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MRMDecoy Class Reference

This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMDecoy.h>

Inheritance diagram for MRMDecoy:
ProgressLogger

Public Types

typedef std::vector< OpenMS::TargetedExperiment::ProteinProteinVectorType
 
typedef std::vector< OpenMS::TargetedExperiment::PeptidePeptideVectorType
 
typedef std::vector< OpenMS::ReactionMonitoringTransitionTransitionVectorType
 
typedef boost::unordered_map< String, boost::unordered_map< String, double > > IonSeries
 
typedef boost::unordered_map< String, IonSeriesIonSeriesMapType
 
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, 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, doublegetDecoyIon (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, doublegetTargetIon (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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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_
 
ProgressLoggerImplcurrent_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

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

Constructor & Destructor Documentation

MRMDecoy ( )
inline

Member Function Documentation

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.

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.

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.

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