OpenMS
FLASHDeconvHelperStructs Struct Reference

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

Referenced by TOPPFLASHDeconv::main_().

◆ getLogMz()

static double getLogMz ( double  mz,
bool  positive 
)
static

calculate log mzs from mzs

Parameters
mzmz
positivedetermines the charge carrier mass