Class and Description |
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CvParam
This object holds additional data in controlled vocabulary.
|
ExperimentMetaData
General descriptions shared or used for the whole file.
|
Parameter
Parameter exist in neither PRIDE XML nor mzML, it created for method sharing.
|
ParamGroup
ParamGroup is a container for CvParams and UserParams.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
Precursor
The method of precursor ion selection and activation
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
Score
Score stores a number of scores from a list of search engines.
|
Spectrum
A peak list including the underlying acquisitions.
|
Class and Description |
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Chromatogram
Chromatogram object.
|
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
ExperimentMetaData
General descriptions shared or used for the whole file.
|
FragmentIon
FragmentIon stores details about peptide fragment ion information.
|
IdentificationMetaData
This class is used to manage and store the information of the metadata for protein and spectrum
identifications.
|
Modification
A molecule modification specification.
|
MzGraphMetaData
This class storage the information related with metadata at the spectrum level.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
ProteinGroup
A set of logically related results from a protein detection, for example to represent conflicting assignments of
peptides to proteins
|
Quantification
Quantitation object is a pseudo object which contains all the cv params related to quantitative data for PRIDE XMLs.
|
QuantitativeSample
QuantitativeSample which contains quantitative related information
This is mainly for PRIDE XMl
|
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
QuantScore
The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
|
Score
Score stores a number of scores from a list of search engines.
|
SearchDataBase
A database for searching mass spectra.
|
Spectrum
A peak list including the underlying acquisitions.
|
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
SubstitutionModification
Substitution Modification is a Modification where One amino acid is replaced by another amino acid.
|
Class and Description |
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Chromatogram
Chromatogram object.
|
CVLookup
CVLookup is referenced in every CvParam.
|
DataProcessing
Description of the way in which a List of Software were used.
|
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
ExperimentMetaData
General descriptions shared or used for the whole file.
|
ExperimentProtocol
Protocol used to generate the dataset, added by PRIDE XML 2.0.
|
FragmentIon
FragmentIon stores details about peptide fragment ion information.
|
IdentificationMetaData
This class is used to manage and store the information of the metadata for protein and spectrum
identifications.
|
InstrumentConfiguration
Description of a particular hardware configuration of a mass spectrometer.
|
Modification
A molecule modification specification.
|
MzGraphMetaData
This class storage the information related with metadata at the spectrum level.
|
Organization
Organizations are entities like companies, universities, government agencies.
|
ParamGroup
ParamGroup is a container for CvParams and UserParams.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
Person
A person's name and contact details.
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
ProteinGroup
A set of logically related results from a protein detection, for example to represent conflicting assignments of
peptides to proteins
|
Protocol
The collection of protocols which include the parameters and settings of the performed analyses.
|
Provider
Provider object.
|
Quantification
Quantitation object is a pseudo object which contains all the cv params related to quantitative data for PRIDE XMLs.
|
QuantitativeSample
QuantitativeSample which contains quantitative related information
This is mainly for PRIDE XMl
|
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
QuantScore
The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
|
Reference
Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
|
ReferenceableParamGroup
Referenceable param group stores a map of reference string to param group.
|
Sample
Description of the sample used to generate the Dataset.
|
ScanSetting
Description of the acquisition settings or the instrument prior to the start of
the run.
|
Score
Score stores a number of scores from a list of search engines.
|
SearchDataBase
A database for searching mass spectra.
|
Software
Software details.
|
SourceFile
Description of source file, including identification file, location and type.
|
SpectraData
A data set containing spectra data (consisting of one or more spectra).
|
Spectrum
A peak list including the underlying acquisitions.
|
SpectrumIdentificationProtocol
The parameters and settings of a SpectrumIdentification analysis.
|
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
SubstitutionModification
Substitution Modification is a Modification where One amino acid is replaced by another amino acid.
|
Class and Description |
---|
BinaryDataArray
BinaryDataArray is a slim down version of binaryDataArray in mzML
ParamGroup of this object must have the followings in mzML 1.1.0.1 definition:
For Chromatograms (once each):
1.
|
Chromatogram
Chromatogram object.
|
CVLookup
CVLookup is referenced in every CvParam.
|
CvParam
This object holds additional data in controlled vocabulary.
|
DataProcessing
Description of the way in which a List of Software were used.
|
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
ExperimentProtocol
Protocol used to generate the dataset, added by PRIDE XML 2.0.
|
IdentifiableParamGroup
Other classes in the model can be specified as sub-classes, inheriting from IdentifiablePraramGroup.
|
InstrumentConfiguration
Description of a particular hardware configuration of a mass spectrometer.
|
Organization
Organizations are entities like companies, universities, government agencies.
|
ParamGroup
ParamGroup is a container for CvParams and UserParams.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
Person
A person's name and contact details.
|
Precursor
The method of precursor ion selection and activation
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
ProteinGroup
A set of logically related results from a protein detection, for example to represent conflicting assignments of
peptides to proteins
|
Protocol
The collection of protocols which include the parameters and settings of the performed analyses.
|
Provider
Provider object.
