OpenMS
FLASHDeconvAlgorithm Class Reference

FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) More...

#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.h>

Inheritance diagram for FLASHDeconvAlgorithm:
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Collaboration diagram for FLASHDeconvAlgorithm:
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Public Types

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine
 
typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak
 

Public Member Functions

 FLASHDeconvAlgorithm ()
 default constructor More...
 
 FLASHDeconvAlgorithm (const FLASHDeconvAlgorithm &)=default
 copy constructor More...
 
 FLASHDeconvAlgorithm (FLASHDeconvAlgorithm &&other)=default
 move constructor More...
 
FLASHDeconvAlgorithmoperator= (const FLASHDeconvAlgorithm &fd)=default
 assignment operator More...
 
FLASHDeconvAlgorithmoperator= (FLASHDeconvAlgorithm &&fd)=default
 move assignment operator More...
 
 ~FLASHDeconvAlgorithm ()=default
 destructor More...
 
void performSpectrumDeconvolution (const MSSpectrum &spec, const std::vector< DeconvolvedSpectrum > &survey_scans, int scan_number, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_FLASHIda)
 main deconvolution function that generates the deconvolved target and dummy spectrum based on the original spectrum. More...
 
DeconvolvedSpectrumgetDeconvolvedSpectrum ()
 return deconvolved spectrum More...
 
const PrecalculatedAveraginegetAveragine ()
 get calculated averagine. Call after calculateAveragine is called. More...
 
void setAveragine (const PrecalculatedAveragine &avg)
 set calculated averagine More...
 
void setTargetMasses (const std::vector< double > &masses, bool exclude=false)
 set targeted or excluded masses for targeted deconvolution. Masses are targeted or excluded in all ms levels. More...
 
void calculateAveragine (bool use_RNA_averagine)
 precalculate averagine (for predefined mass bins) to speed up averagine generation More...
 
void setTargetDummyType (PeakGroup::TargetDummyType target_dummy_type, DeconvolvedSpectrum &target_dspec_for_dummy_calcualtion)
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Static Public Member Functions

static int getNominalMass (double mass)
 convert double to nominal mass More...
 
static float getCosine (const std::vector< float > &a, int a_start, int a_end, const IsotopeDistribution &b, int b_size, int offset, int min_iso_size)
 
static float getIsotopeCosineAndDetermineIsotopeIndex (double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift=0, int window_width=-1, int allowed_iso_error_for_second_best_cos=0, PeakGroup::TargetDummyType target_dummy_type=PeakGroup::TargetDummyType::target)
 Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass. More...
 
static void addMZsToExcludsionList (const DeconvolvedSpectrum &dspec, std::unordered_set< double > &excluded_mzs)
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 

Protected Member Functions

void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Private Member Functions

void updateLogMzPeaks_ ()
 generate log mz peaks from the input spectrum More...
 
void updateMzBins_ (Size bin_number, std::vector< float > &mz_bin_intensities)
 generate mz bins and intensity per mz bin from log mz peaks More...
 
double getMassFromMassBin_ (Size mass_bin, double bin_mul_factor) const
 get mass value for input mass bin More...
 
double getMzFromMzBin_ (Size mass_bin, double bin_mul_factor) const
 get mz value for input mz bin More...
 
void generatePeakGroupsFromSpectrum_ ()
 Generate peak groups from the input spectrum. More...
 
Matrix< int > updateMassBins_ (const std::vector< float > &mz_intensities)
 Update mass_bins_. It select candidate mass bins using the universal pattern, eliminate possible harmonic masses. This function does not perform deisotoping. More...
 
