PeptideIdentification#

class pyopenms.PeptideIdentification#

Bases: object

Cython implementation of _PeptideIdentification

Original C++ documentation is available here: – Inherits from [‘MetaInfoInterface’]

Represents peptide identification results for a single spectrum or feature

PeptideIdentification stores the results of peptide identification from database search engines (e.g., Mascot, X!Tandem, MSGF+). Each PeptideIdentification contains:

A list of peptide hits (candidate sequences) ranked by score
The precursor m/z and retention time
Score type and significance threshold
Link to the ProteinIdentification (via identifier)

Multiple PeptideIdentifications can belong to one ProteinIdentification, which stores the search parameters and protein-level results.

Example usage:

pep_id = oms.PeptideIdentification()
pep_id.setRT(1234.5)  # Set retention time
pep_id.setMZ(445.678)  # Set precursor m/z
pep_id.setScoreType("XTandem")
# Add a peptide hit
hit = oms.PeptideHit()
hit.setScore(50.5)
hit.setRank(1)
hit.setSequence(oms.AASequence.fromString("PEPTIDE"))
hit.setCharge(2)
pep_id.insertHit(hit)
# Access hits
for hit in pep_id.getHits():
    print(f"Sequence: {hit.getSequence().toString()}, Score: {hit.getScore()}")

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeptideIdentification) → None

Methods

`__init__`
`clearMetaInfo`(self)	Removes all meta values
`empty`(self)
`getBaseName`(self)
`getExperimentLabel`(self)
`getHits`(self)	Returns all peptide hits (candidate sequences)
`getIdentifier`(self)	Returns the identifier linking to the parent ProteinIdentification
`getKeys`(self, keys)	Fills the given vector with a list of all keys for which a value is set
`getMZ`(self)	Returns the precursor m/z value
`getMetaValue`(self, in_0)	Returns the value corresponding to a string, or
`getRT`(self)	Returns the retention time of the precursor
`getReferencingHits`(self, in_0, in_1)	Returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession).
`getScoreType`(self)	Returns the type of score (e.g., "Mascot", "XTandem", "q-value")
`getSignificanceThreshold`(self)	Returns the significance threshold value
`hasMZ`(self)	Checks if m/z value is set
`hasRT`(self)	Checks if retention time is set
`insertHit`(self, in_0)	Appends a peptide hit to the list
`isHigherScoreBetter`(self)	Returns whether higher scores are better
`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
`setBaseName`(self, in_0)
`setExperimentLabel`(self, in_0)
`setHigherScoreBetter`(self, in_0)	Sets whether higher scores are better
`setHits`(self, in_0)	Sets all peptide hits at once
`setIdentifier`(self, in_0)	Sets the identifier linking to a ProteinIdentification
`setMZ`(self, in_0)	Sets the precursor m/z value
`setMetaValue`(self, in_0, in_1)	Sets the DataValue corresponding to a name
`setRT`(self, in_0)	Sets the retention time of the precursor
`setScoreType`(self, in_0)	Sets the score type
`setSignificanceThreshold`(self, value)	Sets the significance threshold value
`sort`(self)

clearMetaInfo(self) → None#: Removes all meta values

empty(self) → bool#

getBaseName(self) → bytes | str | String#

getExperimentLabel(self) → bytes | str | String#

getHits(self) → List[PeptideHit]#

Returns all peptide hits (candidate sequences)

Returns:: List of peptide candidates ranked by score

Hits are typically sorted by score, with the best hit at index 0

getIdentifier(self) → bytes | str | String#

Returns the identifier linking to the parent ProteinIdentification

Returns:: Unique identifier string

Use this to find the corresponding ProteinIdentification with search parameters

getKeys(self, keys: List[bytes]) → None#: Fills the given vector with a list of all keys for which a value is set

getMZ(self) → float#

Returns the precursor m/z value

Returns:: Mass-to-charge ratio of the precursor ion

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

getRT(self) → float#

Returns the retention time of the precursor

Returns:: Retention time in seconds

getReferencingHits(self, in_0: List[PeptideHit], in_1: Set[bytes]) → List[PeptideHit]#: Returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession)

getScoreType(self) → bytes | str | String#

Returns the type of score (e.g., “Mascot”, “XTandem”, “q-value”)

Returns:: Name of the score type

getSignificanceThreshold(self) → float#

Returns the significance threshold value

Returns:: The threshold value (interpretation depends on score type)

Hits with scores below/above this threshold (depending on score direction) may be considered insignificant

hasMZ(self) → bool#

Checks if m/z value is set

Returns:: True if m/z is available, False otherwise

hasRT(self) → bool#

Checks if retention time is set

Returns:: True if RT is available, False otherwise

insertHit(self, in_0: PeptideHit) → None#

Appends a peptide hit to the list

Parameters:: hit – The peptide hit to add

isHigherScoreBetter(self) → bool#

Returns whether higher scores are better

Returns:: True if higher scores indicate better matches, False if lower is better

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

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

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

setHigherScoreBetter(self, in_0: bool) → None#

Sets whether higher scores are better

Parameters:: higher_better – True if higher scores are better, False otherwise

setHits(self, in_0: List[PeptideHit]) → None#

Sets all peptide hits at once

Parameters:: hits – List of peptide hits to store

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

Sets the identifier linking to a ProteinIdentification

Parameters:: identifier – Unique identifier string

setMZ(self, in_0: float) → None#

Sets the precursor m/z value

Parameters:: mz – Mass-to-charge ratio of the precursor

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

setRT(self, in_0: float) → None#

Sets the retention time of the precursor

Parameters:: rt – Retention time in seconds

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

Sets the score type

Parameters:: score_type – Name of the score type (e.g., “Mascot”, “XTandem”)

setSignificanceThreshold(self, value: float) → None#

Sets the significance threshold value

Parameters:: value – The threshold value to set

sort(self) → None#