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MRMAssay Class Reference

Generate assays from a TargetedExperiment. More...

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

Inheritance diagram for MRMAssay:
ProgressLogger

Public Types

typedef std::vector< OpenMS::TargetedExperiment::ProteinProteinVectorType
 
typedef std::vector< OpenMS::TargetedExperiment::PeptidePeptideVectorType
 
typedef std::vector< OpenMS::ReactionMonitoringTransitionTransitionVectorType
 
- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 

Public Member Functions

void reannotateTransitions (OpenMS::TargetedExperiment &exp, double mz_threshold, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_alternative_localizations, bool enable_reannotation, bool enable_losses, int round_decPow=-4)
 Annotates and filters transitions in a TargetedExperiment. More...
 
void restrictTransitions (OpenMS::TargetedExperiment &exp, double lower_mz_limit, double upper_mz_limit, std::vector< std::pair< double, double > > swathes)
 Restrict and filter transitions in a TargetedExperiment. More...
 
void detectingTransitions (OpenMS::TargetedExperiment &exp, int min_transitions, int max_transitions)
 Select detecting fragment ions. More...
 
void uisTransitions (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, bool enable_uis_scoring, bool enable_site_scoring, double mz_threshold, std::vector< std::pair< double, double > > swathes)
 Annotate UIS / site-specific transitions. More...
 
void insilicoTransitions (OpenMS::TargetedExperiment &exp, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4)
 Generates in silico transitions. More...
 
 MRMAssay ()
 Constructor. More...
 
 ~MRMAssay ()
 Destructor. 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...
 

Protected Member Functions

bool isUIS_ (const double fragment_ion, std::vector< double > ions, const double mz_threshold)
 Check whether fragment ion are unique ion signatures in vector within threshold. More...
 
void isSiteUIS_ (const AASequence sequence, ReactionMonitoringTransition &tr)
 Annotate fragment ions with site-specific attributes. More...
 
int getSwath_ (const std::vector< std::pair< double, double > > swathes, const double precursor_mz)
 Get swath index (precursor isolation window ordinal) for a particular precursor. More...
 
bool isInSwath_ (const std::vector< std::pair< double, double > > swathes, const double precursor_mz, const double product_mz)
 Check whether the product m/z of a transition falls into the precursor isolation window. More...
 
std::vector< std::vector< size_t > > nchoosekcombinations_ (std::vector< size_t > n, size_t k)
 Computes all N choose K combinations. More...
 
std::vector< OpenMS::AASequencecombineModifications_ (OpenMS::AASequence sequence)
 Generate alternative modified peptide forms according to ModificationsDB. More...
 
std::vector< OpenMS::AASequenceaddModificationsSequences_ (std::vector< OpenMS::AASequence > sequences, std::vector< std::vector< size_t > > mods_combs, OpenMS::String modification)
 Generate alternative modified peptide forms according to ModificationsDB. More...
 
void addModification_ (std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, ResidueModification &rmod, const String &name)
 Adds ResidueModification to vector of modifications. 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

Generate assays from a TargetedExperiment.

Will generate assays from a raw, unfiltered TargetedExperiment, as can be generated by ConvertTSVToTraML.

Transitions can be selected according to a set of rules, as described in Schubert et al., 2015 (PMID: 25675208).

In addition, unique ion signature (UIS) (Sherman et al., 2009 (PMID: 19556279)) or site-specific transitions can be generated based on empirically observed or in silico generated ion series.

Member Typedef Documentation

Constructor & Destructor Documentation

MRMAssay ( )

Constructor.

~MRMAssay ( )

Destructor.

Member Function Documentation

void addModification_ ( std::vector< TargetedExperiment::Peptide::Modification > &  mods,
int  location,
ResidueModification rmod,
const String name 
)
protected

Adds ResidueModification to vector of modifications.

Parameters
modsa vector of targeted experiment modifications
locationthe residue location of the modification
rmodthe residue modification
namethe name of the residue modification
std::vector<OpenMS::AASequence> addModificationsSequences_ ( std::vector< OpenMS::AASequence sequences,
std::vector< std::vector< size_t > >  mods_combs,
OpenMS::String  modification 
)
protected

Generate alternative modified peptide forms according to ModificationsDB.

Parameters
sequencetemplate AASequence

a vector of all alternative modified peptides.

std::vector<OpenMS::AASequence> combineModifications_ ( OpenMS::AASequence  sequence)
protected

Generate alternative modified peptide forms according to ModificationsDB.

