massdash.loaders.access.MzMLDataAccess

class massdash.loaders.access.MzMLDataAccess(filename: str, readOptions='ondisk', verbose=False)

Bases: object

Class for data loading and extracting operations of an .mzML file

filename

The mzML file to load.

Type:

str

readOptions

The readOptions to use, either ‘ondisk’ or ‘cached’.

Type:

str

exp

The on disk experiment.

Type:

OnDiscMSExperiment

meta_data

The meta data.

Type:

MSExperiment

has_im

Whether the data has ion mobility.

Type:

bool

load_data()

Loads data from an mzML file as an on disc experiment for memory efficiency and meta data access without loading full data.

get_target_ms_level_indices()

Extract spectrum indices for a specific mslevel(s).

get_spectra_rt_list()

Get a list of RT for all the spectra using meta_exp.

check_ion_mobility(num_lines_to_check=10000000)

Check if the mzML file contains ion mobility data

Args: mzml_file: (str) mzML file to load num_lines_to_check: (int) Number of lines to check for “Ion Mobility”

Returns: Return a boolean indicating if the mzML file contains ion mobility data

filter_single_spectrum(spec_indice: int, feature: TransitionGroupFeature, config: TargetedDIAConfig) → _MSSpectrumDF

Filter a single spectrum for a given spectrum indice.

Parameters:

  • spec_indice – (int) an interger of the spectrum indice to extra a spectrum for

  • feature – (TransitionGroupFeature) metadata on feature

  • config – (TargetedDIAConfig object) an object of TargetedDIAConfig that contains configuration parameters of how wide filtering windows should be

Returns:

po.MSSpectrum() a MSSpectrum object

get_spectra_rt_list() → array

Get a list of RT for all the spectra using meta_exp

Parameters:

self – (object) self object containing meta_data

Returns:

Return a list of RT values for spectra

get_target_ms_level_indices(mslevel=[1, 2]) → array

Extract spectrum indices for a specific mslevel(s).

Parameters:

  • self – (object) self object containing meta_data

  • mslevel – (list) list of mslevel(s) to extract indices for

Returns:

Return mslevel_indices a list of indices with request mslevel(s) to self

load_data()

Method to load data from an mzML file as an on disc experiment for memory efficiency and meta data access without loading full data

load_spectrum(spec_indice: int) → Tuple[array, array, array]

Load a single spectrum for a given spectrum indice.

Parameters:

spec_indice – (int) an interger of the spectrum indice to extra a spectrum for

Returns:

mz array int_array: intensity array im_array: ion mobility array

Return type:

mz_array

msExperimentToFeatureMap(msExperiment: _MSExperimentDF, feature: TransitionGroupFeature, config: TargetedDIAConfig) → FeatureMap

Convert filtered spectra to Pandas DataFrame

Parameters:

  • msExperiment – (MSExperiment) MSExperiment object that contains filtered data

  • feature – (TransitionGroupFeature) metadata on feature

  • config – (TargetedDIAConfig object) an object of TargetedDIAConfig that contains configuration parameters of how wide filtering windows should be

Returns:

a FeatureMap object that contains filtered spectra

Return type:

FeatureMap

reduce_spectra(feature: TransitionGroupFeature, config: TargetedDIAConfig) → FeatureMap

Main method for filtering raw mzML DIA/diaPASEF data given specific set of coordinates to filter for.

Parameters:

  • feature – (TransitionGroupFeature) a TransitionGroupFeature object that contains coordinates to filter for

  • config – (TargetedDIAConfig object) an object of TargetedDIAConfig that contains configuration parameters of how wide filtering windows should be

Returns:

a FeatureMap object that contains filtered spectra

Return type:

FeatureMap