Matrix< int > filterMassBins_ (const std::vector< float > &mass_intensities)
 Subfunction of updateMassBins_. More...
 
void updateCandidateMassBins_ (std::vector< float > &mass_intensities, const std::vector< float > &mz_intensities)
 Subfunction of updateMassBins_. It select candidate masses and update mass_bins_ using the universal pattern, eliminate possible harmonic masses. More...
 
void getCandidatePeakGroups_ (const Matrix< int > &per_mass_abs_charge_ranges)
 For selected masses in mass_bins_, select the peaks from the original spectrum. Also isotopic peaks are clustered in this function. More...
 
void setFilters_ ()
 Make the universal pattern. More...
 
void scoreAndFilterPeakGroups_ ()
 function for peak group scoring and filtering More...
 
void removeChargeErrorPeakGroups_ (DeconvolvedSpectrum &dspec) const
 filter out charge error masses More...
 
void removeOverlappingPeakGroups_ (DeconvolvedSpectrum &dspec, double tol)
 filter out overlapping masses More...
 
bool registerPrecursor_ (const std::vector< DeconvolvedSpectrum > &survey_scans, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_real_time_acquisition)
 register the precursor peak as well as the precursor peak group (or mass) if possible for MSn (n>1) spectrum. Given a precursor peak (found in the original MS n-1 Spectrum) the masses containing the precursor peak are searched. If multiple masses are detected, the one with the best Qscore is selected. For the selected mass, its corresponding peak group (along with precursor peak) is registered. If no such mass exists, only the precursor peak is registered. More...
 

Static Private Member Functions

static double getBinValue_ (Size bin, double min_value, double bin_mul_factor)
 static function that converts bin to value More...
 
static Size getBinNumber_ (double value, double min_value, double bin_mul_factor)
 static function that converts value to bin More...
 

Private Attributes

int allowed_iso_error_ = 1
 allowed isotope error in deconvolved mass to calculate qvalue More...
 
double min_rt_
 range of RT subject to analysis (in seconds) More...
 
double max_rt_
 
double min_mz_
 range of mz subject to analysis More...
 
double max_mz_
 
int min_abs_charge_
 min charge and max charge subject to analysis, set by users More...
 
int max_abs_charge_
 
bool is_positive_
 is positive mode More...
 
double min_mass_
 mass ranges of deconvolution, set by users More...
 
double max_mass_
 
int current_max_charge_
 current_max_charge_: controlled by precursor charge for MSn n>1; otherwise just max_abs_charge_ More...
 
double current_max_mass_
 max mass is controlled by precursor mass for MSn n>1; otherwise just max_mass More...
 
double current_min_mass_
 max mass is max_mass for MS1 and 50 for MS2 More...
 
double intensity_threshold_
 peak intensity threshold subject to analysis More...
 
DoubleList tolerance_
 tolerance in ppm for each MS level More...
 
DoubleList bin_mul_factors_
 bin multiplication factor (log mz * bin_mul_factors_ = bin number) - for fast convolution, binning is used More...
 
DoubleList min_isotope_cosine_
 cosine threshold between observed and theoretical isotope patterns for each MS level More...
 
DeconvolvedSpectrumtarget_dspec_for_dummy_calcualtion_
 the deconvolved spectrum from normal run. This is used when dummy masses are generated. More...
 
PeakGroup::TargetDummyType target_dummy_type_ = PeakGroup::TargetDummyType::target
 PeakGroup::TargetDummyType values. More...
 
FLASHDeconvHelperStructs::PrecalculatedAveragine avg_
 precalculated averagine distributions for fast averagine generation More...
 
boost::dynamic_bitset target_mass_bins_
 mass bins that are targeted for FLASHIda global targeting mode More...
 
std::vector< double > target_mono_masses_
 
std::vector< double > excluded_masses_
 mass bins that are excluded for FLASHIda global targeting mode More...
 
boost::dynamic_bitset previously_deconved_mass_bins_for_dummy_
 mass bins that are previsouly deconvolved and excluded for dummy mass generation More...
 
std::vector< double > previously_deconved_mono_masses_for_dummy_
 
std::unordered_set< double > excluded_peak_mzs_
 
std::vector< LogMzPeaklog_mz_peaks_
 Stores log mz peaks. More...
 
