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

Collaboration diagram for Targeted Quantitation (MRM/SRM):

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