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Classes | Public Types | Public Member Functions | Private Types | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
IDFreeMassErrorEstimator Class Reference

Identification-free precursor and fragment mass-precision estimator. More...

#include <OpenMS/QC/IDFreeMassErrorEstimator.h>

Classes

struct  Diagnostics
 Estimator support/accounting counters. More...
 
struct  FragmentFingerprint
 
struct  GaussianUniformFit
 
struct  Parameters
 Tunable estimator thresholds. Defaults match the validated prideQC implementation. More...
 
struct  PrecursorCluster
 
struct  Result
 Current precision estimates, optional tolerance suggestions and diagnostics. More...
 
struct  RobustError
 Robust summary of pairwise repeated-measurement differences. More...
 
struct  ToleranceSuggestion
 Precision-derived search-tolerance suggestion for one unit system. More...
 

Public Types

enum class  FragmentResolutionRegime { UNAVAILABLE , HIGH_RESOLUTION , LOW_RESOLUTION }
 

Public Member Functions

 IDFreeMassErrorEstimator ()
 
 IDFreeMassErrorEstimator (const Parameters &parameters)
 
void setParameters (const Parameters &parameters)
 Replace estimator parameters and clear all accumulated evidence.
 
const Parameters & getParameters () const
 
void reset ()
 Clear all accumulated evidence while retaining the current parameters.
 
void consumeSpectrum (const MSSpectrum &spectrum)
 
Result compute (const MSExperiment &experiment)
 Reset, consume all spectra in experiment, and return the resulting estimate.
 
Result getResult () const
 Return the current complete estimate without mutating accumulated state.
 
std::optional< RobustError > getPrecursorPrecisionPPM () const
 Return only the current precursor-ppm precision summary.
 

Private Types

using BinKey = std::pair< Int, Int >
 

Private Member Functions

void commitPrecursorCluster_ (PrecursorCluster &cluster)
 
void consumePrecursor_ (const MSSpectrum &spectrum, double precursor_mz, Int charge)
 
std::pair< std::vector< double >, std::vector< double > > fragmentPeaks_ (const MSSpectrum &spectrum)
 
void consumeFragments_ (const MSSpectrum &spectrum, double precursor_mz, Int charge)
 

Static Private Member Functions

static void validateParameters_ (const Parameters &parameters)
 
static std::optional< RobustError > robustError_ (const std::vector< double > &values)
 
static std::optional< GaussianUniformFit > gaussianUniformFit_ (const std::vector< double > &values)
 
static RobustError errorFromGaussianUniformFit_ (const std::vector< double > &values, const GaussianUniformFit &fit)
 
static std::pair< std::vector< double >, std::vector< double > > centroidTopPeaks_ (const MSSpectrum &spectrum, Size limit)
 
static std::pair< std::vector< double >, std::vector< double > > profilePeakCenters_ (const MSSpectrum &spectrum, Size limit)
 
static std::pair< std::vector< double >, std::vector< double > > matchedDeltas_ (const std::vector< double > &left_mz, const std::vector< double > &right_mz, double tolerance_da)
 
static std::pair< std::vector< double >, std::vector< double > > coarseBinnedDeltas_ (const std::vector< double > &left_mz, const std::vector< double > &left_relative_intensity, const std::vector< double > &right_mz, const std::vector< double > &right_relative_intensity, double bin_width_da, std::vector< double > &shared_relative_intensity)
 

Private Attributes

Parameters parameters_
 
std::map< BinKey, std::vector< PrecursorCluster > > precursor_bins_
 
std::map< BinKey, std::deque< FragmentFingerprint > > fragment_bins_
 
std::vector< double > precursor_errors_ppm_
 
std::vector< double > precursor_errors_da_
 
std::vector< double > fragment_errors_da_
 
std::vector< double > fragment_errors_ppm_
 
std::vector< double > fragment_mixture_errors_ppm_
 
std::vector< double > fragment_mixture_mean_mz_
 
std::vector< double > fragment_mixture_shared_relative_intensity_
 
std::vector< double > fragment_low_res_errors_da_
 
std::vector< double > fragment_low_res_errors_ppm_
 
std::vector< double > fragment_very_low_res_errors_da_
 
std::vector< double > fragment_very_low_res_errors_ppm_
 
Diagnostics diagnostics_
 

Detailed Description

Identification-free precursor and fragment mass-precision estimator.

