peptdeep.mass_spec.ms_reader¶

Classes:

`AlphaPept_HDF_MS1_Reader`()	MS1 from AlphaPept HDF
`AlphaPept_HDF_MS2_Reader`()	MS2 from AlphaPept HDF
`MGFReader`()	MGF Reader (MS2)
`MSReaderBase`()
`MSReaderProvider`()	Factory class to register and get MS Readers
`MZMLReader`()
`ThermoRawMS1Reader`()	Thermo Raw MS1 Reader
`ThermoRawMS2Reader`()	Thermo RAW MS2 Reader

Functions:

`find_line`(lines, start)
`index_ragged_list`(ragged_list)	Create lookup indices for a list of arrays for concatenation.
`is_pfind_mgf`(mgf)
`parse_pfind_scan_from_TITLE`(pfind_title)
`read_until`(file, until)

class peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS1_Reader[source][source]¶

Bases: MSReaderBase

MS1 from AlphaPept HDF

Methods:

load(file_path)

load(file_path)[source][source]¶

class peptdeep.mass_spec.ms_reader.AlphaPept_HDF_MS2_Reader[source][source]¶

Bases: MSReaderBase

MS2 from AlphaPept HDF

Methods:

load(file_path)

load(file_path)[source][source]¶

class peptdeep.mass_spec.ms_reader.MGFReader[source][source]¶

Bases: MSReaderBase

MGF Reader (MS2)

Methods:

load(mgf)

load(mgf)[source][source]¶

class peptdeep.mass_spec.ms_reader.MSReaderBase[source][source]¶

Bases: object

Methods:

`__init__`()
`build_spectrum_df`(scan_list, scan_indices, ...)	Build spectrum_df by the given information
`get_peaks`(spec_idx)	Get peak (mz and intensity) values by spec_idx
`get_peaks_by_scan_num`(scan_num)	Get peak (mz and intensity) values by spec_idx
`load`(file_path)

__init__()[source][source]¶

build_spectrum_df(scan_list: list, scan_indices: ndarray, rt_list: list, mobility_list: list = None, nce_list: list = None)[source][source]¶

Build spectrum_df by the given information

Parameters:

scan_list (list) – scan number list
scan_indices (np.array) – starts and end positions of ms2 peaks for each scan
rt_list (list) – retention time (minutes) for each scan
mobility_list (list, optional) – mobility for each scan. Defaults to None.