Generate assays from a TargetedExperiment. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMAssay.h>
Public Types | |
typedef std::vector< OpenMS::TargetedExperiment::Protein > | ProteinVectorType |
typedef std::vector< OpenMS::TargetedExperiment::Peptide > | PeptideVectorType |
typedef std::vector< OpenMS::ReactionMonitoringTransition > | TransitionVectorType |
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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... | |
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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... | |
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::AASequence > | combineModifications_ (OpenMS::AASequence sequence) |
Generate alternative modified peptide forms according to ModificationsDB. More... | |
std::vector< OpenMS::AASequence > | addModificationsSequences_ (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 | |
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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_ |
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.
typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType |
typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType |
typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType |
MRMAssay | ( | ) |
Constructor.
~MRMAssay | ( | ) |
Destructor.
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protected |
Adds ResidueModification to vector of modifications.
mods | a vector of targeted experiment modifications |
location | the residue location of the modification |
rmod | the residue modification |
name | the name of the residue modification |
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protected |
Generate alternative modified peptide forms according to ModificationsDB.
sequence | template AASequence |
a vector of all alternative modified peptides.
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protected |
Generate alternative modified peptide forms according to ModificationsDB.
sequence | template AASequence |
a vector of all alternative modified peptides.
void detectingTransitions | ( | OpenMS::TargetedExperiment & | exp, |
int | min_transitions, | ||
int | max_transitions | ||
) |
Select detecting fragment ions.
exp | the input, unfiltered transitions |
min_transitions | the minimum number of transitions required per assay |
max_transitions | the maximum number of transitions required per assay |
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protected |
Get swath index (precursor isolation window ordinal) for a particular precursor.
swathes | the swath window settings |
precursor_mz | the 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.
exp | the input, unfiltered transitions |
fragment_types | the fragment types to consider for annotation |
fragment_charges | the fragment charges to consider for annotation |
enable_losses | whether neutral losses for the fragment ion (according to SpectraST) should be enabled |
round_decPow | round product m/z values to decimal power (default: -4) |
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protected |
Check whether the product m/z of a transition falls into the precursor isolation window.
swathes | the swath window settings |
precursor_mz | the query precursor m/z |
precursor_mz | the query product m/z |
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protected |
Annotate fragment ions with site-specific attributes.
sequence | the corresponding AASequence including modifications |
tr | a reference to the query transition |
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protected |
Check whether fragment ion are unique ion signatures in vector within threshold.
fragment_ion | the queried fragment ion |
ions | a vector of fragment ions which could interfere with fragment_ion |
mz_threshold | the threshold within which to search for interferences |
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protected |
Computes all N choose K combinations.
n | vector of N indices |
k | number 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.
exp | the input, unfiltered transitions |
mz_threshold | the product m/z threshold in Th for annotation |
fragment_types | the fragment types to consider for annotation |
fragment_charges | the fragment charges to consider for annotation |
enable_alternative_localizations | whether to trust the site-localizations of the transitions or whether alternative options should be generated |
enable_reannotation | whether the original annotation should be taken or reannotation should be conducted |
enable_losses | whether neutral losses for the fragment ion (according to SpectraST) should be enabled |
round_decPow | round 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.
exp | the input, unfiltered transitions |
lower_mz_limit | the lower product m/z limit in Th |
upper_mz_limit | the upper product m/z limit in Th |
swathes | the 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.
exp | the input, unfiltered transitions |
mz_threshold | the product m/z threshold in Th for annotation |
fragment_types | the fragment types to consider for annotation |
fragment_charges | the fragment charges to consider for annotation |
enable_losses | whether neutral losses for the fragment ion (according to SpectraST) should be enabled |
enable_uis_scoring | whether UIS transitions should be annotated |
enable_site_scoring | whether site-specific transitions should be annotated |
mz_threshold | the product m/z threshold in Th for annotation |
swathes | the swath window settings (to exclude fragment ions falling |
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |