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

Collaboration diagram for Targeted Quantitation (MRM/SRM):

Classes
class	ConfidenceScoring
	Confidence scoring for SRM/MRM/PRM features against a targeted assay library. More...

class	DIAScoring
	Scoring of an spectrum at the peak apex of an chromatographic elution peak. More...

class	LevelContextInference
	Shared OpenSwath analysis context inference for peptide, protein, and gene rows. More...

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	MRMFeatureSelectorQMIP
	MRMFeatureSelector implementation that selects MRM features via a quadratic-programming formulation over relative retention time. More...

class	MRMFeatureSelectorScore
	MRMFeatureSelector implementation that selects MRM features via a linear program with score-weighted per-feature variables. More...

struct	OpenSwathExportFilterConfig
	Shared filter configuration for OpenSWATH export readers. More...

struct	OpenSwathResultsExportConfig
	Configuration for user-facing feature results exports. More...

struct	OpenSwathMatrixExportConfig
	Configuration for matrix exports. More...

struct	OpenSwathParquetExportConfig
	Configuration for scored feature Parquet exports. More...

struct	OpenSwathExportRow
	Filtered feature-level row used by results and matrix exports. More...

struct	OpenSwathFeatureScoreRow
	Feature-level scored row for Parquet export. More...

struct	OpenSwathFeatureScoreTable
	Feature-level Parquet export table with dynamically discovered FEATURE_MS1 / FEATURE_MS2 columns. More...

struct	OpenSwathTransitionScoreRow
	Transition-level scored row for optional Parquet export. More...

struct	OpenSwathTransitionScoreTable
	Transition-level Parquet export table with dynamically discovered FEATURE_TRANSITION columns. More...

struct	OpenSwathQuantMatrix
	Dense matrix representation used by matrix exports. More...

class	OpenSwathGeneInference
	OpenSwath gene-level context inference. More...

struct	ErrorEstimationConfig
	Configuration for OpenSwath analyte level inference global and local error estimation. More...

struct	PeptidoformInferenceConfig
	Configuration for peptidoform inference. More...

struct	LevelContextInferenceConfig
	Configuration for peptide-, protein-, and gene-level context inference. More...

struct	IPFPrecursorRow
	Peak-group and precursor evidence for peptidoform inference. More...

struct	IPFPrecursorProbabilityRow
	Precursor-layer posterior error probability used by IPF. More...

struct	IPFTransitionRow
	Transition-layer evidence for peptidoform inference. More...

struct	IPFAlignmentRow
	Alignment-group membership for cross-run IPF signal propagation. More...

struct	IPFResultRow
	Final peptidoform inference result row. More...

struct	LevelContextInputRow
	Compact level-context input row independent of file format. More...

struct	LevelContextResultRow
	Final level-context result row. More...

class	OpenSwathMatrixExporter
	Build and write OpenSWATH quantification matrices. More...

class	OpenSwathParquetExporter
	Write scored OpenSWATH feature and transition tables to Parquet. More...

class	OpenSwathPeptideInference
	OpenSwath peptide-level context inference. More...

class	OpenSwathPeptidoformInference
	OpenSwath inference of peptidoforms (IPF). More...

struct	OpenSwathPeptidoformInference::BayesianModelRow
	Compact Bayesian model row used by the public helper methods. More...

struct	OpenSwathPeptidoformInference::PosteriorRow
	Posterior probability row returned by applyBM. More...

class	OpenSwathProteinInference
	OpenSwath protein-level context inference. More...

class	OpenSwathResultsExporter
	Write filtered OpenSWATH feature results to TSV or Parquet. More...

class	OpenSwathWorkflowScheduler
	Plans memory-bounded OpenSwathWorkflow work waves and exposes a small concurrency-limiter pair. 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	ChromatogramProcessor
	Convenience entry point that runs MRMFeatureFinderScoring on a list of already-extracted chromatograms. More...

class	DefaultChromHandler
	Dispatching chromatogram handler that picks SRM/MRM or DIA at runtime based on the input maps. More...

class	DIAChromHandler
	IChromatogramHandler implementation for DIA / SWATH / PRM / PASEF-DIA acquisitions, where chromatograms are extracted from full-scan MS2 data rather than being directly acquired as SRM/MRM traces. More...

class	TOPPOpenSwathBase
	Shared TOPPBase scaffolding for OpenSWATH-family CLI tools (currently OpenSwathWorkflow). More...

struct	OSWHierarchy
	Hierarchy levels of the OSWData tree. More...

struct	OSWIndexTrace
	Index path into the OSWData tree from the root down to a specific node. More...

struct	OSWTransition
	High-level meta-data of one fragment-ion transition referenced by an OSWPeakGroup. More...

class	OSWPeakGroup
	A peak group (also called feature) is defined on a small RT range (leftWidth to rightWidth) in a group of extracted transitions (chromatograms). More...

class	OSWPeptidePrecursor
	A peptide with a charge state. More...

class	OSWProtein
	A Protein is the highest entity and contains one or more peptides which were found/traced. More...

class	OSWData
	Holds all or partial information from an OSW file. More...

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

Enumerations
enum class	OpenSwathExportFileFormat { TSV , Parquet }
	Output file format for OpenSWATH export tables. More...

enum class	OpenSwathIPFExportMode { Peptidoform , Augmented , Disable }
	IPF handling mode for OpenSWATH exports. More...

enum class	OpenSwathMatrixLevel { Precursor , Peptide , Protein , Gene }
	Quantification matrix level for OpenSWATH matrix exports. More...

enum class	OpenSwathMatrixNormalization { None , Median , MedianMedian }
	Normalization method for OpenSWATH matrix exports. More...

enum class	InferenceLevel { Peptidoform , Peptide , Protein , Gene }
	Inference level for OpenSWATH-derived confidence inference. More...

enum class	InferenceContext { Global , ExperimentWide , RunSpecific }
	Context for peptide-, protein-, and gene-level inference. 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

Class Documentation

◆ OpenMS::OpenSwathExportFilterConfig

struct OpenMS::OpenSwathExportFilterConfig

Shared filter configuration for OpenSWATH export readers.

Defaults mirror the corresponding PyProphet export CLI defaults

Collaboration diagram for OpenSwathExportFilterConfig:

Class Members
bool	exclude_decoys = true
bool	gene = false
double	ipf_max_peptidoform_pep = 0.4	Filter results to maximum run-specific peptidoform-level PEP.
OpenSwathIPFExportMode	ipf_mode = OpenSwathIPFExportMode::Peptidoform
double	max_alignment_pep = 0.7
double	max_global_gene_qvalue = 0.01
double	max_global_peptide_qvalue = 0.01
double	max_global_protein_qvalue = 0.01
double	max_rs_peakgroup_qvalue = 0.05	Filter results to maximum run-specific peak group-level q-value.
double	max_transition_pep = 0.7	Maximum PEP to retain scored transitions for quantification (requires transition-level scoring)
bool	peptide = true
bool	protein = true
bool	transition_quantification = true	Report aggregated transition-level quantification.
bool	use_alignment = false

Class Members
OpenSwathExportFilterConfig	filters
OpenSwathExportFileFormat	format = OpenSwathExportFileFormat::TSV

Class Members
bool	consistent_top = true
OpenSwathExportFilterConfig	filters
OpenSwathExportFileFormat	format = OpenSwathExportFileFormat::TSV
OpenSwathMatrixLevel	level = OpenSwathMatrixLevel::Peptide
OpenSwathMatrixNormalization	normalization = OpenSwathMatrixNormalization::None
Size	top_n = 3

Class Members
string	aggr_fragment_annotation
string	aggr_peak_apex
string	aggr_peak_area
optional< double >	aggr_prec_peak_apex
optional< double >	aggr_prec_peak_area
optional< Int64 >	alignment_group_id
optional< double >	alignment_pep
optional< double >	alignment_qvalue
optional< Int64 >	alignment_reference_feature_id
optional< double >	alignment_reference_rt
double	assay_irt = 0.0
double	assay_rt = 0.0
Int32	charge = 0
double	d_score = 0.0
bool	decoy = false
double	delta_irt = 0.0
double	delta_rt = 0.0
optional< double >	exp_im
Int64	feature_id = -1
string	filename
bool	from_alignment = false
string	full_peptide_name
optional< double >	gene_experiment_wide_qvalue
optional< double >	gene_global_qvalue
string	gene_name
optional< double >	gene_run_specific_qvalue
optional< double >	im_left_width
optional< double >	im_right_width
double	intensity = 0.0
string	ipf_full_peptide_name
optional< double >	ipf_pep
optional< double >	ipf_peptidoform_m_score
optional< double >	ipf_peptidoform_pep
optional< double >	ipf_precursor_peakgroup_pep
double	irt = 0.0
double	left_width = 0.0
double	m_score = 0.0
optional< double >	ms1_pep
optional< double >	ms2_m_score
optional< double >	ms2_pep
double	mz = 0.0
Int32	peak_group_rank = 0
optional< double >	pep
optional< double >	peptide_experiment_wide_qvalue
optional< double >	peptide_global_qvalue
Int64	peptide_id = -1
optional< double >	peptide_run_specific_qvalue
Int64	precursor_id = -1
optional< double >	precursor_pep
optional< double >	protein_experiment_wide_qvalue
optional< double >	protein_global_qvalue
string	protein_name
optional< double >	protein_run_specific_qvalue
double	right_width = 0.0
double	rt = 0.0
Int64	run_id = -1
string	run_name
string	sequence
string	transition_group_id

Class Members
vector< string >	feature_ms1_column_names
vector< string >	feature_ms2_column_names
vector< OpenSwathFeatureScoreRow >	rows

Class Members
string	annotation
optional< Int64 >	feature_id
vector< optional< double > >	feature_transition_values
optional< Int64 >	ipf_peptide_id
Int64	precursor_id = -1
double	product_mz = 0.0
optional< Int64 >	run_id
optional< double >	score_transition_pep
optional< double >	score_transition_pvalue
optional< double >	score_transition_qvalue
optional< Int32 >	score_transition_rank
optional< double >	score_transition_score
Int32	transition_charge = 0
bool	transition_decoy = false
bool	transition_detecting = false
Int64	transition_id = -1
optional< double >	transition_library_intensity
Int32	transition_ordinal = 0
string	transition_traml_id
string	transition_type

Class Members
vector< string >	feature_transition_column_names
vector< OpenSwathTransitionScoreRow >	rows

Class Members
vector< string >	identifier_column_names
vector< vector< string > >	identifier_rows
vector< string >	sample_column_names
vector< vector< optional< double > > >	values

Class Members
double	lfdr_adj = 1.5	Smoothing bandwidth multiplier used during local FDR density estimation.
double	lfdr_eps = 1e-8	Tail clipping threshold used during local FDR calculation.
bool	lfdr_monotone = true	If true, enforce non-decreasing local FDR values with increasing p-values.
string	lfdr_transformation = "probit"	Transformation applied to p-values for local FDR estimation ("probit", "logit").
bool	lfdr_truncate = true	If true, local FDR values above one are truncated to one.
bool	parametric = false	If true, perform parametric estimation of p-values.
bool	pfdr = false	If true, compute positive false discovery rate (pFDR) instead of FDR.
vector< double >	pi0_lambda {0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45}	Lambda grid for pi0 estimation for non-parametric p-value estimation.
string	pi0_method = "bootstrap"	Method for choosing the pi0 tuning parameter ("smoother", "bootstrap").
Int32	pi0_smooth_df = 3	Degrees of freedom for smoother-based pi0 estimation.
bool	pi0_smooth_log_pi0 = false	If true, smooth log(pi0) instead of pi0 directly.

