Chemistry

Classes
class	AAIndex
	Representation of selected AAIndex properties. More...
class	AASequence
	Representation of a peptide/protein sequence. More...
class	AdductInfo
	Mass-arithmetic helper for ionizing adducts (e.g. [M+H]+, [2M-H]-, [M+2K-H]+). More...
class	BuiltInProteaseDataProvider
	Data provider for built-in protease definitions. More...
class	CrossLinksDB
	Process-wide singleton database of cross-linking modifications. More...
class	DigestionEnzyme
	Base class for digestion enzymes. More...
class	DigestionEnzymeDataProvider< EnzymeType >
	Abstract interface for providing digestion enzyme data. More...
class	InMemoryDigestionEnzymeDataProvider< EnzymeType >
	In-memory data provider for digestion enzymes (primarily for testing) More...
class	DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
	Digestion enzyme database (base class) More...
class	DigestionEnzymeProtein
	Representation of a digestion enzyme for proteins (protease) More...
class	DigestionEnzymeRNA
	Representation of a digestion enzyme for RNA (RNase) More...
class	Element
	Representation of an element. More...
class	ElementDB
	Singleton that stores elements and isotopes. More...
class	EmpiricalFormula
	Representation of an empirical formula. More...
class	EnzymaticDigestion
	Class for the enzymatic digestion of sequences. More...
class	EnzymeXMLDataProvider< EnzymeType >
	Data provider that loads digestion enzymes from an XML file. More...
class	HydrophobicityProfile
	This class is used for hydrophobicity profiling of peptides. More...
class	CoarseIsotopePatternGenerator
	Isotope pattern generator for coarse isotope distributions. More...
class	FineIsotopePatternGenerator
	Isotope pattern generator for fine isotope distributions. More...
class	ModificationDataProvider
	Interface for providing ResidueModification data to ModificationsDB. More...
class	InMemoryDataProvider
	Data provider that serves pre-built modifications from memory. More...
class	ModificationDefinition
class	ModificationDefinitionsSet
class	ModificationsDB
	database which holds all residue modifications from UniMod More...
class	ModifiedNASequenceGenerator
	Generator of modified nucleic-acid sequences for fixed and variable modification placement. More...
class	ModifiedPeptideGenerator
	Generate fixed- and variable-modification variants of an AASequence, lock-free. More...
class	ModomicsJSONDataProvider
	Loads Ribonucleotide data from a Modomics JSON file. More...
class	MonosaccharideDB
	Singleton database of monosaccharides for glycan notation. More...
struct	MzPAFNeutralLoss
	Neutral loss in an mzPAF annotation. More...
struct	MzPAFMassDelta
	Mass delta in an mzPAF annotation. More...
struct	MzPAFAnnotation
	A single mzPAF peak annotation. More...
struct	MzPAFPeakAnnotations
	Multiple mzPAF annotations for a single peak. More...
class	MzPAFParseError
	Parse error for mzPAF notation. More...
class	MzPAF
	Parser and writer for mzPAF (Peak Annotation Format) notation. More...
class	NASequence
	Representation of a nucleic acid sequence. More...
class	NucleicAcidSpectrumGenerator
	Generates theoretical spectra for nucleic acid sequences. More...
class	OBODataProvider
	Loads ResidueModification data from an OBO ontology file (PSI-MOD or XLMOD). More...
class	ProForma
	ProForma v2 peptidoform notation parser and data structures. More...
class	ProteaseDB
	Database for enzymes that digest proteins (proteases) More...
class	ProteaseDigestion
	Class for the enzymatic digestion of proteins represented as AASequence or String. More...
class	Residue
	Representation of an amino acid residue. More...
class	ResidueDB
	OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. More...
class	Ribonucleotide
	Representation of a ribonucleotide (modified or unmodified) More...
struct	RibonucleotideEntry
	Holds a Ribonucleotide together with optional ambiguity codes. More...
class	RibonucleotideDataProvider
	Interface for providing Ribonucleotide data to RibonucleotideDB. More...
class	InMemoryRibonucleotideDataProvider
	Data provider that serves pre-built ribonucleotides from memory. More...
class	RibonucleotideDB
	Database of ribonucleotides (modified and unmodified) More...
class	RibonucleotideTSVDataProvider
	Loads Ribonucleotide data from a tab-separated values (TSV) file. More...
class	RNaseDB
	Database for enzymes that digest RNA (RNases) More...
class	RNaseDigestion
	Class for the enzymatic digestion of RNAs. More...
class	SequenceCoverage
	Compute sequence coverage of a protein by peptide sequences. More...
class	SimpleTSGXLMS
	Generates theoretical spectra for cross-linked peptides. More...
class	SpectrumAnnotator
	Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...
class	TheoreticalSpectrumGenerator
	Generates theoretical spectra for peptides with various options. More...
class	UnimodXMLDataProvider
	Loads ResidueModification data from a Unimod XML file. More...

