massdash.loaders.GenericSpectrumLoader

class massdash.loaders.GenericSpectrumLoader(libraryFile=None, **kwargs)

Bases: GenericRawDataLoader

Abstract class for loading raw spectrum data

rsltsFile

(str) The path to the report file (DIANN-TSV or OSW)

dataFiles

(str/List[str]) The path to the mzML file(s)

libraryFile

(str) The path to the library file (.tsv or .pqp)

abstract loadFeatureMaps(pep_id: str, charge: int, config=<class 'massdash.structs.TargetedDIAConfig.TargetedDIAConfig'>, runNames: None | str | ~typing.List[str] = None) → Dict[str, FeatureMap]

Loads a dictionary of FeatureMaps (where the keys are the filenames) from the results file

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • runNames (None | str | List[str]) – Name of the run to extract the feature map from. If None, all runs are extracted. If str, only the specified run is extracted. If List[str], only the specified runs are extracted.

Returns:

FeatureMap object containing peak boundaries, intensity and confidence

Return type:

FeatureMap

abstract loadTransitionGroups(pep_id: str, charge: int, config: TargetedDIAConfig, runNames: None | str | List[str] = None) → Dict[str, TransitionGroup]

Loads the transition group for a given peptide ID and charge across all files

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • config (TargetedDIAConfig) – Configuration object containing the extraction parameters

  • runNames (None | str | List[str]) – Name of the run to extract the transition group from. If None, all runs are extracted. If str, only the specified run is extracted. If List[str], only the specified runs are extracted.

Returns:

Dictionary of TransitionGroups, with keys as filenames

Return type:

dict[str, TransitionGroup]

abstract loadTransitionGroupsDf(pep_id: str, charge: int, config: TargetedDIAConfig) → Dict[str, DataFrame]

Loads the transition group for a given peptide ID and charge across all files into a pandas DataFrame

Parameters:

  • pep_id (str) – Peptide ID

  • charge (int) – Charge

  • config (TargetedDIAConfig) – Configuration object containing the extraction parameters

Returns:

Dictionary of TransitionGroups, with keys as filenames

Return type:

dict[str, pd.DataFrame]

plotChromatogram(seq: str, charge: int, runName: str | None = None, includeBoundaries: bool = True, include_ms1: bool = False, smooth: bool = True, sgolay_polynomial_order: int = 3, sgolay_frame_length: int = 11, mz_tol: float = 20, rt_window: float = 50, im_window: float | None = None, **kwargs) → bokeh.plotting.figure.Figure

Plots a chromatogram for a given peptide sequence and charge state for a given run

Parameters:

  • seq (str) – Peptide sequence

  • charge (int) – Charge state

  • runName (str) – Name of the run to extract the chromatogram from

  • includeBoundaries (bool, optional) – Whether to include peak boundaries. Defaults to True.

  • include_ms1 (bool, optional) – Whether to include MS1 data. Defaults to False.

  • smooth (bool, optional) – Whether to smooth the chromatogram. Defaults to True.

  • sgolay_polynomial_order (int, optional) – Order of the polynomial to use for smoothing. Defaults to 3.

  • sgolay_frame_length (int, optional) – Frame length to use for smoothing. Defaults to 11.

  • mz_tol (float, optional) – m/z tolerance for extraction (in ppm). Defaults to 20.

  • rt_tol (float, optional) – RT tolerance for extraction (in seconds). Defaults to 50.

  • im_tol (float, optional) – IM tolerance for extraction (in 1/k0). Defaults to None.

Returns:

Bokeh figure object

Return type:

bokeh.plotting.figure.Figure