Classes that capture meta data about a MS or HPLC-MS experiment. More...

Classes
class	Acquisition
	Information about one raw data spectrum that was combined with several other raw data spectra. More...

class	AcquisitionInfo
	Description of the combination of raw data to a single spectrum. More...

class	ChromatogramSettings
	Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...

class	ContactPerson
	Contact person information. More...

class	CVTerm
	Representation of controlled vocabulary term. More...

class	CVTermList
	Representation of controlled vocabulary term list. More...

class	CVTermListInterface
	Interface to the controlled vocabulary term list. More...

class	DataProcessing
	Description of the applied preprocessing steps. More...

class	Digestion
	Meta information about digestion of a sample. More...

class	DocumentIdentifier
	Manage source document information. More...

class	ExperimentalDesign
	Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesignFile class. More...

class	ExperimentalSettings
	Description of the experimental settings. More...

class	Gradient
	Representation of a HPLC gradient. More...

class	HPLC
	Representation of a HPLC experiment. More...

class	Identification
	Represents a object which can store the information of an analysisXML instance. More...

class	IdentificationHit
	Represents a object which can store the information of an analysisXML instance. More...

class	Instrument
	Description of a MS instrument. More...

class	InstrumentSettings
	Description of the settings a MS Instrument was run with. More...

class	IonDetector
	Description of a ion detector (part of a MS Instrument) More...

class	IonSource
	Description of an ion source (part of a MS Instrument) More...

class	MassAnalyzer
	Description of a mass analyzer (part of a MS Instrument) More...

class	MetaInfo
	A Type-Name-Value tuple class. More...

class	MetaInfoDescription
	Description of the meta data arrays of MSSpectrum. More...

class	MetaInfoInterface
	Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). More...

class	MetaInfoRegistry
	Registry which assigns unique integer indices to strings. More...

class	Modification
	Meta information about chemical modification of a sample. More...

class	PeptideEvidence
	Representation of a peptide evidence. More...

class	PeptideHit
	Representation of a peptide hit. More...

class	PeptideIdentification
	Represents the peptide hits for a spectrum. More...

class	Precursor
	Precursor meta information. More...

class	Product
	Product meta information. More...

class	ProteinHit
	Representation of a protein hit. More...

class	ProteinIdentification
	Representation of a protein identification run. More...

class	Sample
	Meta information about the sample. More...

class	SampleTreatment
	Base class for sample treatments (Digestion, Modification, Tagging, ...) More...

struct	ScanWindow
	Scan window description. More...

class	Software
	Description of the software used for processing. More...

class	SourceFile
	Description of a file location, used to store the origin of (meta) data. More...

class	SpectrumIdentification
	Represents a object which can store the information of an analysisXML instance. More...

class	SpectrumSettings
	Representation of 1D spectrum settings. More...

class	Tagging
	Meta information about tagging of a sample e.g. ICAT labeling. More...

class	MQEvidence
	Builds a MaxQuant Evidence.txt. More...

class	MQExporterHelper
	Helper class for common functions and NON trivial values needed for exporting MaxQuant outputs. More...

class	MQMsms
	Builds a MaxQuant msms.txt. More...

Functions
template<typename ContainerType , typename PredicateType >
static void	removeFromSetIf_ (ContainerType &container, PredicateType predicate)
	Representation of spectrum identification results and associated data. More...

Detailed Description

Classes that capture meta data about a MS or HPLC-MS experiment.

The top-level classes are OpenMS::ExperimentalSettings and OpenMS::SpectrumSettings .

Function Documentation

◆ removeFromSetIf_()

static void OpenMS::removeFromSetIf_	(	ContainerType &	container,
		PredicateType	predicate
	)

static

Representation of spectrum identification results and associated data.

This class provides capabilities for storing spectrum identification results from different types of experiments/molecules (proteomics: peptides/proteins, metabolomics: small molecules, "nucleomics": RNA).

The class design has the following goals:

Provide one structure for storing all relevant data for spectrum identification results.
Store data non-redundantly.
Ensure consistency (e.g. no conflicting information; no "dangling references").
Allow convenient and efficient querying.
Support different types of experiments, as mentioned above, in one common framework.

The following important subordinate classes are provided to represent different types of data:

Class	Represents	Key	Proteomics example	Corresponding legacy class
ProcessingStep	Information about a data processing step that was applied (e.g. input files, software used, parameters)	Combined information	Mascot search	ProteinIdentification
Observation	A search query (with identifier, RT, m/z) from an input file, i.e. an MS2 spectrum or feature (for accurate mass search)	File/Identifier	MS2 spectrum	PeptideIdentification
ParentSequence	An entry in a FASTA file with associated information (sequence, coverage, etc.)	Accession	Protein	ProteinHit
IdentifiedPeptide/-Oligo/-Compound	An identified molecule of the respective type	Sequence (or identifier for a compound)	Peptide	PeptideHit
ObservationMatch	A match between a query (Observation), identified molecule (Identified...), and optionally adduct	Combination of query/molecule/adduct references	Peptide-spectrum match (PSM)	PeptideIdentification/PeptideHit

To populate an IdentificationData instance with data, "register..." functions are used. These functions return "references" (implemented as iterators) that can be used to refer to stored data items and thus form connections. For example, a protein can be stored using registerParentSequence, which returns a corresponding reference. This reference can be used to build an IdentifiedPeptide object that references the protein. An identified peptide referencing a protein can only be registered if that protein has been registered already, to ensure data consistency. Given the identified peptide, information about the associated protein can be retrieved efficiently by simply dereferencing the reference.

To ensure non-redundancy, many data types have a "key" (see table above) to which a uniqueness constraint applies. This means only one item of such a type with a given key can be stored in an IdentificationData object. If items with an existing key are registered subsequently, attempts are made to merge new information (e.g. additional scores) into the existing entry. The details of this merging are handled in the merge function in each data class.

Warning: This class is not thread-safe while being modified. Remove elements from a set (or ordered multi_index_container) if they fulfill a predicate (TODO: deprecate and use std::erase_if with C++20 adoption)

Referenced by IdentificationData::removeObservationMatchesIf(), and IdentificationData::removeParentSequencesIf().

Classes

Functions

Detailed Description

Function Documentation

◆ removeFromSetIf_()