| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
MRMFragmentSelection Class Reference

This class can select appropriate fragment ions of an MS/MS spectrum of a peptide. More...

`#include <OpenMS/ANALYSIS/MRM/MRMFragmentSelection.h>`

Inheritance diagram for MRMFragmentSelection:

## Public Member Functions

MRMFragmentSelection & | operator= (const MRMFragmentSelection &rhs)
| assignment operator More...
void | selectFragments (std::vector< Peak1D > &selected_peaks, const PeakSpectrum &spec)
| selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks More...
Constructors and destructors
| MRMFragmentSelection ()
| default constructor More...
| MRMFragmentSelection (const MRMFragmentSelection &rhs)
| copy constructor More...
| ~MRMFragmentSelection () override
| destructor More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Protected Member Functions

bool | peakselectionIsAllowed_ (const String &name, const int charge)
| returns true if the selection of peak is allowed, according to the parameters set and the ion name More...
Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Additional Inherited Members

Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## 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 | 80.0 |  | Minimal ion position the ion should have, relative to the precursor position
min_mz | float | 400.0 |  | Minimal m/z value that is allowed for selection.
max_mz | float | 1200.0 |  | 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

## ◆ MRMFragmentSelection() [1/2]

MRMFragmentSelection | ( |  | ) |

default constructor

## ◆ MRMFragmentSelection() [2/2]

MRMFragmentSelection | ( | const MRMFragmentSelection & | rhs | ) |

copy constructor

## ◆ ~MRMFragmentSelection()

~MRMFragmentSelection | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ operator=()

MRMFragmentSelection& operator= | ( | const MRMFragmentSelection & | rhs | ) |

assignment operator

## ◆ peakselectionIsAllowed_()

bool peakselectionIsAllowed_ | ( | const String & | name,
|  | const int | charge
| ) |  |

protected

returns true if the selection of peak is allowed, according to the parameters set and the ion name

## ◆ selectFragments()

void selectFragments | ( | std::vector< Peak1D > & | selected_peaks,
|  | const PeakSpectrum & | spec
| ) |  |

selects accordingly to the parameters the best peaks of spec and writes them into selected_peaks