Class Members
double	across_run_confidence_threshold = 0.5	Maximum transition PEP eligible for across-run evidence propagation.
bool	ipf_grouped_fdr = false	If true, compute grouped FDR instead of pooled FDR.
bool	ipf_h0 = true	If true, include the null hypothesis that no peptidoform explains the peak group.
double	ipf_max_peakgroup_pep = 0.7	Maximum peakgroup PEP to consider scored peak groups in IPF.
double	ipf_max_precursor_peakgroup_pep = 0.4	Maximum precursor-peakgroup PEP retained for transition-level IPF.
double	ipf_max_precursor_pep = 0.7	Maximum precursor PEP to consider scored precursor evidence in IPF.
double	ipf_max_transition_pep = 0.6	Maximum transition PEP to consider scored transition evidence in IPF.
double	ipf_min_alignment_mapping_confidence = 0.5	Minimum mapping confidence retained from FEATURE_MS2_ALIGNMENT_CANDIDATE.
bool	ipf_ms1_scoring = false	If true, use MS1 precursor data for IPF.
bool	ipf_ms2_scoring = false	If true, use MS2 precursor data for IPF.
bool	propagate_signal_across_runs = false	If true, propagate confident transition evidence across aligned runs.

Class Members
InferenceContext	context = InferenceContext::RunSpecific	The context in which to perform inference (global, experiment-wide, or run-specific).
ErrorEstimationConfig	error	Error-estimation settings applied during inference.
InferenceLevel	level = InferenceLevel::Peptide	The analyte level to perform inference on.

Class Members
double	evidence = 0.0
Int64	feature_id = -1
Int64	hypothesis = -1
double	prior = 0.0

Enumerator
Peptidoform	Report results on peptidoform-level.
Augmented	Augment OpenSWATH results with IPF scores.
Disable	Ignore IPF scores, report standard OpenSWATH results only.

Classes

Enumerations

Detailed Description

Workflow Overview

Core Components

Peak Detection and Integration

Quality Control

Feature Selection (Linear Programming)

Absolute Quantitation

Spectrum Extraction

References

Class Documentation

◆ OpenMS::OpenSwathExportFilterConfig

◆ OpenMS::OpenSwathResultsExportConfig

◆ OpenMS::OpenSwathMatrixExportConfig

◆ OpenMS::OpenSwathParquetExportConfig

◆ OpenMS::OpenSwathExportRow

◆ OpenMS::OpenSwathFeatureScoreRow

◆ OpenMS::OpenSwathFeatureScoreTable

◆ OpenMS::OpenSwathTransitionScoreRow

◆ OpenMS::OpenSwathTransitionScoreTable

◆ OpenMS::OpenSwathQuantMatrix

◆ OpenMS::ErrorEstimationConfig

◆ OpenMS::PeptidoformInferenceConfig

◆ OpenMS::LevelContextInferenceConfig

◆ OpenMS::IPFPrecursorRow

◆ OpenMS::IPFPrecursorProbabilityRow

◆ OpenMS::IPFTransitionRow

◆ OpenMS::IPFAlignmentRow

◆ OpenMS::IPFResultRow

◆ OpenMS::LevelContextInputRow

◆ OpenMS::LevelContextResultRow

◆ OpenMS::OpenSwathPeptidoformInference::BayesianModelRow

◆ OpenMS::OpenSwathPeptidoformInference::PosteriorRow

Enumeration Type Documentation

◆ InferenceContext

◆ InferenceLevel

◆ OpenSwathExportFileFormat

◆ OpenSwathIPFExportMode

◆ OpenSwathMatrixLevel

◆ OpenSwathMatrixNormalization