| OpenMS 2.5.0

Public Member Functions | List of all members
MassTraceDetection Class Reference

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More...

`#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>`

Inheritance diagram for MassTraceDetection:

## Public Member Functions

| MassTraceDetection ()
| Default constructor. More...
| ~MassTraceDetection () override
| Default destructor. More...
Helper methods
void | updateIterativeWeightedMeanMZ (const double &, const double &, double &, double &, double &)
| Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z. More...
Main computation methods
void | run (const PeakMap &, std::vector< MassTrace > &, const Size max_traces=0)
| Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container. More...
void | run (PeakMap::ConstAreaIterator &begin, PeakMap::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
| Invokes the run method (see above) on merely a subregion of a MSExperiment map. 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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. More...
void | setLogType (LogType type) const
| Sets the progress log that should be used. The default type is NONE! More...
LogType | getLogType () const
| Returns the type of progress log being used. More...
void | startProgress (SignedSize begin, SignedSize end, const String &label) const
| Initializes the progress display. More...
void | setProgress (SignedSize value) const
| Sets the current progress. More...
void | endProgress () const
| Ends the progress display. More...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Private methods and members

typedef std::multimap< double, std::pair< Size, Size > > | MapIdxSortedByInt
double | mass_error_ppm_
double | noise_threshold_int_
double | chrom_peak_snr_
MassTrace::MT_QUANTMETHOD | quant_method_
String | trace_termination_criterion_
Size | trace_termination_outliers_
double | min_sample_rate_
double | min_trace_length_
double | max_trace_length_
bool | reestimate_mt_sd_
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | run_ (const MapIdxSortedByInt &chrom_apices, const Size peak_count, const PeakMap &work_exp, const std::vector< Size > &spec_offsets, std::vector< MassTrace > &found_masstraces, const Size max_traces=0)
| The internal run method. More...

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. 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< 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...
Protected Attributes inherited from ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.

Peaks of a MSExperiment are sorted by their intensity and stored in a list of potential chromatographic apex positions. Only peaks that are above the noise threshold (user-defined) are analyzed and only peaks that are n times above this minimal threshold are considered as apices. This saves computational resources and decreases the noise in the resulting output.

Starting with these, mass traces are extended in- and decreasingly in retention time. During this extension phase, the centroid m/z is computed on-line as an intensity-weighted mean of peaks.

The extension phase ends when either the frequency of gathered peaks drops below a threshold (min_sample_rate, see MassTraceDetection parameters) or when the number of missed scans exceeds a threshold (trace_termination_outliers, see MassTraceDetection parameters).

Finally, only mass traces that pass a filter (a certain minimal and maximal length as well as having the minimal sample rate criterion fulfilled) get added to the result.

## Member Typedef Documentation

## ◆ MapIdxSortedByInt

typedef std::multimap<double, std::pair<Size, Size> > MapIdxSortedByInt

private

## Constructor & Destructor Documentation

## ◆ MassTraceDetection()

MassTraceDetection | ( |  | ) |

Default constructor.

## ◆ ~MassTraceDetection()

~MassTraceDetection | ( |  | ) |

override

Default destructor.

## Member Function Documentation

## ◆ run() [1/2]

void run | ( | const PeakMap & | ,
|  | std::vector< MassTrace > & | ,
|  | const Size | max_traces = `0`
| ) |  |

Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.

Referenced by UTILProteomicsLFQ::estimateMedianChromatographicFWHM_().

## ◆ run() [2/2]

void run | ( | PeakMap::ConstAreaIterator & | begin,
|  | PeakMap::ConstAreaIterator & | end,
|  | std::vector< MassTrace > & | found_masstraces
| ) |  |

Invokes the run method (see above) on merely a subregion of a MSExperiment map.

## ◆ run_()

void run_ | ( | const MapIdxSortedByInt & | chrom_apices,
|  | const Size | peak_count,
|  | const PeakMap & | work_exp,
|  | const std::vector< Size > & | spec_offsets,
|  | std::vector< MassTrace > & | found_masstraces,
|  | const Size | max_traces = `0`
| ) |  |

private

The internal run method.

## ◆ updateIterativeWeightedMeanMZ()

void updateIterativeWeightedMeanMZ | ( | const double & | ,
|  | const double & | ,
|  | double & | ,
|  | double & | ,
|  | double & |
| ) |  |

Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ chrom_peak_snr_

double chrom_peak_snr_

private

## ◆ mass_error_ppm_

double mass_error_ppm_

private

## ◆ max_trace_length_

double max_trace_length_

private

## ◆ min_sample_rate_

double min_sample_rate_

private

## ◆ min_trace_length_

double min_trace_length_

private

## ◆ noise_threshold_int_

double noise_threshold_int_

private

## ◆ quant_method_

MassTrace::MT_QUANTMETHOD quant_method_

private

## ◆ reestimate_mt_sd_

bool reestimate_mt_sd_

private

## ◆ trace_termination_criterion_

String trace_termination_criterion_

private

## ◆ trace_termination_outliers_

Size trace_termination_outliers_

private