A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.
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| MassTraceDetection () |
| Default constructor. More...
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| ~MassTraceDetection () override |
| Default destructor. More...
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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...
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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...
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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...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More...
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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.