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, std::vector< double > &spectrum_precursors, 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, Size count_proteins=0, Size count_peptides=0, bool n_term_linker=false, bool c_term_linker=false) |
| 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< 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, double precursor_mass, double allowed_error, String cross_link_name, bool n_term_linker, bool c_term_linker) |
| 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 spectrum4. 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... | |
The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code.
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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.
| 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 |
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Fills up the given FragmentAnnotation vector with annotations from a theoretical spectrum4.
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.
| 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 specrum |
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Builds PeptideIdentifications and PeptideHits.
| 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 |
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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.
| 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 |
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Enumerates precursor masses for all candidates in an XL-MS search.
| 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_mass_tolerance | The precursor mass tolerance |
| precursor_mass_tolerance_unit_ppm | The unit of the precursor mass tolerance ("Da" or "ppm") |
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A helper function, that turns a StringList with modification names into a vector of ResidueModifications.
| modNames | The list of modification names |
| OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:11 using doxygen 1.8.13 |