Interface | Description |
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MassSpecObject |
All core objects should implement this interface.
|
Class | Description |
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AbundanceAssay |
Abundance Assay is the Class to storage the abundance variables for each Protein.
|
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.
|
Chromatogram |
Chromatogram object.
|
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.
|
ContactRole |
Contact Role is a class to define the role of an Specific Contact (Organization or Person)in the context
of the Experiment a role is defined as CvParams ()
The role that a Contact plays in an organization or with respect to the associating class.
|
CVLookup |
CVLookup is referenced in every CvParam.
|
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.
|
ExperimentMetaData |
General descriptions shared or used for the whole file.
|
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.
|
IdentificationMetaData |
This class is used to manage and store the information of the metadata for protein and spectrum
identifications.
|
InstrumentComponent |
InstrumentComponent is key to keep the order of different instrument
component.
|
InstrumentConfiguration |
Description of a particular hardware configuration of a mass spectrometer.
|
IonType |
IonType defines the index of fragmentation ions being reported,
importing a CV term for the type of ion e.g.
|
MassTable | |
Modification |
A molecule modification specification.
|
MzGraph |
Abstract object can be extended by both Spectrum and Chromatogram.
|
MzGraphMetaData |
This class storage the information related with metadata at the spectrum level.
|
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
|
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.
|
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.
|
SpectrumIdentificationList |
Represents the set of all search results from SpectrumIdentification.
|
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.
|
Enum | Description |
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Quantification.Type |
The type of the identification;
|
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