Uses of Package
com.compomics.util.experiment.massspectrometry

Packages that use com.compomics.util.experiment.massspectrometry

Package	Description
com.compomics.util.experiment	Gene factory classes.
com.compomics.util.experiment.identification	Experiment classes related to identifications.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.identification_parameters	Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.identification_parameters.tool_specific	Parameters settings for the search algorithms.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.ptm	Additional PSM scoring classes.
com.compomics.util.experiment.identification.ptm.ptmscores	PTM scores.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	Spectrum annotation.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.io.massspectrometry	Reading and indexing of mgf files.
com.compomics.util.experiment.io.massspectrometry.export	Experiment classes related to exporting mass spectrometry files.
com.compomics.util.experiment.massspectrometry	Experiment classes related to spectra.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment

Class and Description
FragmentationMethod Enum for the different fragmentation methods.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification

Class and Description
Charge This class models a charge.
Peak This class represents a peak.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.filtering

Class and Description
SpectrumFactory This factory will provide the spectra when needed.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.identification_parameters

Class and Description
Charge This class models a charge.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.identification_parameters.tool_specific

Class and Description
Charge This class models a charge.
FragmentationMethod Enum for the different fragmentation methods.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.matches

Class and Description
Charge This class models a charge.
Peak This class represents a peak.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.psm_scoring

Class and Description
MSnSpectrum This class models an MSn spectrum.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.psm_scoring.psm_scores

Class and Description
MSnSpectrum This class models an MSn spectrum.
Precursor This class models a precursor.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.ptm

Class and Description
MSnSpectrum This class models an MSn spectrum.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.ptm.ptmscores

Class and Description
MSnSpectrum This class models an MSn spectrum.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.spectrum_annotation

Class and Description
MSnSpectrum This class models an MSn spectrum.
Peak This class represents a peak.
Spectrum This class models a spectrum.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Class and Description
MSnSpectrum This class models an MSn spectrum.
Peak This class represents a peak.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.identification.spectrum_assumptions

Class and Description
Charge This class models a charge.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.io.massspectrometry

Class and Description
MSnSpectrum This class models an MSn spectrum.
Precursor This class models a precursor.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.io.massspectrometry.export

Class and Description
FragmentationMethod Enum for the different fragmentation methods.
MSnSpectrum This class models an MSn spectrum.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.experiment.massspectrometry

Class and Description
Charge This class models a charge.
FragmentationMethod Enum for the different fragmentation methods.
Peak This class represents a peak.
Precursor This class models a precursor.
Spectrum This class models a spectrum.
SpectrumFactory This factory will provide the spectra when needed.

Classes in com.compomics.util.experiment.massspectrometry used by com.compomics.util.gui.spectrum

Class and Description
MSnSpectrum This class models an MSn spectrum.