CalibrationWorkflow.h File Reference

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/APPLICATIONS/OpenSwathBase.h>

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Classes
class	CalibrationWorkflow
	Orchestrates calibration workflows for OpenSWATH analysis. More...
struct	CalibrationWorkflow::CalibrationResult
	Results from calibration workflow. More...
struct	CalibrationWorkflow::IrtExperiments
	Prepared iRT experiments ready for calibration. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Enumerations
enum class	IrtStrategy {   NULL_TRANSFORMATION , STATIC_FILES , SAMPLE_ONCE , SAMPLE_PER_RUN ,   RUN_SPECIFIC }
	Strategy for obtaining iRT (indexed Retention Time) calibrant peptides across multiple runs. More...

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Class Documentation

OpenMS::CalibrationWorkflow::CalibrationResult

struct OpenMS::CalibrationWorkflow::CalibrationResult

Results from calibration workflow.

Collaboration diagram for CalibrationWorkflow::CalibrationResult:

Class Members
double	estimated_rt_window {-1.0}	Estimated RT extraction window (full width, seconds)
TransformationDescription	im_trafo	Ion mobility transformation (fitted). May be empty if no IM calibration performed.
double	ms1_im_window {-1.0}	MS1 ion mobility extraction window (full width). -1 if not applicable.
double	ms1_mz_window_ppm {-1.0}	MS1 m/z extraction window (full width, ppm). -1 if not computed.
double	ms2_im_window {-1.0}	MS2 ion mobility extraction window (full width). -1 if not applicable.
double	ms2_mz_window_ppm {-1.0}	MS2 m/z extraction window (full width, ppm). -1 if not computed.
TransformationDescription	rt_trafo	RT normalization transformation (fitted)

OpenMS::CalibrationWorkflow::IrtExperiments

struct OpenMS::CalibrationWorkflow::IrtExperiments

Prepared iRT experiments ready for calibration.

Collaboration diagram for CalibrationWorkflow::IrtExperiments:

Class Members
bool	is_prepared {false}	Whether experiments are available and ready for calibration.
LightTargetedExperiment	linear_irt	Linear iRT experiment (always required for calibration)
LightTargetedExperiment	nonlinear_irt	Nonlinear iRT experiment (optional, empty if not used)
IrtStrategy	strategy {IrtStrategy::STATIC_FILES}	Strategy used to prepare these experiments.