This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMDecoy.h>
Public Types | |
| typedef std::vector< OpenMS::TargetedExperiment::Protein > | ProteinVectorType |
| typedef std::vector< OpenMS::TargetedExperiment::Peptide > | PeptideVectorType |
| typedef std::vector< OpenMS::ReactionMonitoringTransition > | TransitionVectorType |
| typedef std::map< String, std::vector< const ReactionMonitoringTransition * > > | PeptideTransitionMapType |
 Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Public Member Functions | |
| MRMDecoy () | |
| void | generateDecoys (OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, String method, String decoy_tag, double identity_threshold, int max_attempts, double mz_threshold, double mz_shift, bool exclude_similar, double similarity_threshold, bool remove_CNterm_mods, double precursor_mass_shift, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_specific_losses, bool enable_unspecific_losses, bool remove_unannotated, int round_decPow=-4) |
| Generate decoys from a TargetedExperiment. More... | |
| std::vector< std::pair< std::string::size_type, std::string > > | find_all_tryptic (std::string sequence) |
| Find all tryptic sites in a sequence. More... | |
| float | AASequenceIdentity (const String &sequence, const String &decoy) |
| Compute relative identity (relative number of matches of amino acids at the same position) between two sequences. More... | |
| bool | has_CNterminal_mods (const OpenMS::TargetedExperiment::Peptide &peptide) |
| Check if a peptide has C or N terminal modifications. More... | |
| OpenMS::TargetedExperiment::Peptide | shufflePeptide (OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed=-1, int max_attempts=10, bool replace_aa_instead_append=false) |
| Shuffle a peptide (with its modifications) sequence. More... | |
| OpenMS::TargetedExperiment::Peptide | pseudoreversePeptide (OpenMS::TargetedExperiment::Peptide peptide) |
| Pseudo-reverse a peptide sequence (with its modifications) More... | |
| OpenMS::TargetedExperiment::Peptide | reversePeptide (OpenMS::TargetedExperiment::Peptide peptide) |
| Reverse a peptide sequence (with its modifications) More... | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
Additional Inherited Members | |
| Static Protected Member Functions inherited from ProgressLogger | |
| static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Detailed Description
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.
Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.
First, the algorithm goes through all peptides and applies the decoy method to the target peptide sequence (pseudo-reverse, reverse or shuffle) in order to produce the decoy sequence. Then, for each peptide, the fragment ions in the target library are matched to their most likely origin (e.g. the ions are annotated with their ion series (a,b,y) and the fragment number and optionally a neutral loss (10 different neutral losses are currently implemented)). For each fragment ion from the target peptide, an equivalent ion is created for the decoy peptide with the same intensity (e.g. if the target peptide sequence has a b5 ion with a normalized intensity of 200, an equivalent b5 ion for the decoy sequence is created and assigned the intensity 200). Optionally, the m/z values are corrected to reflect the theoretical value rather than the experimental value in the library.
Member Typedef Documentation
◆ PeptideTransitionMapType
| typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType |
◆ PeptideVectorType
| typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType |
◆ ProteinVectorType
| typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType |
◆ TransitionVectorType
| typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType |
Constructor & Destructor Documentation
◆ MRMDecoy()
|
inline |
Member Function Documentation
◆ AASequenceIdentity()
Compute relative identity (relative number of matches of amino acids at the same position) between two sequences.
◆ find_all_tryptic()
| std::vector<std::pair<std::string::size_type, std::string> > find_all_tryptic | ( | std::string | sequence | ) |
Find all tryptic sites in a sequence.
◆ generateDecoys()
| void generateDecoys | ( | OpenMS::TargetedExperiment & | exp, |
| OpenMS::TargetedExperiment & | dec, | ||
| String | method, | ||
| String | decoy_tag, | ||
| double | identity_threshold, | ||
| int | max_attempts, | ||
| double | mz_threshold, | ||
| double | mz_shift, | ||
| bool | exclude_similar, | ||
| double | similarity_threshold, | ||
| bool | remove_CNterm_mods, | ||
| double | precursor_mass_shift, | ||
| std::vector< String > | fragment_types, | ||
| std::vector< size_t > | fragment_charges, | ||
| bool | enable_specific_losses, | ||
| bool | enable_unspecific_losses, | ||
| bool | remove_unannotated, | ||
| int | round_decPow = -4 |
||
| ) |
Generate decoys from a TargetedExperiment.
Will generate decoy peptides for each target peptide provided in exp and write them into the decoy experiment.
Valid methods: shuffle, reverse, pseudo-reverse
If theoretical is true, the target transitions will be returned but their masses will be adjusted to match the theoretical value of the fragment ion that is the most likely explanation for the product.
mz_threshold is used for the matching of theoretical ion series to the observed one
◆ has_CNterminal_mods()
| bool has_CNterminal_mods | ( | const OpenMS::TargetedExperiment::Peptide & | peptide | ) |
Check if a peptide has C or N terminal modifications.
◆ pseudoreversePeptide()
| OpenMS::TargetedExperiment::Peptide pseudoreversePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide | ) |
Pseudo-reverse a peptide sequence (with its modifications)
Pseudo reverses a peptide sequence, leaving the last AA constant
◆ reversePeptide()
| OpenMS::TargetedExperiment::Peptide reversePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide | ) |
Reverse a peptide sequence (with its modifications)
◆ shufflePeptide()
| OpenMS::TargetedExperiment::Peptide shufflePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide, |
| double | identity_threshold, | ||
| int | seed = -1, |
||
| int | max_attempts = 10, |
||
| bool | replace_aa_instead_append = false |
||
| ) |
Shuffle a peptide (with its modifications) sequence.
This function will shuffle the given peptide sequences and its modifications such that the resulting relative sequence identity is below identity_threshold.