OpenMS
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:
[legend]
Collaboration diagram for MRMFragmentSelection:
[legend]

Constructors and destructors

 MRMFragmentSelection ()
 default constructor More...
 
 MRMFragmentSelection (const MRMFragmentSelection &rhs)
 copy constructor More...
 
 ~MRMFragmentSelection () override
 destructor More...
 
MRMFragmentSelectionoperator= (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...
 
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...
 

Additional Inherited Members

- 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. 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...
 
- 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
num_top_peaks int4  Number of most intense peak to pick
min_pos_precursor_percentage float80.0  Minimal ion position the ion should have, relative to the precursor position
min_mz float400.0  Minimal m/z value that is allowed for selection.
max_mz float1200.0  Maximal m/z value that is allowed for selection.
consider_names stringtrue true, falseShould names be considered when selecting ions?
allow_loss_ions stringfalse true, falseShould 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]

default constructor

◆ MRMFragmentSelection() [2/2]

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