Enumerations
enum class	ProteomicsPkaScale {   LEHNINGER = 0 , EMBOSS = 1 , SILLERO = 2 , BJELLQVIST = 3 ,   SIZE_OF_PROTEOMICS_PKA_SCALES }
	Utility class for computing the isoelectric point (pI) and net charge of peptides. More...
enum class	MzPAFIonSeries {   A , B , C , X ,   Y , Z , PRECURSOR , IMMONIUM ,   INTERNAL , REPORTER , FORMULA , NAMED ,   UNKNOWN }
	Ion series types for mzPAF peak annotations. More...
enum class	MzPAFDeltaUnit { DALTON , PPM }
	Unit for mass delta values in mzPAF annotations. More...
enum class	MzPAFErrorCode {   UNEXPECTED_CHARACTER , UNCLOSED_BRACKET , INVALID_ION_SERIES , INVALID_NUMBER ,   INVALID_FORMULA , INVALID_CHARGE , INVALID_DELTA , INVALID_CONFIDENCE ,   EMPTY_INPUT , UNEXPECTED_END_OF_INPUT , INTERNAL_ERROR }
	Error codes for mzPAF parsing errors. More...

Detailed Description

Enumeration Type Documentation

MzPAFDeltaUnit

enum class MzPAFDeltaUnit

strong

Unit for mass delta values in mzPAF annotations.

Enumerator
DALTON	Mass delta in Daltons (Da)
PPM	Mass delta in parts per million.

MzPAFErrorCode

enum class MzPAFErrorCode

strong

Error codes for mzPAF parsing errors.

Enumerator
UNEXPECTED_CHARACTER	Unexpected character encountered.
UNCLOSED_BRACKET	Opening bracket without matching close.
INVALID_ION_SERIES	Invalid ion series character.
INVALID_NUMBER	Invalid numeric value.
INVALID_FORMULA	Invalid chemical formula.
INVALID_CHARGE	Invalid charge specification.
INVALID_DELTA	Invalid mass delta specification.
INVALID_CONFIDENCE	Invalid confidence score.
EMPTY_INPUT	Empty input string.
UNEXPECTED_END_OF_INPUT	Unexpected end of input.
INTERNAL_ERROR	Internal parser error.

MzPAFIonSeries

enum class MzPAFIonSeries

strong

Ion series types for mzPAF peak annotations.

Identifies the type of fragment ion or special ion in an mzPAF annotation.

Enumerator
A	a-ion (N-terminal, loses CO)
B	b-ion (N-terminal)
C	c-ion (N-terminal, ETD)
X	x-ion (C-terminal)
Y	y-ion (C-terminal)
Z	z-ion (C-terminal, ETD)
PRECURSOR	Precursor ion (p)
IMMONIUM	Immonium ion (I)
INTERNAL	Internal fragment (m)
REPORTER	Reporter ion (r)
FORMULA	Chemical formula ion (f)
NAMED	Named compound (_)
UNKNOWN	Unknown or unrecognized ion type.

ProteomicsPkaScale

enum class ProteomicsPkaScale

strong

Utility class for computing the isoelectric point (pI) and net charge of peptides.

This class provides methods to compute:

• The net charge of an amino acid sequence at a given pH using the Henderson-Hasselbalch equation
• The isoelectric point (pI), i.e. the pH at which the net charge is zero, found via bisection

The calculation considers:

• The N-terminal amino group (pKa), unless the peptide has an N-terminal modification
• The C-terminal carboxyl group (pKa), unless the peptide has a C-terminal modification
• Ionizable side chains of D, E, C, U, Y, H, K, R

The default pK values follow the Lehninger scale (Nelson & Cox, Lehninger Principles of Biochemistry). Other supported scales (EMBOSS, Sillero, Bjellqvist) can be selected via the ProteomicsPkaScale enum.

The Bjellqvist scale uses N-terminal-residue-dependent pKa values for the N-terminus (one value per N-terminal residue identity) and residue-dependent C-terminal pKas for D and E.

Side-chain PTM-specific pKa shifts are currently not modeled; modified residues are evaluated using the parent residue one-letter code. Pyrrolysine (O) is not supported and raises Exception::InvalidValue. If the zero crossing lies outside the searched pH interval [0, 14], computePI() returns the closer boundary and logs a warning.

References:

• Nelson DL, Cox MM. Lehninger Principles of Biochemistry. 6th ed. (2013).
• Sillero A, Ribeiro JM. Isoelectric points of proteins... Anal Biochem. 1989;179:319-325.
• Bjellqvist B et al. Isoelectric focusing in immobilized pH gradients... Electrophoresis 1993;14:1023-1031.

Enum for pKa scales used in isoelectric point calculation

Enumerator
LEHNINGER	Lehninger (Nelson & Cox) scale.
EMBOSS	EMBOSS scale (used by pepstats)
SILLERO	Sillero & Ribeiro scale.
BJELLQVIST	Bjellqvist scale with N-terminal-residue-dependent pKa values.
SIZE_OF_PROTEOMICS_PKA_SCALES