|
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
Reference
Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
|
ReferenceableParamGroup
Referenceable param group stores a map of reference string to param group.
|
Sample
Description of the sample used to generate the Dataset.
|
ScanSetting
Description of the acquisition settings or the instrument prior to the start of
the run.
|
SearchDataBase
A database for searching mass spectra.
|
Software
Software details.
|
SourceFile
Description of source file, including identification file, location and type.
|
SpectraData
A data set containing spectra data (consisting of one or more spectra).
|
Spectrum
A peak list including the underlying acquisitions.
|
SpectrumIdentification
PSM Spectrum identification match.
|
SpectrumIdentificationProtocol
The parameters and settings of a SpectrumIdentification analysis.
|
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
UserParam
Uncontrolled user parameters, allowing free text.
|
Class and Description |
---|
Assay
Assay In the mzTab experiment with the corresponding Reagent and sample
|
BinaryDataArray
BinaryDataArray is a slim down version of binaryDataArray in mzML
ParamGroup of this object must have the followings in mzML 1.1.0.1 definition:
For Chromatograms (once each):
1.
|
Contact
This class is just to organize the code, the ConstantRole class have to kind of instance,
one of then is Organization and the Other one if the person both objects extend the IdentifiableParamGroup
in order to organize the code we create a new abstract class named AbstractContact to separate the Contacts types
from the IdentifiableParamGroup.
|
CvParam
This object holds additional data in controlled vocabulary.
|
DataBaseTranslation
DataBaseTranslation control and storage the information of Nucleotide Databases.
|
DataProcessing
Description of the way in which a List of Software were used.
|
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
Enzyme
Enzyme used during the search in Databases.
|
ExperimentProtocol
Protocol used to generate the dataset, added by PRIDE XML 2.0.
|
ExternalData
Data external to the XML instance document.
|
Filter
Filter controlled the database filters with CVParams and UserParams.
|
FragmentIon
FragmentIon stores details about peptide fragment ion information.
|
Gel
Gel is a class to Describe the Gel Spot for each Protein.
|
Identifiable
Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
|
IdentifiableParamGroup
Other classes in the model can be specified as sub-classes, inheriting from IdentifiablePraramGroup.
|
InstrumentComponent
InstrumentComponent is key to keep the order of different instrument
component.
|
InstrumentConfiguration
Description of a particular hardware configuration of a mass spectrometer.
|
MassSpecObject
All core objects should implement this interface.
|
MassTable |
Modification
A molecule modification specification.
|
MzGraph
Abstract object can be extended by both Spectrum and Chromatogram.
|
Organization
Organizations are entities like companies, universities, government agencies.
|
Parameter
Parameter exist in neither PRIDE XML nor mzML, it created for method sharing.
|
ParamGroup
ParamGroup is a container for CvParams and UserParams.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
PeptideSequence
One (poly)peptide (a sequence with modifications).
|
Person
A person's name and contact details.
|
Precursor
The method of precursor ion selection and activation
|
ProcessingMethod
Description of the default peak processing method.
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
Protocol
The collection of protocols which include the parameters and settings of the performed analyses.
|
Provider
Provider object.
|
Quantification.Type
The type of the identification;
|
QuantPeptide
Quantitative Peptide is a Peptide with Quantitation information and is used in mzTab file formats.
|
QuantScore
The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
|
Reference
Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
|
Sample
Description of the sample used to generate the Dataset.
|
Scan
Scan or acquisition from original raw file used to create this
peak list, as specified in sourceFile.
|
ScanList
List and descriptions of scans.
|
ScanSetting
Description of the acquisition settings or the instrument prior to the start of
the run.
|
Score
Score stores a number of scores from a list of search engines.
|
SearchDataBase
A database for searching mass spectra.
|
SearchModification
Search Modification is the variable or fixed modification defined in the Identification Search
by the user.
|
Software
Software details.
|
SourceFile
Description of source file, including identification file, location and type.
|
SpectraData
A data set containing spectra data (consisting of one or more spectra).
|
Spectrum
A peak list including the underlying acquisitions.
|
SpectrumIdentification
PSM Spectrum identification match.
|
SpectrumIdentificationProtocol
The parameters and settings of a SpectrumIdentification analysis.
|
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
SubstitutionModification
Substitution Modification is a Modification where One amino acid is replaced by another amino acid.
|
UserParam
Uncontrolled user parameters, allowing free text.
|
Class and Description |
---|
CvParam
This object holds additional data in controlled vocabulary.
|
Peptide
The class Peptide Manage the information for peptide Identifications
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
UserParam
Uncontrolled user parameters, allowing free text.
|
Class and Description |
---|
Peptide
The class Peptide Manage the information for peptide Identifications
|
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
Class and Description |
---|
CvParam
This object holds additional data in controlled vocabulary.
|
ParamGroup
ParamGroup is a container for CvParams and UserParams.
|
Score
Score stores a number of scores from a list of search engines.
|
SpectraData
A data set containing spectra data (consisting of one or more spectra).
|
UserParam
Uncontrolled user parameters, allowing free text.
|
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