The estimator derives measurement precision from repeated precursor observations and likely repeated MS2 spectra without requiring peptide identifications. Precursor evidence uses repeated observations with the same positive charge in a bounded RT/m/z neighbourhood. Fragment evidence compares strong peak centres from likely repeated spectra. High-resolution fragment precision is estimated from unambiguous coarse-bin peak pairs with a Gaussian plus uniform-background mixture in ppm, avoiding dependence on a narrow fragment-match window. Centroided spectra use their native peaks; profile spectra use an ephemeral three-point quadratic fit in log-intensity space around local maxima. Input spectra are never modified.

The returned precision describes random measurement variation. It does not recover a historical database-search tolerance, fixed calibration bias, or isotope-error policy.

The class is stateful so callers can stream spectra through consumeSpectrum. The convenience compute overload resets the estimator and processes a complete experiment.

Class Documentation

◆ OpenMS::IDFreeMassErrorEstimator::Diagnostics

struct OpenMS::IDFreeMassErrorEstimator::Diagnostics

Estimator support/accounting counters.

Class Members
Size excluded_fragment_profile_or_unknown {0}
Size excluded_fragment_unknown {0}
Size excluded_low_fragment_peaks {0}
Size excluded_missing_precursor {0}
Size excluded_profile_peak_pick_failure {0}
Size fragment_centroid_spectra {0}
Size fragment_eligible_ms2 {0}
bool fragment_high_intensity_fallback_used {false}
bool fragment_high_intensity_mixture_converged {false}
Size fragment_high_intensity_pairs {0}
double fragment_high_intensity_signal_fraction {0.0}
Size fragment_high_intensity_signal_pairs {0}
double fragment_high_intensity_threshold {0.0}
Size fragment_low_res_pairs {0}
bool fragment_mixture_converged {false}
Size fragment_mixture_iterations {0}
double fragment_mixture_mean_ppm {0.0}
Size fragment_mixture_pairs {0}
double fragment_mixture_reference_mz {0.0}
bool fragment_mixture_rejected_zero_quantization {false}
double fragment_mixture_signal_fraction {0.0}
Size fragment_mixture_signal_pairs {0}
Size fragment_paired_spectra {0}
Size fragment_pairs {0}
Size fragment_profile_centroids {0}
Size fragment_profile_spectra {0}
Size fragment_very_low_res_pairs {0}
double fragment_zero_delta_fraction {0.0}
Size fragment_zero_delta_pairs {0}
Size precursor_clusters_used {0}
Size precursor_eligible_ms2 {0}
Size precursor_paired_spectra {0}

◆ OpenMS::IDFreeMassErrorEstimator::FragmentFingerprint

struct OpenMS::IDFreeMassErrorEstimator::FragmentFingerprint
Class Members
vector< double > mz
double precursor_mz {0.0}
vector< double > relative_intensity
double rt {0.0}

◆ OpenMS::IDFreeMassErrorEstimator::GaussianUniformFit

struct OpenMS::IDFreeMassErrorEstimator::GaussianUniformFit
Class Members
bool converged {false}
Size iterations {0}
double log_likelihood {-std::numeric_limits<double>::infinity()}
double mean {0.0}
double pairwise_sigma {0.0}
double signal_fraction {0.0}

◆ OpenMS::IDFreeMassErrorEstimator::Parameters

struct OpenMS::IDFreeMassErrorEstimator::Parameters

Tunable estimator thresholds. Defaults match the validated prideQC implementation.

