Topdown

Topdown-related classes. More...

Collaboration diagram for Topdown:

Classes
class	FLASHDeconvAlgorithm
	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 deisotoping - peak groups are defined here iii) scoring and filter out low scoring masses (i.e., peak groups) More...
class	MassFeatureTrace
	Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by SpectralDeconvolution In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. This class also comes with tsv, TopFD feature file formats. More...
class	PeakGroup
	Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used for PeakGroupScoring calculation. DeconvolvedSpectrum consists of PeakGroups. More...
class	PeakGroupScoring
	scoring functions for PeakGroup. For now, only Qscore has been implemented. For Qscore, the weight vector has been determined by logistic regression. In the future, other technique such as deep learning would be used. More...
class	Qvalue
	Qvalue : contains functions to calculate Qvalues from deconvolution quality score (Qscore) defined in PeakGroupScoring. More...
class	SpectralDeconvolution
	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...
class	TopDownIsobaricQuantification
	Isobaric quantification for Top down proteomics. The report ion ratios from multiple MS2 are merged when their precursor masses belong to the same deconvolved features (MassFeature instances). More...

Detailed Description

Topdown-related classes.