Identification

Protein and peptide identification classes. More...

Collaboration diagram for Identification:

Classes
class	AccurateMassSearchResult
	One small-molecule hit produced by AccurateMassSearchEngine. More...
class	AccurateMassSearchEngine
	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB). More...
class	BasicProteinInferenceAlgorithm
	Simple protein inference by aggregation of per-peptide PSM scores. More...
struct	CometModification
	Helper struct that represents one Comet variable_modXX entry and supports merging compatible entries. More...
class	ConsensusIDAlgorithm
	Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs). More...
class	ConsensusIDAlgorithmAverage
	Calculates a consensus from multiple ID runs by averaging the search scores. More...
class	ConsensusIDAlgorithmBest
	Calculates a consensus from multiple ID runs by taking the best search score. More...
class	ConsensusIDAlgorithmIdentity
	Abstract base class for ConsensusID algorithms that compare only identical sequences. More...
class	ConsensusIDAlgorithmPEPIons
	Calculates a consensus from multiple ID runs based on PEPs and shared ions. More...
class	ConsensusIDAlgorithmPEPMatrix
	Calculates a consensus from multiple ID runs based on PEPs and sequence similarities. More...
class	ConsensusIDAlgorithmRanks
	Calculates a consensus from multiple ID runs based on the ranks of the search hits. More...
class	ConsensusIDAlgorithmSimilarity
	Abstract base class for ConsensusID algorithms that take peptide similarity into account. More...
class	ConsensusIDAlgorithmWorst
	Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach). More...
class	FalseDiscoveryRate
	Calculates false discovery rates (FDR) from identifications. More...
class	FIAMSDataProcessor
	Data processing pipeline for one Flow Injection Analysis MS (FIA-MS) sample. More...
class	FIAMSScheduler
	Batch driver for FIA-MS analyses. Dispatches each sample of a CSV-described batch to FIAMSDataProcessor. More...
class	IDBoostGraph
	Creates and maintains a boost graph based on the OpenMS ID datastructures. More...
class	IDDecoyProbability
	IDDecoyProbability calculates probabilities using decoy approach. More...
class	IDRipper
	Ripping protein/peptide identification according their file origin. More...
class	IonIdentityMolecularNetworking
	Helpers for the Ion Identity Molecular Networking (IIMN) workflow on GNPS. More...
class	SpectralMatch
	One library-search match record: the observed spectrum, the matching DB spectrum, the score, and the metabolite metadata copied from the hit. More...
class	MetaboliteSpectralMatching
	Metabolomics spectral-library search by hyperscore. More...
class	NeighborSeq
	Subset-neighbor peptide search: find peptides from a wider pool (typically a FASTA digest) that are spectral neighbors of a smaller "relevant" peptide set, useful when only part of a complex sample is of interest. More...
class	PeptideProteinResolution
	Resolves shared peptides based on protein scores. More...
class	PrecursorPurity
	Precursor purity or noise estimation. More...
class	Scores
	Utility class for score type handling in identification and quantification workflows. More...
class	SimpleSearchEngineAlgorithm
	Minimal in-memory peptide-spectrum search engine. More...
class	SiriusExportAlgorithm
	Algorithm class behind the SiriusExport tool: writes a SIRIUS .ms input file from MS data and (optionally) a featureXML. More...
class	SiriusMSFile
	Writes a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations. More...
class	NuXLAnnotateAndLocate
	Post-scoring step of the OpenNuXL pipeline: annotates fragment-ion peaks of each candidate hit and localises the NA cross-link to a residue. More...
class	NuXLConstants
	Index positions of the per-peak IntegerDataArrays used by the OpenNuXL pipeline. More...
class	NuXLFDR
	Class-separated FDR calculation for nucleic-acid cross-links (NuXL). More...
class	NuXLFragmentIonGenerator
	Augments a peptide-cross-link fragment spectrum with NuXL-specific ions that TheoreticalSpectrumGenerator does not produce. More...
struct	NuXLModificationMassesResult
	Result of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup. More...
class	NuXLModificationsGenerator
	Enumerator of precursor-adduct masses for NuXL cross-link searches. More...
class	DDAWorkflowCommons
	Common functions for DDA workflows. More...
class	NeedlemanWunsch
	Global-alignment similarity score for two amino-acid sequences using the Needleman-Wunsch algorithm. More...
class	OpenPepXLAlgorithm
	Search for peptide pairs linked with a labeled cross-linker. More...
class	OPXLDataStructs
	Namespace-style container holding the data types shared across the OpenPepXL cross-linking pipeline. More...
class	OPXLSpectrumProcessingAlgorithms
	Spectrum preprocessing and theoretical-vs-experimental peak alignment helpers used by the OpenPepXL cross-link search engines. More...
class	SearchEngineBase
	Base class for TOPP search-engine adapters. More...

Detailed Description

Protein and peptide identification classes.

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Class Documentation

OpenMS::NuXLModificationMassesResult

struct OpenMS::NuXLModificationMassesResult

Result of NuXLModificationsGenerator::initModificationMassesNA — empirical formulas with their monoisotopic mass and the disambiguating nucleotide-composition lookup.

Two parallel maps keyed by the same empirical-formula string:

• formula2mass — empirical formula → monoisotopic mass.
• mod_combinations — empirical formula → set of nucleotide-composition strings that produce that formula. A set rather than a single value because different oligos can share a chemical formula, e.g. C18H22N4O16P2 → {CU-H3N1, UU-H2O1}.

The nested MyStringLengthCompare comparator orders the composition strings primarily by length and lexicographically within the same length so the shortest (most likely) composition appears first when iterating a value.

Collaboration diagram for NuXLModificationMassesResult:

Class Members
typedef map< string, NucleotideFormulas >	MapSumFormulaToNucleotideFormulas	Empirical formula → NucleotideFormulas.
typedef set< string, MyStringLengthCompare >	NucleotideFormulas	Length-ordered set of nucleotide-composition strings producing the same empirical formula.

Class Members
map< string, double >	formula2mass	Empirical formula → monoisotopic mass.
MapSumFormulaToNucleotideFormulas	mod_combinations	Empirical formula → all nucleotide compositions yielding that formula (kept as a set because mutations / losses can make the mapping ambiguous).