Class Members
double fragment_high_intensity_quantile {0.75}
double fragment_high_res_max_sigma_da {0.01}
double fragment_high_res_max_sigma_ppm {10.0}
double fragment_low_res_match_da {0.5}
double fragment_low_res_min_sigma_da {0.01}
double fragment_low_res_min_sigma_ppm {20.0}
double fragment_match_da {0.2}
double fragment_tolerance_sigma_multiplier {6.0}
double fragment_very_low_res_match_da {1.0}
Size max_candidates_per_bin {32}
Size min_fragment_pairs {200}
Size min_fragment_tolerance_pairs {1000}
Size min_fragment_tolerance_spectra {50}
Size min_matched_peaks {8}
double min_overlap_fraction {0.25}
Size min_precursor_cluster_size {3}
Size min_precursor_clusters {10}
Size min_spectrum_pairs {25}
Size min_tolerance_clusters {100}
Size min_tolerance_pairs {200}
double precursor_candidate_ppm {20.0}
double rt_window_seconds {120.0}
double tolerance_sigma_multiplier {6.0}
Size top_peaks {50}

◆ OpenMS::IDFreeMassErrorEstimator::PrecursorCluster

struct OpenMS::IDFreeMassErrorEstimator::PrecursorCluster
Class Members
bool committed {false}
Size count {1}
double last_mz {0.0}
double last_rt {0.0}
double mean_mz {0.0}
vector< double > pending_da
vector< double > pending_ppm

◆ OpenMS::IDFreeMassErrorEstimator::Result

struct OpenMS::IDFreeMassErrorEstimator::Result

Current precision estimates, optional tolerance suggestions and diagnostics.

Class Members
Diagnostics diagnostics
optional< RobustError > fragment_da
double fragment_match_window_da {0.2}
optional< RobustError > fragment_ppm
FragmentResolutionRegime fragment_resolution_regime {FragmentResolutionRegime::UNAVAILABLE}
optional< ToleranceSuggestion > fragment_tolerance_da
optional< ToleranceSuggestion > fragment_tolerance_ppm
bool fragment_window_censored {false}
optional< RobustError > precursor_da
optional< RobustError > precursor_ppm
optional< ToleranceSuggestion > precursor_tolerance_ppm

◆ OpenMS::IDFreeMassErrorEstimator::RobustError

struct OpenMS::IDFreeMassErrorEstimator::RobustError

Robust summary of pairwise repeated-measurement differences.

Class Members
double pairwise_median {0.0}
double pairwise_p95_abs {0.0}
double pairwise_sigma {0.0}
Size robust_inlier_count {0}
double robust_inlier_fraction {0.0}
double robust_inlier_p95_abs_centered {0.0}
double robust_inlier_threshold_3sigma {0.0}
Size robust_outlier_count {0}
double single_measurement_sigma {0.0}

◆ OpenMS::IDFreeMassErrorEstimator::ToleranceSuggestion

struct OpenMS::IDFreeMassErrorEstimator::ToleranceSuggestion

Precision-derived search-tolerance suggestion for one unit system.

Class Members
string confidence
double sigma_multiplier {0.0}
double single_measurement_sigma {0.0}
Size support {0}
double tolerance {0.0}
string unit

Member Typedef Documentation

◆ BinKey

using BinKey = std::pair<Int, Int>
private

Member Enumeration Documentation

◆ FragmentResolutionRegime

enum class FragmentResolutionRegime
strong
Enumerator
UNAVAILABLE 
HIGH_RESOLUTION 
LOW_RESOLUTION 

Constructor & Destructor Documentation

◆ IDFreeMassErrorEstimator() [1/2]

IDFreeMassErrorEstimator ( )

◆ IDFreeMassErrorEstimator() [2/2]

IDFreeMassErrorEstimator ( const Parameters &  parameters)
explicit

Member Function Documentation

◆ centroidTopPeaks_()

static std::pair< std::vector< double >, std::vector< double > > centroidTopPeaks_ ( const MSSpectrum &  spectrum,
Size  limit 
)
staticprivate

◆ coarseBinnedDeltas_()

static std::pair< std::vector< double >, std::vector< double > > coarseBinnedDeltas_ ( const std::vector< double > &  left_mz,
const std::vector< double > &  left_relative_intensity,
const std::vector< double > &  right_mz,
const std::vector< double > &  right_relative_intensity,
double  bin_width_da,
std::vector< double > &  shared_relative_intensity 
)
staticprivate

◆ commitPrecursorCluster_()

void commitPrecursorCluster_ ( PrecursorCluster &  cluster)
private

◆ compute()

Result compute ( const MSExperiment &  experiment)

Reset, consume all spectra in experiment, and return the resulting estimate.