DeconvolvedSpectrum deconvolved_spectrum_
 selected_peak_groups_ stores the deconvolved mass peak groups More...
 
boost::dynamic_bitset mass_bins_
 mass_bins_ stores the selected bins for this spectrum + overlapped spectrum (previous a few spectra). More...
 
boost::dynamic_bitset mz_bins_
 mz_bins_ stores the binned log mz peaks More...
 
std::vector< double > filter_
 This stores the "universal pattern". More...
 
Matrix< double > harmonic_filter_matrix_
 This stores the patterns for harmonic reduction. More...
 
double iso_da_distance_
 isotope dalton distance More...
 
std::vector< int > bin_offsets_
 This stores the "universal pattern" in binned dimension. More...
 
Matrix< int > harmonic_bin_offset_matrix_
 This stores the patterns for harmonic reduction in binned dimension. More...
 
double mass_bin_min_value_
 minimum mass and mz values representing the first bin of massBin and mzBin, respectively: to save memory space More...
 
double mz_bin_min_value_
 
uint ms_level_
 current ms Level More...
 
double isolation_window_size_
 default precursor isolation window size. More...
 

Static Private Attributes

static const int min_iso_size_ = 2
 FLASHDeconv parameters. More...
 
static const int min_support_peak_count_ = 2
 minimum number of peaks supporting a mass minus one More...
 

Additional Inherited Members

- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

FLASHDeconv algorithm: ultrafast mass deconvolution algorithm for top down mass spectrometry dataset From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps: i) decharging and select candidate masses - speed up via binning ii) collecting isotopes from the candidate masses and deisotope - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups)

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Constructor & Destructor Documentation

◆ FLASHDeconvAlgorithm() [1/3]

default constructor

◆ FLASHDeconvAlgorithm() [2/3]

copy constructor

◆ FLASHDeconvAlgorithm() [3/3]

move constructor

◆ ~FLASHDeconvAlgorithm()

~FLASHDeconvAlgorithm ( )
default

destructor

Member Function Documentation

◆ addMZsToExcludsionList()

static void addMZsToExcludsionList ( const DeconvolvedSpectrum dspec,
std::unordered_set< double > &  excluded_mzs 
)
static

add m/zs in input DeconvolvedSpectrum into exclusion list. The exclusion list is used to generate noise dummy masses.

Parameters
dspecinput DeconvolvedSpectrum
excluded_mzsmz exclusion list to be updated

◆ calculateAveragine()

void calculateAveragine ( bool  use_RNA_averagine)

precalculate averagine (for predefined mass bins) to speed up averagine generation

Parameters
use_RNA_averagineif set, averagine for RNA (nucleotides) is calculated

◆ filterMassBins_()

Matrix<int> filterMassBins_ ( const std::vector< float > &  mass_intensities)
private

Subfunction of updateMassBins_.

Parameters
mass_intensitiesper mass bin intensity
Returns
a matrix containing charge ranges for all found masses

◆ generatePeakGroupsFromSpectrum_()

void generatePeakGroupsFromSpectrum_ ( )
private

Generate peak groups from the input spectrum.

◆ getAveragine()

const PrecalculatedAveragine& getAveragine ( )

get calculated averagine. Call after calculateAveragine is called.

◆ getBinNumber_()

static Size getBinNumber_ ( double  value,
double  min_value,
double  bin_mul_factor 
)
staticprivate

static function that converts value to bin

Parameters
valuevalue
min_valueminimum value (corresponding to bin number = 0)
bin_mul_factorbin multiplication factor: bin_number = (bin_value * bin_mul_factors_ - min_value)
Returns
bin corresponding to value

◆ getBinValue_()

static double getBinValue_ ( Size  bin,
double  min_value,
double  bin_mul_factor 
)
staticprivate

static function that converts bin to value

Parameters
binbin number
min_valueminimum value (corresponding to bin number = 0)
bin_mul_factorbin multiplication factor: bin_value = (min_value + bin_number/ bin_mul_factors_)
Returns
value corresponding to bin

◆ getCandidatePeakGroups_()

void getCandidatePeakGroups_ ( const Matrix< int > &  per_mass_abs_charge_ranges)
private

For selected masses in mass_bins_, select the peaks from the original spectrum. Also isotopic peaks are clustered in this function.

