OpenMS
|
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, const EnzymaticDigestion &digestor, Size min_peptide_length, const StringList &cross_link_residue1, const 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, const 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, const DoubleList &cross_link_mass_mono_link, const StringList &cross_link_residue1, const 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 (const 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, const DataArrays::IntegerDataArray &num_iso_peaks_array, const std::vector< std::pair< Size, Size > > &matched_spec_linear_alpha, const std::vector< std::pair< Size, Size > > &matched_spec_linear_beta, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks_alpha, const std::vector< std::pair< Size, Size > > &matched_spec_xlinks_beta) |
Computes the mean of alpha, beta, xlinks-alpha and xlinks-beta respectively and store means in csm . 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... | |
The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code.
|
static |
adds accessions_beta MetaValue to alpha peptides for TOPPView visualization and CSV table output
peptide_ids | The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins |
|
static |
Adds the list of features that percolator should use for OpenPepXL.
prot_id | Receives updated search parameters ('feature_extractor' and 'extra_features') as meta value for OpenPepXL |
|
static |
adds MetaValues for cross-link positions to PeptideHits
peptide_ids | The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins |
|
static |
adds xl_target_decoy MetaValue that combines alpha and beta target_decoy info
peptide_ids | The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits, after mapping of peptides to proteins |
|
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.
candidates | The XLPrecursors containing indices of two peptides |
precursor_corrections | Same size as candidates |
precursor_correction_positions | Same size as candidates ; A vector of the position of the used precursor correction |
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 |
spectrum_precursor_vector | The precursor masses of the experimental spectrum (used to filter out certain candidates, e.g. mono- and loop-links have a different mass) |
allowed_error_vector | Allowed mass error in Da for the respective precursor in spectrum_precursor_vector . |
cross_link_name | The name of the cross-linker |
|
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.
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 |
|
static |
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 |
|
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.
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 |
|
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.
peptide_ids | PeptideIdentifications from a Cross-Linking MS search with labeled linkers |
number_top_hits | The chosen number of reported top hits |
|
static |
sorts PeptideHits for each PeptideIdentification by score and adds the delta score as a MetaValue
peptide_ids | The vector of peptide_ids containing XL-MS search results without beta PeptideHits |
|
static |
Computes the mass error of a precursor mass to a hit.
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 |
|
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.
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 |
|
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.
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") |
|
static |
Filters the list of candidates for cases that include at least one of the tags in at least one of the two sequences.
candidates | The list of XLPrecursors as enumerated by e.g. enumerateCrossLinksAndMasses |
precursor_correction_positions | |
tags | The list of tags for the current spectrum produced by the Tagger |
|
static |
Computes the mean of alpha, beta, xlinks-alpha and xlinks-beta respectively and store means in csm
.
|
static |
removes beta peptides from cross-link IDs, since all info is already contained in the alpha peptide hits
peptide_ids | The vector of peptide_ids containing XL-MS search results with alpha and beta PeptideHits |