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| OpenPepXLAlgorithm () |
| Default constructor. More...
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| ~OpenPepXLAlgorithm () override |
| Default destructor. More...
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ExitCodes | run (PeakMap &unprocessed_spectra, ConsensusMap &cfeatures, std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, std::vector< std::pair< Size, Size > > &spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, PeakMap &spectra) |
| Performs the main function of this class, the search for cross-linked peptides. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More...
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Search for peptide pairs linked with a labeled cross-linker.
This tool performs a search for cross-links in the given mass spectra. It uses linked MS1 features to pair up MS2 spectra and uses these pairs to find the fragment peaks that contain the linker and those that do not.
It executes the following steps in order:
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Processing of spectra: deisotoping and filtering
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Digesting and preprocessing the protein database, building a peptide pair index dependent on the precursor masses of the MS2 spectra
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Generating theoretical spectra of cross-linked peptides and aligning the experimental spectra against those
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Scoring of cross-link spectrum matches
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Using PeptideIndexer to map the peptides to all possible source proteins
See below for available parameters and more functionality.
Input: MS2 spectra, linked features from FeatureFinderMultiplex and fasta database of proteins expected to be cross-linked in the sample
The spectra should be provided as one PeakMap. If you have multiple files, e.g. for multiple fractions, you should run this tool on each file separately. The database should be provided as a vector of FASTAEntrys containing the target and decoy proteins. A ConsensusMap, that links the MS1 feature pairs from heavy and light cross-linkers is also required. This can be generated by the tool FeatureFinderMultiplex. Setting up FeatureFinderMultiplex: In the FeatureFinderMultiplex parameters you have to change the mass of one of the labels to the difference between the light and heavy (e.g. change the mass of Arg6 to 12.075321 for labeled DSS) in the advanced options. The parameter -labels should have one empty label ( [] ) and the label you adapted (e.g. [][Arg6]). For the other settings refer to the documentation of FeatureFinderMultiplex.
Parameters
The parameters for fixed and variable modifications refer to additional modifications beside the cross-linker. The linker used in the experiment has to be described using the cross-linker specific parameters. Only one mass is allowed for a cross-linker, that links two peptides (cross_linker:mass_light), while multiple masses are possible for mono-links of the same cross-linking reagent. Mono-links are cross-linkers, that are linked to one peptide by one of their two reactive groups. The masses refer to the light version of the linker. The parameter cross_linker:mass_iso_shift defines the difference between the light and heavy versions of the cross-linker and the mono-links. The parameters cross_linker:residue1 and cross_linker:residue2 are used to enumerate the amino acids, that each end of the linker can react with. This way any heterobifunctional cross-linker can be defined. To define a homobifunctional cross-linker, these two parameters should have the same value. The parameter cross_linker:name is used to solve ambiguities arising from different cross-linkers having the same mass after the linking reaction (see section on output for clarification).
Output: XL-MS Identifications with scores and linked positions in the proteins
The input parameters protein_ids and peptide_ids are filled with XL-MS search parameters and IDs
pot. predecessor tools | OpenPepXL | pot. successor tools |
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