51 Contact(
const std::string&
id =
"");
78 Software(
const std::string& _id =
"");
82 const std::string& _version);
178 Protein(
const std::string&
id =
"");
230 Peptide(
const std::string&
id =
"");
248 Compound(
const std::string&
id =
"");
347 namespace IO {
struct HandlerTraData;}
390 const std::string& version()
const;
402 friend struct IO::HandlerTraData;
413 #endif // _TRADATA_HPP_
std::vector< Modification > modifications
List of modifications on this peptide.
std::vector< CompoundPtr > compoundPtrs
Precursor (Q1) of the transition.
List of precursor m/z targets to include or exclude.
std::vector< ProteinPtr > proteinPtrs
Reference to zero or more proteins which this peptide is intended to identify.
double averageMassDelta
Atomic mass delta when considering the natural distribution of isotopes in Daltons.
std::vector< InstrumentPtr > instrumentPtrs
List of instruments on which transitions are validated.
boost::shared_ptr< Protein > ProteinPtr
std::vector< Interpretation > interpretationList
List of possible interprations of fragment ions for a transition.
double monoisotopicMassDelta
Atomic mass delta when assuming only the most common isotope of elements in Daltons.
Precursor precursor
Precursor (Q1) of the target.
std::vector< Target > targetExcludeList
List of precursor m/z targets to exclude.
Information about the state of validation of a transition on a given instrument model.
PWIZ_API_DECL std::vector< CV > defaultCVList()
returns a default list of CVs used in an TraML document; currently includes PSI-MS, Unit Ontology, and UNIMOD
std::string id
Identifier for the protein to be used for referencing within a document.
std::string id
Identifier for the compound to be used for referencing within a document.
Instrument on which transitions are validated.
Prediction prediction
Information about a prediction for a suitable transition using some software.
Information about a prediction for a suitable transition using some software.
TargetList targets
List of precursor m/z targets to include or exclude.
A peptide or compound that is to be included or excluded from a target list of precursor m/z values...
Instrument configuration used in the validation or optimization of the transitions.
std::string id
String label for this transition.
std::string version
Version of the software program described.
std::vector< SoftwarePtr > softwarePtrs
List of software packages used in the generation of one of more transitions described in the document...
Information about empirical mass spectrometer observations of the peptide.
std::string sequence
Amino acid sequence of the protein.
std::string id
Identifier for the software to be used for referencing within a document.
PeptidePtr peptidePtr
Reference to a peptide for which this target is the trigger.
std::string id
String label for this target.
represents a post-translational modification (PTM) modification formula or masses must be provided at...
RetentionTime retentionTime
Information about predicted or calibrated retention time.
CompoundPtr compoundPtr
Reference to a compound for which this target is the trigger.
std::string id
Identifier for the instrument to be used for referencing within a document.
A possible interpration of the product ion for a transition.
std::string sequence
Amino acid sequence of the peptide being described.
boost::shared_ptr< Compound > CompoundPtr
SoftwarePtr softwarePtr
Reference to a software package from which this prediction is derived.
Chemical compound other than a peptide for which one or more transitions.
represents a peptide or polypeptide (a sequence of amino acids)
ContactPtr contactPtr
Reference to a contact person that generated this prediction.
RetentionTime retentionTime
Information about predicted or calibrated retention time.
InstrumentPtr instrumentPtr
Reference to an instrument for which this configuration information is appropriate.
std::vector< Publication > publications
List of publications from which the transitions were collected or wherein they are published...
The base class for elements that may contain cvParams, userParams, or paramGroup references.
boost::shared_ptr< Contact > ContactPtr
ContactPtr contactPtr
Reference to a contact person originating this information.
std::vector< CV > cvs
List of controlled vocabularies used in a TraML document note: one of the <cv> elements in this list ...
Product (Q3) of the transition.
Product product
Product (Q3) of the transition.
PeptidePtr peptidePtr
Reference to a peptide which this transition is intended to identify.
std::string id
Identifier for the peptide to be used for referencing within a document.
boost::shared_ptr< Peptide > PeptidePtr
std::vector< Validation > validations
CompoundPtr compoundPtr
Reference to a compound for this transition.
boost::shared_ptr< TraData > TraDataPtr
std::vector< Transition > transitions
List of transitions.
std::vector< Configuration > configurationList
List of insutrument configurations used in the validation or optimization of the transitions.
boost::shared_ptr< Instrument > InstrumentPtr
SoftwarePtr softwarePtr
Software used to determine the retention time.
std::vector< Configuration > configurationList
List of instrument configurations used in the validation or optimization of the target.
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
Precursor precursor
Precursor (Q1) of the transition.
std::vector< PeptidePtr > peptidePtrs
List of compounds (including peptides) for which one or more transitions are intended to identify...
std::vector< Target > targetIncludeList
List of precursor m/z targets to include.
boost::shared_ptr< Software > SoftwarePtr
std::vector< ProteinPtr > proteinPtrs
List of proteins for which one or more transitions are intended to identify.
std::string id
Identifier for the publication to be used for referencing within a document.
int location
Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.
std::string id
for internal use: not currently in the schema
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
std::vector< ContactPtr > contactPtrs
List of contacts referenced in the generation or validation of transitions.
represents a tag-value pair, where the tag comes from the controlled vocabulary