ getModificationsFromStringList()

static std::vector<ResidueModification> getModificationsFromStringList ( StringList modNames )

static

A helper function, that turns a StringList with modification names into a vector of ResidueModifications.

Parameters

modNames The list of modification names

Returns: A vector of modifications

Static Public Member Functions

Static Private Member Functions

Detailed Description

Member Function Documentation

◆ addProteinPositionMetaValues()

◆ buildCandidates()

◆ buildFragmentAnnotations()

◆ buildPeptideIDs()

◆ digestDatabase()

◆ enumerateCrossLinksAndMasses()

◆ filter_and_add_candidate()

◆ getModificationsFromStringList()