Classes for targeted quantitation workflows using MRM/SRM and SWATH/DIA data. More...

Collaboration diagram for Targeted Quantitation (MRM/SRM):

Classes
class	MRMBatchFeatureSelector
	Batch processing wrapper for MRMFeatureSelector. More...

class	MRMFeatureFilter
	The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria. More...

class	MRMFeatureQC
	The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter. More...

class	MRMFeatureSelector
	A base class for selection of MRM Features through Linear Programming optimization. More...

class	PeakIntegrator
	Compute the area, background and shape metrics of a peak. More...

class	TargetedSpectraExtractor
	This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on a target list. More...

class	AbsoluteQuantitation
	AbsoluteQuantitation is a class to support absolute or relative quantitation for targeted or untargeted quantitation workflows (e.g., Isotope Dilution Mass Spectrometry). More...

class	AbsoluteQuantitationMethod
	AbsoluteQuantitationMethod is a class to hold information about the quantitation method and for applying and/or generating the quantitation method. More...

class	EmgGradientDescent
	Fit peaks to an Exponentially Modified Gaussian (EMG) model using gradient descent. More...

Detailed Description

Classes for targeted quantitation workflows using MRM/SRM and SWATH/DIA data.

This module provides a comprehensive set of algorithms for processing targeted mass spectrometry data, including Multiple Reaction Monitoring (MRM), Selected Reaction Monitoring (SRM), and SWATH/DIA acquisitions. These classes form the computational foundation used by tools like SmartPeaks for automated metabolomics and fluxomics data processing.

Workflow Overview

The typical targeted quantitation workflow proceeds through these stages:

Core Components

Peak Detection and Integration

MRMTransitionGroupPicker - Consensus peak picking across multiple chromatograms
PeakIntegrator - Peak area calculation with multiple integration methods (trapezoid, Simpson's rule)
EmgGradientDescent - Exponentially Modified Gaussian peak fitting for saturated/cutoff peaks

Quality Control

MRMFeatureQC - Data structure for QC criteria at component, component group, and pair levels
MRMFeatureFilter - Filters features based on QC criteria, RSD, and background interference
MRMFeatureQCFile - File I/O for QC parameters

Feature Selection (Linear Programming)

MRMFeatureSelector - Base class for LP-based feature selection
MRMFeatureSelectorQMIP - Quadratic Mixed Integer Programming selector
MRMFeatureSelectorScore - Score-weighted linear programming selector
MRMBatchFeatureSelector - Iterative batch processing

Absolute Quantitation

AbsoluteQuantitation - Calibration curve fitting and concentration calculation
AbsoluteQuantitationMethod - Method parameters (LOD, LOQ, transformation model)
AbsoluteQuantitationStandards - Standard concentration management

Spectrum Extraction

TargetedSpectraExtractor - Extract and score spectra from DDA experiments

References

These algorithms are described in:

McCloskey D, et al. "SmartPeaks: An Open Source Tool for Automated Processing of LC-MS Metabolomics and Fluxomics Data" (2020)

See also: MRMTransitionGroupPicker; OpenSwathWorkflow