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 boost::unordered_map< String, boost::unordered_map< String, double > > | IonSeries |
typedef boost::unordered_map< String, IonSeries > | IonSeriesMapType |
typedef std::map< String, std::vector< const ReactionMonitoringTransition * > > | PeptideTransitionMapType |
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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, bool theoretical, double mz_shift, bool exclude_similar, double similarity_threshold, bool remove_CNterm_mods, double precursor_mass_shift, bool enable_losses, bool remove_unannotated) |
Generate decoys from a TargetedExperiment. More... | |
void | restrictTransitions (OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions) |
Remove transitions s.t. all peptides have a defined set of transitions. More... | |
std::pair< String, double > | getDecoyIon (String ionid, boost::unordered_map< String, boost::unordered_map< String, double > > &decoy_ionseries) |
Selects a decoy ion from a set of ions. More... | |
std::pair< String, double > | getTargetIon (double ProductMZ, double mz_threshold, boost::unordered_map< String, boost::unordered_map< String, double > > target_ionseries, bool enable_losses) |
Selects a target ion from a set of ions. More... | |
boost::unordered_map< String, boost::unordered_map< String, double > > | getIonSeries (AASequence sequence, int precursor_charge) |
Generate all ion series for an input AASequence. 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... | |
void | correctMasses (OpenMS::TargetedExperiment &exp, double mz_threshold, bool enable_losses) |
Correct the masses according to theoretically computed masses. More... | |
OpenMS::TargetedExperiment::Peptide | shufflePeptide (OpenMS::TargetedExperiment::Peptide peptide, double identity_threshold, int seed=-1, int max_attempts=10) |
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... | |
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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 | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
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.
typedef boost::unordered_map<String, IonSeries> IonSeriesMapType |
typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType |
typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType |
typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType |
typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType |
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inline |
Compute relative identity (relative number of matches of amino acids at the same position) between two sequences.
void correctMasses | ( | OpenMS::TargetedExperiment & | exp, |
double | mz_threshold, | ||
bool | enable_losses | ||
) |
Correct the masses according to theoretically computed masses.
std::vector<std::pair<std::string::size_type, std::string> > find_all_tryptic | ( | std::string | sequence | ) |
Find all tryptic sites in a sequence.
void generateDecoys | ( | OpenMS::TargetedExperiment & | exp, |
OpenMS::TargetedExperiment & | dec, | ||
String | method, | ||
String | decoy_tag, | ||
double | identity_threshold, | ||
int | max_attempts, | ||
double | mz_threshold, | ||
bool | theoretical, | ||
double | mz_shift, | ||
bool | exclude_similar, | ||
double | similarity_threshold, | ||
bool | remove_CNterm_mods, | ||
double | precursor_mass_shift, | ||
bool | enable_losses, | ||
bool | remove_unannotated | ||
) |
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
std::pair<String, double> getDecoyIon | ( | String | ionid, |
boost::unordered_map< String, boost::unordered_map< String, double > > & | decoy_ionseries | ||
) |
Selects a decoy ion from a set of ions.
boost::unordered_map<String, boost::unordered_map<String, double> > getIonSeries | ( | AASequence | sequence, |
int | precursor_charge | ||
) |
Generate all ion series for an input AASequence.
Currently generated are:
bionseries, bionseries_loss, yionseries, yionseries_loss, aionseries
for each of these, the following neutral losses are calculated: -17, -18, -34, -35, -36, -44, -45, -46, -64, -98.
FEATURE (george): a more generic mechanism to specify which series and losses should be generated. possible integration with TheoreticalSpectrumGenerator?
std::pair<String, double> getTargetIon | ( | double | ProductMZ, |
double | mz_threshold, | ||
boost::unordered_map< String, boost::unordered_map< String, double > > | target_ionseries, | ||
bool | enable_losses | ||
) |
Selects a target ion from a set of ions.
bool has_CNterminal_mods | ( | const OpenMS::TargetedExperiment::Peptide & | peptide | ) |
Check if a peptide has C or N terminal modifications.
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
void restrictTransitions | ( | OpenMS::TargetedExperiment & | exp, |
int | min_transitions, | ||
int | max_transitions | ||
) |
Remove transitions s.t. all peptides have a defined set of transitions.
All transitions of a peptide above max_transitions get deleted, all peptides with less than min_transitions also get deleted.
OpenMS::TargetedExperiment::Peptide reversePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide | ) |
Reverse a peptide sequence (with its modifications)
OpenMS::TargetedExperiment::Peptide shufflePeptide | ( | OpenMS::TargetedExperiment::Peptide | peptide, |
double | identity_threshold, | ||
int | seed = -1 , |
||
int | max_attempts = 10 |
||
) |
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.
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:37 using doxygen 1.8.9.1 |