Parameters
sequencetemplate AASequence

a vector of all alternative modified peptides.

void detectingTransitions ( OpenMS::TargetedExperiment exp,
int  min_transitions,
int  max_transitions 
)

Select detecting fragment ions.

Parameters
expthe input, unfiltered transitions
min_transitionsthe minimum number of transitions required per assay
max_transitionsthe maximum number of transitions required per assay
int getSwath_ ( const std::vector< std::pair< double, double > >  swathes,
const double  precursor_mz 
)
protected

Get swath index (precursor isolation window ordinal) for a particular precursor.

Parameters
swathesthe swath window settings
precursor_mzthe query precursor m/z
void insilicoTransitions ( OpenMS::TargetedExperiment exp,
std::vector< String fragment_types,
std::vector< size_t fragment_charges,
bool  enable_losses,
int  round_decPow = -4 
)

Generates in silico transitions.

Parameters
expthe input, unfiltered transitions
fragment_typesthe fragment types to consider for annotation
fragment_chargesthe fragment charges to consider for annotation
enable_losseswhether neutral losses for the fragment ion (according to SpectraST) should be enabled
round_decPowround product m/z values to decimal power (default: -4)
bool isInSwath_ ( const std::vector< std::pair< double, double > >  swathes,
const double  precursor_mz,
const double  product_mz 
)
protected

Check whether the product m/z of a transition falls into the precursor isolation window.

Parameters
swathesthe swath window settings
precursor_mzthe query precursor m/z
precursor_mzthe query product m/z
void isSiteUIS_ ( const AASequence  sequence,
ReactionMonitoringTransition tr 
)
protected

Annotate fragment ions with site-specific attributes.

Parameters
sequencethe corresponding AASequence including modifications
tra reference to the query transition
bool isUIS_ ( const double  fragment_ion,
std::vector< double ions,
const double  mz_threshold 
)
protected

Check whether fragment ion are unique ion signatures in vector within threshold.

Parameters
fragment_ionthe queried fragment ion
ionsa vector of fragment ions which could interfere with fragment_ion
mz_thresholdthe threshold within which to search for interferences
std::vector<std::vector<size_t> > nchoosekcombinations_ ( std::vector< size_t n,
size_t  k 
)
protected

Computes all N choose K combinations.

Parameters
nvector of N indices
knumber of K

a vector of all N index combinations

void reannotateTransitions ( OpenMS::TargetedExperiment exp,
double  mz_threshold,
std::vector< String fragment_types,
std::vector< size_t fragment_charges,
bool  enable_alternative_localizations,
bool  enable_reannotation,
bool  enable_losses,
int  round_decPow = -4 
)

Annotates and filters transitions in a TargetedExperiment.

Parameters
expthe input, unfiltered transitions
mz_thresholdthe product m/z threshold in Th for annotation
fragment_typesthe fragment types to consider for annotation
fragment_chargesthe fragment charges to consider for annotation
enable_alternative_localizationswhether to trust the site-localizations of the transitions or whether alternative options should be generated
enable_reannotationwhether the original annotation should be taken or reannotation should be conducted
enable_losseswhether neutral losses for the fragment ion (according to SpectraST) should be enabled
round_decPowround product m/z values to decimal power (default: -4)
void restrictTransitions ( OpenMS::TargetedExperiment exp,
double  lower_mz_limit,
double  upper_mz_limit,
std::vector< std::pair< double, double > >  swathes 
)

Restrict and filter transitions in a TargetedExperiment.

Parameters
expthe input, unfiltered transitions
lower_mz_limitthe lower product m/z limit in Th
upper_mz_limitthe upper product m/z limit in Th
swathesthe swath window settings (to exclude fragment ions falling into the precursor isolation window)
void uisTransitions ( OpenMS::TargetedExperiment exp,
std::vector< String fragment_types,
std::vector< size_t fragment_charges,
bool  enable_losses,
bool  enable_uis_scoring,
bool  enable_site_scoring,
double  mz_threshold,
std::vector< std::pair< double, double > >  swathes 
)

Annotate UIS / site-specific transitions.

Parameters
expthe input, unfiltered transitions
mz_thresholdthe product m/z threshold in Th for annotation
fragment_typesthe fragment types to consider for annotation
fragment_chargesthe fragment charges to consider for annotation
enable_losseswhether neutral losses for the fragment ion (according to SpectraST) should be enabled
enable_uis_scoringwhether UIS transitions should be annotated
enable_site_scoringwhether site-specific transitions should be annotated
mz_thresholdthe product m/z threshold in Th for annotation
swathesthe swath window settings (to exclude fragment ions falling

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:03 using doxygen 1.8.9.1