 |
OpenMS
|
Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMIonSeries.h>
Public Types | |
| typedef std::unordered_map< String, double > | IonSeries |
| An MRM ion series which maps: "ion_type" -> "fragment m/z". More... | |
Public Member Functions | |
| MRMIonSeries () | |
| Constructor. More... | |
| ~MRMIonSeries () | |
| Destructor. More... | |
| std::pair< String, double > | getIon (IonSeries &ionseries, const String &ionid) |
| Selects ion from IonSeries according to annotation string. More... | |
| std::pair< String, double > | annotateIon (const IonSeries &ionseries, const double product_mz, const double mz_threshold) |
| Selects ion from IonSeries according to product m/z. More... | |
| void | annotateTransitionCV (ReactionMonitoringTransition &tr, const String &annotation) |
| Annotates transition with CV terms. More... | |
| void | annotateTransition (ReactionMonitoringTransition &tr, const TargetedExperiment::Peptide &peptide, const double precursor_mz_threshold, const double product_mz_threshold, const bool enable_reannotation, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) |
| Annotates transition. More... | |
| IonSeries | getIonSeries (const AASequence &sequence, size_t precursor_charge, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) |
| Computed theoretical fragment ion series. More... | |
Private Member Functions | |
| TargetedExperiment::Interpretation | annotationToCVTermList_ (const 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 uses internally an annotation format that is compatible with SpectraST, which is derived from Roepstoff and Fohlman (1984, PMID: 6525415). An annotation tag starts with ion type (a, b, c, x, y, z) followed by the ordinal (number of amino acids). The caret symbol follows "^" with a positive integer indicating the fragment ion charge. If no caret symbol is present, a charge of 1 is assumed. In case of neutral loss, a negative symbol "-" followed by the integer mass (e.g. 17 for ammonia) OR the molecular composition, compatible with EmpiricalFormula (e.g. N1H3 for ammonia) is allowed.
Valid examples: y3, y3^1, y3^1-18, y3^1-H2O, y3-H2O
Limitations: Special SpectraST multi-assignments, immonium, precursors are not supported.
An MRM ion series which maps: "ion_type" -> "fragment m/z".
| MRMIonSeries | ( | ) |
Constructor.
| ~MRMIonSeries | ( | ) |
Destructor.
| std::pair<String, double> annotateIon | ( | const IonSeries & | ionseries, |
| const double | product_mz, | ||
| const double | mz_threshold | ||
| ) |
Selects ion from IonSeries according to product m/z.
| ionseries | the IonSeries from which to choose |
| product_mz | the product m/z of the queried fragment ion |
| mz_threshold | the m/z threshold for annotation of the fragment ion |
| void annotateTransition | ( | ReactionMonitoringTransition & | tr, |
| const TargetedExperiment::Peptide & | peptide, | ||
| const double | precursor_mz_threshold, | ||
| const double | product_mz_threshold, | ||
| const bool | enable_reannotation, | ||
| const std::vector< String > & | fragment_types, | ||
| const std::vector< size_t > & | fragment_charges, | ||
| const bool | enable_specific_losses, | ||
| const bool | enable_unspecific_losses, | ||
| const int | round_decPow = -4 |
||
| ) |
Annotates transition.
| tr | the transition to annotate |
| peptide | the corresponding peptide |
| precursor_mz_threshold | the m/z threshold for annotation of the precursor ion |
| product_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_specific_losses | whether specific neutral losses should be considered |
| enable_unspecific_losses | whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered |
| round_decPow | round precursor and product m/z values to decimal power (default: -4) |
| void annotateTransitionCV | ( | ReactionMonitoringTransition & | tr, |
| const String & | annotation | ||
| ) |
Annotates transition with CV terms.
| tr | the transition to annotate |
| annotation | the fragment ion annotation. |
|
private |
|
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 |
| IonSeries getIonSeries | ( | const AASequence & | sequence, |
| size_t | precursor_charge, | ||
| const std::vector< String > & | fragment_types, | ||
| const std::vector< size_t > & | fragment_charges, | ||
| const bool | enable_specific_losses, | ||
| const bool | enable_unspecific_losses, | ||
| const 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_specific_losses | whether specific neutral losses should be considered |
| enable_unspecific_losses | whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered |
| round_decPow | round product m/z values to decimal power (default: -4) |
1.9.1 
