FineIsotopePatternGenerator Class Reference

Isotope pattern generator for fine isotope distributions. More...

#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/FineIsotopePatternGenerator.h>

Inheritance diagram for FineIsotopePatternGenerator:

Collaboration diagram for FineIsotopePatternGenerator:

Public Member Functions
	FineIsotopePatternGenerator ()=default
	Default Constructor. More...
	FineIsotopePatternGenerator (double stop_condition, bool use_total_prob=true, bool absolute=false)
	Constructor. More...
IsotopeDistribution	run (const EmpiricalFormula &) const
	Creates an isotope distribution from an empirical sum formula. More...
void	setThreshold (double stop_condition)
	Set probability stop condition (lower values generate fewer results) More...
double	getThreshold () const
	Get probability stop condition (lower values generate fewer results) More...
void	setAbsolute (bool absolute)
	Set whether threshold is absolute or relative probability (ignored if use_total_prob is true, see class docu) More...
bool	getAbsolute () const
	Returns whether threshold is absolute or relative probability (ignored if use_total_prob is true, see class docu) More...
void	setTotalProbability (bool total)
	Set whether total probability should be computed. More...
bool	getTotalProbability () const
	Returns whether total probability should be computed. More...
Public Member Functions inherited from IsotopePatternGenerator
	IsotopePatternGenerator ()
	IsotopePatternGenerator (double probability_cutoff)
virtual	~IsotopePatternGenerator ()

Protected Attributes
double	stop_condition_ = 0.01
bool	absolute_ = false
bool	use_total_prob_ = true
Protected Attributes inherited from IsotopePatternGenerator
double	min_prob_

Detailed Description

Isotope pattern generator for fine isotope distributions.

This algorithm generates theoretical pattern distributions for empirical formulas with high resolution (while the CoarseIsotopePatternGenerator will generate low-resolution patterns). The output is a list of pairs containing isotope probabilities paired with the accurate m/z for the analyte isotopic composition.

For example, for a C100H202 molecule (at 0.01 threshold), you will get:

m/z 1403.5806564438 : INT 0.333207070827484
m/z 1404.5840114438 : INT 0.360387712717056
m/z 1404.5869331919 : INT 0.00774129061028361
m/z 1405.5873664438 : INT 0.19294385612011
m/z 1405.5902881919 : INT 0.00837276969105005
m/z 1406.5907214438 : INT 0.0681697279214859
m/z 1406.5936431919 : INT 0.00448260130360723
m/z 1407.5940764438 : INT 0.0178796537220478
m/z 1407.5969981919 : INT 0.00158376491162926
...

For comparison, the CoarseIsotopePatternGenerator will produce the following result for a C100H202 molecule:

m/z 1403.58 INT: 0.333489
m/z 1404.58 INT: 0.36844
m/z 1405.59 INT: 0.201576
m/z 1406.59 INT: 0.0728113
m/z 1407.59 INT: 0.0195325
...

One important value to set is the threshold with tells the algorithm when to stop calculating isotopic peaks to calculate. The default stop condition is to stop when only a small portion (such as 0.01) of the total probability is unexplained and the reported values cover most of the probability (e.g. 0.99).

Another way to stop the search is when any new peak would be less than 0.01 in height (absolute) or when it would be less than 0.01 of the highest isotopic peak (relative). This is how the stop_condition parameter is interpreted when use_total_prob is set to false.

Note

Computation of fine isotope patterns can be slow for large molecules, if you don't need fine isotope distributions consider using CoarseIsotopePatternGenerator.

Consider using IsoSpec directly or the OpenMS IsoSpecWrapper / IsoSpecGeneratorWrapper classes defined in IsoSpecWrapper.h for increased performance.

The computation is based on the IsoSpec algorithm

Łącki MK, Startek M, Valkenborg D, Gambin A.
IsoSpec: Hyperfast Fine Structure Calculator.
Anal Chem. 2017 Mar 21;89(6):3272-3277. doi: 10.1021/acs.analchem.6b01459.

See also method run()

Constructor & Destructor Documentation

FineIsotopePatternGenerator() [1/2]

FineIsotopePatternGenerator ( )

default

Default Constructor.

FineIsotopePatternGenerator() [2/2]

FineIsotopePatternGenerator ( double  stop_condition, bool  use_total_prob = true, bool  absolute = false  )

inline

Constructor.

Parameters

stop_condition	The total probability (if use_total_prob == true) or threshold (if use_total_prob is false) (see class docu)
use_total_prob	Whether the stop_condition should be interpreted as a probability threshold (only configurations with intensity above this threshold will be returned) or as a total probability that the distribution should cover.
absolute	Whether threshold is absolute or relative (ignored if use_total_prob is true, see class docu)

Member Function Documentation

getAbsolute()

bool getAbsolute ( ) const

inline

Returns whether threshold is absolute or relative probability (ignored if use_total_prob is true, see class docu)

getThreshold()

double getThreshold ( ) const

inline

Get probability stop condition (lower values generate fewer results)

getTotalProbability()

bool getTotalProbability ( ) const

inline

Returns whether total probability should be computed.

run()

IsotopeDistribution run ( const EmpiricalFormula &  ) const

virtual

Creates an isotope distribution from an empirical sum formula.

Iterates through all elements, convolves them according to the number of atoms from that element and sums up the result.

Note

The constructed isotope distribution is sorted by m/z which slows down processing, consider using IsoSpec (IsoSpecWrapper / IsoSpecGeneratorWrapper) directly for increased performance.

Implements IsotopePatternGenerator.

setAbsolute()

void setAbsolute ( bool  absolute )

inline

Set whether threshold is absolute or relative probability (ignored if use_total_prob is true, see class docu)

setThreshold()

void setThreshold ( double  stop_condition )

inline

Set probability stop condition (lower values generate fewer results)

setTotalProbability()

void setTotalProbability ( bool  total )

inline

Set whether total probability should be computed.

Member Data Documentation

absolute_

bool absolute_ = false

protected

stop_condition_

double stop_condition_ = 0.01

protected

use_total_prob_

bool use_total_prob_ = true

protected