◆ consumeFragments_()

void consumeFragments_ ( const MSSpectrum &  spectrum,
double  precursor_mz,
Int  charge 
)
private

◆ consumePrecursor_()

void consumePrecursor_ ( const MSSpectrum &  spectrum,
double  precursor_mz,
Int  charge 
)
private

◆ consumeSpectrum()

void consumeSpectrum ( const MSSpectrum &  spectrum)

Consume one spectrum. Non-MS2 spectra are ignored. Spectrum RT order does not matter. Charge-less MS2 spectra with a valid precursor/isolation m/z contribute fragment evidence, but not charge-specific precursor evidence. A streamed estimator instance represents one run; call reset before consuming spectra from another run.

◆ errorFromGaussianUniformFit_()

static RobustError errorFromGaussianUniformFit_ ( const std::vector< double > &  values,
const GaussianUniformFit &  fit 
)
staticprivate

◆ fragmentPeaks_()

std::pair< std::vector< double >, std::vector< double > > fragmentPeaks_ ( const MSSpectrum &  spectrum)
private

◆ gaussianUniformFit_()

static std::optional< GaussianUniformFit > gaussianUniformFit_ ( const std::vector< double > &  values)
staticprivate

◆ getParameters()

const Parameters & getParameters ( ) const

◆ getPrecursorPrecisionPPM()

std::optional< RobustError > getPrecursorPrecisionPPM ( ) const

Return only the current precursor-ppm precision summary.

◆ getResult()

Result getResult ( ) const

Return the current complete estimate without mutating accumulated state.

◆ matchedDeltas_()

static std::pair< std::vector< double >, std::vector< double > > matchedDeltas_ ( const std::vector< double > &  left_mz,
const std::vector< double > &  right_mz,
double  tolerance_da 
)
staticprivate

◆ profilePeakCenters_()

static std::pair< std::vector< double >, std::vector< double > > profilePeakCenters_ ( const MSSpectrum &  spectrum,
Size  limit 
)
staticprivate

◆ reset()

void reset ( )

Clear all accumulated evidence while retaining the current parameters.

◆ robustError_()

static std::optional< RobustError > robustError_ ( const std::vector< double > &  values)
staticprivate

◆ setParameters()

void setParameters ( const Parameters &  parameters)

Replace estimator parameters and clear all accumulated evidence.

◆ validateParameters_()

static void validateParameters_ ( const Parameters &  parameters)
staticprivate

Member Data Documentation

◆ diagnostics_

Diagnostics diagnostics_
private

◆ fragment_bins_

std::map<BinKey, std::deque<FragmentFingerprint> > fragment_bins_
private

◆ fragment_errors_da_

std::vector<double> fragment_errors_da_
private

◆ fragment_errors_ppm_

std::vector<double> fragment_errors_ppm_
private

◆ fragment_low_res_errors_da_

std::vector<double> fragment_low_res_errors_da_
private

◆ fragment_low_res_errors_ppm_

std::vector<double> fragment_low_res_errors_ppm_
private

◆ fragment_mixture_errors_ppm_

std::vector<double> fragment_mixture_errors_ppm_
private

◆ fragment_mixture_mean_mz_

std::vector<double> fragment_mixture_mean_mz_
private

◆ fragment_mixture_shared_relative_intensity_

std::vector<double> fragment_mixture_shared_relative_intensity_
private

◆ fragment_very_low_res_errors_da_

std::vector<double> fragment_very_low_res_errors_da_
private

◆ fragment_very_low_res_errors_ppm_

std::vector<double> fragment_very_low_res_errors_ppm_
private

◆ parameters_

Parameters parameters_
private

◆ precursor_bins_

std::map<BinKey, std::vector<PrecursorCluster> > precursor_bins_
private

◆ precursor_errors_da_

std::vector<double> precursor_errors_da_
private

◆ precursor_errors_ppm_

std::vector<double> precursor_errors_ppm_
private