FLASHHelperClasses Struct Reference

Wrapper struct for all the structs needed by the FLASHDeconv The following structures/classes are defined: PrecalculatedAveragine, MassFeature, IsobaricQuantities, LogMzPeak, Tag, and DAG for tagging. i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) MassFeature - the feature of the deconvolved masses (instead of m/zs for MS features). iii) IsobaricQuantities - the quantities from isobaric quantification (implemented within FLASHDeconv) iv) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. v) Tag - the sequence tag generated on deconvolved spectra in FLASHTaggerAlgorithm vi) DAG - the graph for sequence tagging in FLASHTaggerAlgorithm and for proteoform characterization in FLASHExtenderAlgorithm. More...

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

Classes
struct	IsobaricQuantities
	Isobaric quantities. More...
class	LogMzPeak
	log transformed peak. After deconvolution, all necessary information from deconvolution such as charge and isotope index is stored. More...
struct	MassFeature
	Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features). More...
class	PrecalculatedAveragine
	Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation. More...

Static Public Member Functions
static double	getLogMz (double mz, bool positive)
	calculate log mzs from mzs More...
static float	getChargeMass (bool positive_ioniziation_mode)
	get charge carrier mass : positive mode mass of (Constants::PROTON_MASS_U) and negative mode mass of (-Constants::PROTON_MASS_U) More...

Detailed Description

Wrapper struct for all the structs needed by the FLASHDeconv The following structures/classes are defined: PrecalculatedAveragine, MassFeature, IsobaricQuantities, LogMzPeak, Tag, and DAG for tagging. i) PrecalculatedAveragine - to match observed isotopic envelope against theoretical one, theoretical envelope from averagine model should be quickly calculated. To do so, precalculate averagines for different masses at the beginning of FLASHDeconv runs ii) MassFeature - the feature of the deconvolved masses (instead of m/zs for MS features). iii) IsobaricQuantities - the quantities from isobaric quantification (implemented within FLASHDeconv) iv) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. v) Tag - the sequence tag generated on deconvolved spectra in FLASHTaggerAlgorithm vi) DAG - the graph for sequence tagging in FLASHTaggerAlgorithm and for proteoform characterization in FLASHExtenderAlgorithm.

See also

SpectralDeconvolution

Member Function Documentation

getChargeMass()

static float getChargeMass ( bool  positive_ioniziation_mode )

static

get charge carrier mass : positive mode mass of (Constants::PROTON_MASS_U) and negative mode mass of (-Constants::PROTON_MASS_U)

Parameters

positive_ioniziation_mode

Determines the charge carrier mass (true = positive or false = negative)

getLogMz()

static double getLogMz ( double  mz, bool  positive  )

static

calculate log mzs from mzs

Parameters

mz	mz
positive	determines the charge carrier mass