massdash.loaders.SpectralLibraryLoader

class massdash.loaders.SpectralLibraryLoader(in_file: str, verbose: bool = False)

Bases: object

Class for loading spectral library files.

in_file

The path to the spectral library file.

Type:

str

data

The spectral library data.

Type:

pd.DataFrame

filter_for_target_transition_list(protein: str, peptide: str, charge: int) → DataFrame

Filters the data for a specific target transition list based on the given protein, peptide, and charge.

Parameters:

  • protein (str) – The protein ID.

  • peptide (str) – The modified peptide sequence.

  • charge (int) – The precursor charge.

Returns:

The filtered data containing the target transition list.

Return type:

pd.DataFrame

get_fragment_library_intensity(peptide: str, charge: int, annotation: str) → float

Retrieves a list of fragment annotations for a given peptide and charge.

Parameters:

  • peptide (str) – The peptide sequence.

  • charge (int) – The precursor charge.

  • annotation (str) – The fragment annotation.

Returns:

The library intensity for the specified fragment annotation.

Return type:

float

get_peptide_fragment_annotation_list(peptide: str, charge: int) → List[str]

Retrieves a list of fragment annotations for a given peptide and charge.

Parameters:

  • peptide (str) – The peptide sequence.

  • charge (int) – The precursor charge.

Returns:

A list of fragment annotations.

Return type:

List[str]

get_peptide_ion_mobility(peptide: str, charge: int) → float

Retrieves the ion mobility of a peptide with a specific charge from the spectral library.

Parameters: peptide (str): The modified peptide sequence. charge (int): The precursor charge.

Returns: float: The precursor ion mobility.

get_peptide_library_intensity(peptide: str, charge: int) → float

Get the library intensity for a specific peptide and charge.

Parameters:

  • peptide (str) – The modified peptide sequence.

  • charge (int) – The precursor charge.

Returns:

The library intensity for the specified peptide and charge.

Return type:

float

get_peptide_precursor_mz(peptide: str, charge: int) → float

Get the precursor m/z value for a given peptide and charge.

Parameters: peptide (str): The modified peptide sequence. charge (int): The precursor charge.

Returns: float: The precursor m/z value.

get_peptide_product_charge_list(peptide: str, charge: int) → List[int]

Retrieve a list of product charges for a given peptide and charge.

Parameters:

  • peptide (str) – The modified peptide sequence.

  • charge (int) – The precursor charge.

Returns:

A list of product charges.

Return type:

List[int]

get_peptide_product_mz_list(peptide: str, charge: int) → List[float]

Retrieve a list of product m/z values for a given peptide and charge.

Parameters:

  • peptide (str) – The modified peptide sequence.

  • charge (int) – The precursor charge.

Returns:

A list of product m/z values.

Return type:

List[float]

get_peptide_retention_time(peptide: str, charge: int) → float

Get the retention time for a given peptide and charge.

Parameters: peptide (str): The modified peptide sequence. charge (int): The precursor charge.

Returns: float: The normalized retention time.

get_unique_charge_states_per_peptide(peptide: str) → List[int]

Returns a list of unique charge states for a given peptide.

Parameters:

peptide (str) – The peptide sequence.

Returns:

A list of unique charge states associated with the peptide.

Return type:

List[int]

get_unique_peptides_per_protein(protein: str) → List[str]

Returns a list of unique peptide sequences for a given protein.

Parameters:

protein (str) – The protein ID.

Returns:

A list of unique peptide sequences.

Return type:

List[str]

get_unique_proteins() → List[str]

Returns a list of unique protein IDs from the data.

Returns:

A list of unique protein IDs.

Return type:

List[str]

load() → DataFrame

Load the transition list file

populateTransitionGroupFeature(transition_group_feature: TransitionGroupFeature) → TransitionGroupFeature

Appends library information to a TransitionGroupFeature object

Parameters:

transition_group_feature (TransitionGroupFeature) – The TransitionGroupFeature object to append library information to.

Returns:

The TransitionGroupFeature object with appended library information.

Return type:

TransitionGroupFeature

populateTransitionGroupFeatures(transition_group_features: List[TransitionGroupFeature]) → List[TransitionGroupFeature]

Populates library information for a list of TransitionGroupFeature objects. *Important:* Assumes that all TransitionGroupFeature objects have the same peptide sequence and precursor charge.

save(file_path: str) → None

Save the data to a file.

Parameters:

file_path (str) – The path to the file where the data will be saved.

Returns:

None