Parameters
per_mass_abs_charge_rangescharge range per mass

◆ getCosine()

static float getCosine ( const std::vector< float > &  a,
int  a_start,
int  a_end,
const IsotopeDistribution b,
int  b_size,
int  offset,
int  min_iso_size 
)
static

calculate cosine between two vectors a and b with additional parameters for fast calculation

Parameters
avector a
a_startnon zero start index of a
a_endnon zero end index of a (exclusive)
bvector b
b_sizesize of b
offsetelement index offset between a and b
min_iso_sizeminimum isotope size. If isotope size is less than this, return 0

◆ getDeconvolvedSpectrum()

DeconvolvedSpectrum& getDeconvolvedSpectrum ( )

return deconvolved spectrum

Referenced by TOPPFLASHDeconv::main_().

◆ getIsotopeCosineAndDetermineIsotopeIndex()

static float getIsotopeCosineAndDetermineIsotopeIndex ( double  mono_mass,
const std::vector< float > &  per_isotope_intensities,
int &  offset,
const PrecalculatedAveragine avg,
int  iso_int_shift = 0,
int  window_width = -1,
int  allowed_iso_error_for_second_best_cos = 0,
PeakGroup::TargetDummyType  target_dummy_type = PeakGroup::TargetDummyType::target 
)
static

Examine intensity distribution over isotope indices. Also determines the most plausible isotope index or, monoisotopic mono_mass.

Parameters
mono_massmonoisotopic mass
per_isotope_intensitiesvector of intensities associated with each isotope - aggregated through charges
offsetoutput offset between input monoisotopic mono_mass and determined monoisotopic mono_mass
avgprecalculated averagine
iso_int_shiftisotope shift in per_isotope_intensities.
window_widthisotope offset value range. If -1, set automatically.
allowed_iso_error_for_second_best_cosallowed isotope error to calculate the second best cos. If target_dummy_type is not PeakGroup::TargetDummyType::target, the second best cosine and its corresponding offset will be output
target_dummy_typeThis target_dummy_type specifies if a PeakGroup is a target (0), charge dummy (1), noise dummy (2), or isotope dummy (3)
Returns
calculated cosine similar score

◆ getMassFromMassBin_()

double getMassFromMassBin_ ( Size  mass_bin,
double  bin_mul_factor 
) const
private

get mass value for input mass bin

◆ getMzFromMzBin_()

double getMzFromMzBin_ ( Size  mass_bin,
double  bin_mul_factor 
) const
private

get mz value for input mz bin

◆ getNominalMass()

static int getNominalMass ( double  mass)
static

convert double to nominal mass

◆ operator=() [1/2]

FLASHDeconvAlgorithm& operator= ( const FLASHDeconvAlgorithm fd)
default

assignment operator

◆ operator=() [2/2]

FLASHDeconvAlgorithm& operator= ( FLASHDeconvAlgorithm &&  fd)
default

move assignment operator

◆ performSpectrumDeconvolution()

void performSpectrumDeconvolution ( const MSSpectrum spec,
const std::vector< DeconvolvedSpectrum > &  survey_scans,
int  scan_number,
const std::map< int, std::vector< std::vector< float >>> &  precursor_map_for_FLASHIda 
)

main deconvolution function that generates the deconvolved target and dummy spectrum based on the original spectrum.

Parameters
specthe original spectrum
survey_scansthe survey scans to assign precursor mass to the deconvolved spectrum.
scan_numberscan number from input spectrum.
precursor_map_for_FLASHIdadeconvolved precursor information from FLASHIda

Referenced by TOPPFLASHDeconv::main_().

◆ registerPrecursor_()

bool registerPrecursor_ ( const std::vector< DeconvolvedSpectrum > &  survey_scans,
const std::map< int, std::vector< std::vector< float >>> &  precursor_map_for_real_time_acquisition 
)
private

register the precursor peak as well as the precursor peak group (or mass) if possible for MSn (n>1) spectrum. Given a precursor peak (found in the original MS n-1 Spectrum) the masses containing the precursor peak are searched. If multiple masses are detected, the one with the best Qscore is selected. For the selected mass, its corresponding peak group (along with precursor peak) is registered. If no such mass exists, only the precursor peak is registered.

Parameters
survey_scansthe candidate precursor spectra - the user may allow search of previous N survey scans.
precursor_map_for_real_time_acquisitionthis contains the deconvolved mass information from FLASHIda runs.

◆ removeChargeErrorPeakGroups_()

void removeChargeErrorPeakGroups_ ( DeconvolvedSpectrum dspec) const
private

filter out charge error masses

◆ removeOverlappingPeakGroups_()

void removeOverlappingPeakGroups_ ( DeconvolvedSpectrum dspec,
double  tol 
)
private

filter out overlapping masses

◆ scoreAndFilterPeakGroups_()

void scoreAndFilterPeakGroups_ ( )
private

function for peak group scoring and filtering

◆ setAveragine()

void setAveragine ( const PrecalculatedAveragine avg)

set calculated averagine

Referenced by TOPPFLASHDeconv::main_().

◆ setFilters_()

void setFilters_ ( )
private

Make the universal pattern.

◆ setTargetDummyType()

void setTargetDummyType ( PeakGroup::TargetDummyType  target_dummy_type,
DeconvolvedSpectrum target_dspec_for_dummy_calcualtion 
)

set target dummy type for the FLASHDeconvAlgorithm run. All masses from the target FLASHDeconvAlgorithm run will have the target_dummy_type_.

Parameters
target_dummy_typeThis target_dummy_type_ specifies if a PeakGroup is a target (0), charge dummy (1), noise dummy (2), or isotope dummy (3)
target_dspec_for_dummy_calcualtiontarget masses from normal deconvolution

Referenced by TOPPFLASHDeconv::main_().

◆ setTargetMasses()

void setTargetMasses ( const std::vector< double > &  masses,
bool  exclude = false 
)

set targeted or excluded masses for targeted deconvolution. Masses are targeted or excluded in all ms levels.

Parameters
massesMasses to be targeted or excluded (exclude=true)
excludeif set, masses are excluded.

◆ updateCandidateMassBins_()

void updateCandidateMassBins_ ( std::vector< float > &  mass_intensities,
const std::vector< float > &  mz_intensities 
)
private

Subfunction of updateMassBins_. It select candidate masses and update mass_bins_ using the universal pattern, eliminate possible harmonic masses.

Parameters
mass_intensitiesmass bin intensities which are updated in this function
mz_intensitiesmz bin intensities

◆ updateLogMzPeaks_()

void updateLogMzPeaks_ ( )
private

generate log mz peaks from the input spectrum

◆ updateMassBins_()

Matrix<int> updateMassBins_ ( const std::vector< float > &  mz_intensities)
private

Update mass_bins_. It select candidate mass bins using the universal pattern, eliminate possible harmonic masses. This function does not perform deisotoping.

Parameters
mz_intensitiesper mz bin intensity
Returns
a matrix containing charge ranges for all found masses

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

◆ updateMzBins_()

void updateMzBins_ ( Size  bin_number,
std::vector< float > &  mz_bin_intensities 
)
private

generate mz bins and intensity per mz bin from log mz peaks

Parameters
bin_numbernumber of mz bins
mz_bin_intensitiesintensity per mz bin

Member Data Documentation

◆ allowed_iso_error_

int allowed_iso_error_ = 1
private

allowed isotope error in deconvolved mass to calculate qvalue

◆ avg_

precalculated averagine distributions for fast averagine generation

◆ bin_mul_factors_

DoubleList bin_mul_factors_
private

bin multiplication factor (log mz * bin_mul_factors_ = bin number) - for fast convolution, binning is used

◆ bin_offsets_

std::vector<int> bin_offsets_
private

This stores the "universal pattern" in binned dimension.

◆ current_max_charge_

int current_max_charge_
private

current_max_charge_: controlled by precursor charge for MSn n>1; otherwise just max_abs_charge_

◆ current_max_mass_

double current_max_mass_
private

max mass is controlled by precursor mass for MSn n>1; otherwise just max_mass

◆ current_min_mass_

double current_min_mass_
private

max mass is max_mass for MS1 and 50 for MS2

◆ deconvolved_spectrum_

DeconvolvedSpectrum deconvolved_spectrum_
private

selected_peak_groups_ stores the deconvolved mass peak groups

◆ excluded_masses_

std::vector<double> excluded_masses_
private

mass bins that are excluded for FLASHIda global targeting mode

◆ excluded_peak_mzs_

std::unordered_set<double> excluded_peak_mzs_
private

◆ filter_

std::vector<double> filter_
private

This stores the "universal pattern".

◆ harmonic_bin_offset_matrix_

Matrix<int> harmonic_bin_offset_matrix_
private

This stores the patterns for harmonic reduction in binned dimension.

◆ harmonic_filter_matrix_

Matrix<double> harmonic_filter_matrix_
private

This stores the patterns for harmonic reduction.

◆ intensity_threshold_

double intensity_threshold_
private

peak intensity threshold subject to analysis

◆ is_positive_

bool is_positive_
private

is positive mode

◆ iso_da_distance_

double iso_da_distance_
private

isotope dalton distance

◆ isolation_window_size_

double isolation_window_size_
private

default precursor isolation window size.

◆ log_mz_peaks_

std::vector<LogMzPeak> log_mz_peaks_
private

Stores log mz peaks.

◆ mass_bin_min_value_

double mass_bin_min_value_
private

minimum mass and mz values representing the first bin of massBin and mzBin, respectively: to save memory space

◆ mass_bins_

boost::dynamic_bitset mass_bins_
private

mass_bins_ stores the selected bins for this spectrum + overlapped spectrum (previous a few spectra).

◆ max_abs_charge_

int max_abs_charge_
private

◆ max_mass_

double max_mass_
private

◆ max_mz_

double max_mz_
private

◆ max_rt_

double max_rt_
private

◆ min_abs_charge_

int min_abs_charge_
private

min charge and max charge subject to analysis, set by users

◆ min_iso_size_

const int min_iso_size_ = 2
staticprivate

FLASHDeconv parameters.

minimum isotopologue count in a peak group

◆ min_isotope_cosine_

DoubleList min_isotope_cosine_
private

cosine threshold between observed and theoretical isotope patterns for each MS level

◆ min_mass_

double min_mass_
private

mass ranges of deconvolution, set by users

◆ min_mz_

double min_mz_
private

range of mz subject to analysis

◆ min_rt_

double min_rt_
private

range of RT subject to analysis (in seconds)

◆ min_support_peak_count_

const int min_support_peak_count_ = 2
staticprivate

minimum number of peaks supporting a mass minus one

◆ ms_level_

uint ms_level_
private

current ms Level

◆ mz_bin_min_value_

double mz_bin_min_value_
private

◆ mz_bins_

boost::dynamic_bitset mz_bins_
private

mz_bins_ stores the binned log mz peaks

◆ previously_deconved_mass_bins_for_dummy_

boost::dynamic_bitset previously_deconved_mass_bins_for_dummy_
private

mass bins that are previsouly deconvolved and excluded for dummy mass generation

◆ previously_deconved_mono_masses_for_dummy_

std::vector<double> previously_deconved_mono_masses_for_dummy_
private

◆ target_dspec_for_dummy_calcualtion_

DeconvolvedSpectrum* target_dspec_for_dummy_calcualtion_
private

the deconvolved spectrum from normal run. This is used when dummy masses are generated.

◆ target_dummy_type_

PeakGroup::TargetDummyType target_dummy_type_ = PeakGroup::TargetDummyType::target
private

◆ target_mass_bins_

boost::dynamic_bitset target_mass_bins_
private

mass bins that are targeted for FLASHIda global targeting mode

◆ target_mono_masses_

std::vector<double> target_mono_masses_
private

◆ tolerance_

DoubleList tolerance_
private

tolerance in ppm for each MS level