Wrapper struct for all the structs needed by the FLASHDeconv Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak 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) TopPicItem - represent TopPic identification. Currently used for Qscore training. TopPic is the top-down proteomics identification tool (https://www.toppic.org/). iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass. More...

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

Classes
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 Three structures are defined: PrecalculatedAveragine, TopPicItem, and LogMzPeak 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) TopPicItem - represent TopPic identification. Currently used for Qscore training. TopPic is the top-down proteomics identification tool (https://www.toppic.org/). iii) LogMzPeak - Log transformed peak from original peak. Contains information such as charge, isotope index, and uncharged mass.

See also: FLASHDeconvAlgorithm @reference: FeatureFinderAlgorithmPickedHelperStructs

Class Documentation

◆ OpenMS::FLASHDeconvHelperStructs::MassFeature

struct OpenMS::FLASHDeconvHelperStructs::MassFeature

Mass feature (Deconvolved masses in spectra are traced by Mass tracing to generate mass features - like LC-MS features).

Collaboration diagram for FLASHDeconvHelperStructs::MassFeature:

[legend]

Class Members
double	avg_mass
int	charge_count
int	iso_offset
double	isotope_score
int	max_charge
int	min_charge
MassTrace	mt
vector< float >	per_charge_intensity
vector< float >	per_isotope_intensity
double	qscore
int	rep_charge
double	rep_mz
int	scan_number

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

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

Referenced by TOPPFLASHDeconv::main_().

◆ getLogMz()

static double getLogMz	(	double	mz,
		bool	positive
	)