PeptideHit

class pyopenms.PeptideHit

Bases: object

Cython implementation of _PeptideHit

Original C++ documentation is available here

– Inherits from [‘MetaInfoInterface’]

Represents a single peptide identification hit from a database search

A PeptideHit stores information about a candidate peptide sequence that was matched to a spectrum. Each hit contains:

• The peptide sequence (as AASequence)

• A score from the search engine

• The rank among all candidates

• The charge state

• Protein mappings (PeptideEvidence objects)

Multiple PeptideHit objects are typically stored in a PeptideIdentification, sorted by score to show the most likely candidates first.

Example usage:

hit = oms.PeptideHit()
hit.setSequence(oms.AASequence.fromString("PEPTIDER"))
hit.setScore(95.5)
hit.setRank(1)
hit.setCharge(2)
# Access information
print(f"Sequence: {hit.getSequence().toString()}")
print(f"Score: {hit.getScore()}, Rank: {hit.getRank()}")
print(f"Charge: {hit.getCharge()}")

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, score: float, rank: int, charge: int, sequence: AASequence) → None

Overload:

__init__(self, in_0: PeptideHit) → None

Methods

__init__
addAnalysisResults(self, aresult)	Adds a search engine sub-score
addPeptideEvidence(self, in_0)	Adds a single protein mapping
clearMetaInfo(self)	Removes all meta values
extractProteinAccessionsSet(self)	Extracts all unique protein accessions
getAnalysisResults(self)	Returns all search engine sub-scores
getCharge(self)	Returns the charge state of the peptide
getKeys(self, keys)	Fills the given vector with a list of all keys for which a value is set
getMetaValue(self, in_0)	Returns the value corresponding to a string, or
getPeakAnnotations(self)	Returns fragment ion annotations
getPeptideEvidences(self)	Returns protein mapping information for this peptide
getRank(self)	Returns the rank of this hit among all candidates
getScore(self)	Returns the score of this peptide-spectrum match (PSM)
getSequence(self)	Returns the peptide sequence
isDecoy(self)	Checks if this hit maps only to decoy proteins
isMetaEmpty(self)	Returns if the MetaInfo is empty
metaRegistry(self)	Returns a reference to the MetaInfoRegistry
metaValueExists(self, in_0)	Returns whether an entry with the given name exists
removeMetaValue(self, in_0)	Removes the DataValue corresponding to name if it exists
setAnalysisResults(self, aresult)	Sets search engine sub-scores
setCharge(self, in_0)	Sets the charge state
setMetaValue(self, in_0, in_1)	Sets the DataValue corresponding to a name
setPeakAnnotations(self, in_0)	Sets fragment ion annotations
setPeptideEvidences(self, in_0)	Sets the protein mapping information
setRank(self, in_0)	Sets the rank of this hit
setScore(self, in_0)	Sets the PSM score
setSequence(self, in_0)	Sets the peptide sequence

addAnalysisResults(self, aresult: PeptideHit_AnalysisResult) → None

Adds a search engine sub-score

Parameters:

aresult – Sub-score to add

addPeptideEvidence(self, in_0: PeptideEvidence) → None

Adds a single protein mapping

Parameters:

evidence – Protein location information to add

clearMetaInfo(self) → None

Removes all meta values

extractProteinAccessionsSet(self) → Set[bytes]

Extracts all unique protein accessions

Returns:

Set of unique protein accession strings

Empty accessions are excluded from the result

getAnalysisResults(self) → List[PeptideHit_AnalysisResult]

Returns all search engine sub-scores

Returns:

Sub-score information

getCharge(self) → int

Returns the charge state of the peptide

Returns:

Charge state (e.g., 2 for doubly charged)

getKeys(self, keys: List[bytes]) → None

Fills the given vector with a list of all keys for which a value is set

getMetaValue(self, in_0: bytes | str | String) → int | float | bytes | str | List[int] | List[float] | List[bytes]

Returns the value corresponding to a string, or

getPeakAnnotations(self) → List[PeptideHit_PeakAnnotation]

Returns fragment ion annotations

Returns:

Annotated fragment peaks

getPeptideEvidences(self) → List[PeptideEvidence]

Returns protein mapping information for this peptide

Returns:

List of proteins where this peptide was found

Each evidence contains protein accession, start/end positions, and if it’s a decoy

getRank(self) → int

Returns the rank of this hit among all candidates

Returns:

Rank (1 = best hit, 2 = second best, etc.)

getScore(self) → float

Returns the score of this peptide-spectrum match (PSM)

Returns:

The search engine score

Interpretation depends on the score type (check isHigherScoreBetter)

getSequence(self) → AASequence

Returns the peptide sequence

Returns:

The peptide amino acid sequence with modifications

isDecoy(self) → bool

Checks if this hit maps only to decoy proteins

Returns:

True if all protein mappings are decoys, False otherwise

Returns False if no target/decoy information is available

isMetaEmpty(self) → bool

Returns if the MetaInfo is empty

metaRegistry(self) → MetaInfoRegistry

Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0: bytes | str | String) → bool

Returns whether an entry with the given name exists

removeMetaValue(self, in_0: bytes | str | String) → None

Removes the DataValue corresponding to name if it exists

setAnalysisResults(self, aresult: List[PeptideHit_AnalysisResult]) → None

Sets search engine sub-scores

Parameters:

aresult – Sub-score information from search engine

setCharge(self, in_0: int) → None

Sets the charge state

Parameters:

charge – Charge state of the peptide ion

setMetaValue(self, in_0: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) → None

Sets the DataValue corresponding to a name

setPeakAnnotations(self, in_0: List[PeptideHit_PeakAnnotation]) → None

Sets fragment ion annotations

Parameters:

annotations – Fragment peak annotations

setPeptideEvidences(self, in_0: List[PeptideEvidence]) → None

Sets the protein mapping information

Parameters:

evidences – Protein locations for this peptide

setRank(self, in_0: int) → None

Sets the rank of this hit

Parameters:

rank – Rank among all candidates (1 = best)

setScore(self, in_0: float) → None

Sets the PSM score

Parameters:

score – The search engine score to set

setSequence(self, in_0: AASequence) → None

Sets the peptide sequence

Parameters:

sequence – The peptide amino acid sequence