Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
Public Types | |
typedef boost::unordered_map< String, double > | IonSeries |
Public Member Functions | |
std::pair< String, double > | getIon (IonSeries ionseries, String ionid) |
Selects ion from IonSeries according to annotation string. More... | |
std::pair< String, double > | annotateIon (IonSeries ionseries, double ProductMZ, double mz_threshold) |
Selects ion from IonSeries according to product m/z. More... | |
void | annotateTransitionCV (ReactionMonitoringTransition &tr, String annotation) |
Annotates transition with CV terms. More... | |
void | annotateTransition (ReactionMonitoringTransition &tr, const TargetedExperiment::Peptide peptide, const double mz_threshold, bool enable_reannotation, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4) |
Annotates transition. More... | |
IonSeries | getIonSeries (AASequence sequence, size_t precursor_charge, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4) |
Computed theoretical fragment ion series. More... | |
MRMIonSeries () | |
Constructor. More... | |
~MRMIonSeries () | |
Destructor. More... | |
Private Member Functions | |
CVTermList | annotationToCVTermList_ (String annotation) |
void | annotationToCV_ (ReactionMonitoringTransition &tr) |
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.
Will generate theoretical fragment ionseries based on AASequence and parameters. Neutral losses are supported according to a model similar to the one in SpectraST. ReactionMonitoringTransition objects can be annotated with the corresponding CV terms.
MRMIonSeries | ( | ) |
Constructor.
~MRMIonSeries | ( | ) |
Destructor.
std::pair<String, double> annotateIon | ( | IonSeries | ionseries, |
double | ProductMZ, | ||
double | mz_threshold | ||
) |
Selects ion from IonSeries according to product m/z.
ionseries | the IonSeries from which to choose |
ProductMz | the product m/z of the queried fragment ion |
mz_threshold | the m/z threshold for annotation of the fragment ion std::pair<String, double> the annotation and product m/z of the queried fragment ion |
void annotateTransition | ( | ReactionMonitoringTransition & | tr, |
const TargetedExperiment::Peptide | peptide, | ||
const double | mz_threshold, | ||
bool | enable_reannotation, | ||
std::vector< String > | fragment_types, | ||
std::vector< size_t > | fragment_charges, | ||
bool | enable_losses, | ||
int | round_decPow = -4 |
||
) |
Annotates transition.
tr | the transition to annotate |
peptide | the corresponding peptide |
mz_threshold | the m/z threshold for annotation of the fragment ion |
enable_reannotation | whether the original (e.g. SpectraST) annotation should be used or reannotation should be conducted |
fragment_types | the fragment ion types for reannotation |
fragment_charges | the fragment ion charges for reannotation |
enable_losses | whether neutral losses should be considered |
round_decPow | round product m/z values to decimal power (default: -4) |
void annotateTransitionCV | ( | ReactionMonitoringTransition & | tr, |
String | annotation | ||
) |
Annotates transition with CV terms.
tr | the transition to annotate |
annotation | the fragment ion annotation. |
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private |
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private |
Selects ion from IonSeries according to annotation string.
ionseries | the IonSeries from which to choose |
ionid | the annotation string of the query fragment ion std::pair<String, double> the annotation and product m/z of the queried fragment ion |
IonSeries getIonSeries | ( | AASequence | sequence, |
size_t | precursor_charge, | ||
std::vector< String > | fragment_types, | ||
std::vector< size_t > | fragment_charges, | ||
bool | enable_losses, | ||
int | round_decPow = -4 |
||
) |
Computed theoretical fragment ion series.
sequence | the peptide amino acid sequence |
precursor_charge | the charge of the peptide precursor |
fragment_types | the fragment ion types for reannotation |
fragment_charges | the fragment ion charges for reannotation |
enable_losses | whether neutral losses should be considered |
round_decPow | round product m/z values to decimal power (default: -4) IonSeries the theoretical fragment ion series |
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |