This class can select appropriate fragment ions of an MS/MS spectrum of a peptide. More...
#include <OpenMS/ANALYSIS/MRM/MRMFragmentSelection.h>
Public Member Functions | |
| MRMFragmentSelection & | operator= (const MRMFragmentSelection &rhs) |
| assignment operator | |
| void | selectFragments (std::vector< RichPeak1D > &selected_peaks, const RichPeakSpectrum &spec) |
| selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks | |
Constructors and destructors | |
| MRMFragmentSelection () | |
| default constructor | |
| MRMFragmentSelection (const MRMFragmentSelection &rhs) | |
| copy constructor | |
| virtual | ~MRMFragmentSelection () |
| destructor | |
Protected Member Functions | |
| bool | peakselectionIsAllowed_ (const RichPeak1D &peak) |
| returns true if the selection of peak is allowed, according to the parameters set | |
Detailed Description
This class can select appropriate fragment ions of an MS/MS spectrum of a peptide.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| num_top_peaks | int | 4 | Number of most intense peak to pick | |
| min_pos_precursor_percentage | float | 80 | Minimal ion position the ion should have, relative to the precursor position | |
| min_mz | float | 400 | Minimal m/z value that is allowed for selection. | |
| max_mz | float | 1200 | Maximal m/z value that is allowed for selection. | |
| consider_names | string | true | true, false | Should names be considered when selecting ions? |
| allow_loss_ions | string | false | true, false | Should loss ions allowed to be selected? |
| allowed_ion_types | string list | [y] | The one-character-typenames of the ion types allowed | |
| allowed_charges | string list | [1] | List of allowed charge states for selection. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Several user choices can influence the selection of the ions from the MS/MS spectrum. These choices can be done using the parameters as described on the parameters page (see below). Basically there are two different ways of selecting suitable ions. One, using standardized names, e.g. given in the meta value "IonName" of each peaks of the spectrum (this can be written from TheoreticalSpectrumGenerator, PILISModel...). The second one is simply using the most abundant peaks in a specified m/z range.
Constructor & Destructor Documentation
default constructor
| MRMFragmentSelection | ( | const MRMFragmentSelection & | rhs | ) |
copy constructor
| virtual ~MRMFragmentSelection | ( | ) | [virtual] |
destructor
Member Function Documentation
| MRMFragmentSelection& operator= | ( | const MRMFragmentSelection & | rhs | ) |
assignment operator
| bool peakselectionIsAllowed_ | ( | const RichPeak1D & | peak | ) | [protected] |
returns true if the selection of peak is allowed, according to the parameters set
| void selectFragments | ( | std::vector< RichPeak1D > & | selected_peaks, | |
| const RichPeakSpectrum & | spec | |||
| ) |
selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |