alphabase.psm_reader.dia_psm_reader#

Classes:

DiannReader(*[, column_mapping, ...])

SpectronautReader(*[, column_mapping, ...])

Reader for Spectronaut's output library TSV/CSV.

SpectronautReportReader(*[, column_mapping, ...])

Reader for Spectronaut's report TSV/CSV.

SwathReader(*[, column_mapping, ...])

class alphabase.psm_reader.dia_psm_reader.DiannReader(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, rt_unit='minute', **kwargs)[source][source]#

Bases: SpectronautReader

Methods:

__init__(*[, column_mapping, ...])

Also similar to MaxQuantReader, but different in column_mapping and modificatin_mapping
__init__(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, rt_unit='minute', **kwargs)[source][source]#

Also similar to MaxQuantReader, but different in column_mapping and modificatin_mapping

class alphabase.psm_reader.dia_psm_reader.SpectronautReader(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, mod_seq_columns=['ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'ModifiedPeptideSequence', 'LabeledSequence', 'FullUniModPeptideName'], rt_unit='minute', **kwargs)[source][source]#

Bases: MaxQuantReader

Reader for Spectronaut’s output library TSV/CSV.

Other parameters, please see MaxQuantReader in alphabase.psm_reader.maxquant_reader

Parameters:

csv_sep (str, optional) – Delimiter for TSV/CSV, by default ‘ ‘

Methods:

__init__(*[, column_mapping, ...])

Reader for MaxQuant msms.txt and evidence.txt
__init__(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, mod_seq_columns=['ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'ModifiedPeptideSequence', 'LabeledSequence', 'FullUniModPeptideName'], rt_unit='minute', **kwargs)[source][source]#

Reader for MaxQuant msms.txt and evidence.txt

Parameters:

  • column_mapping (dict, optional) – By default None. If None, use psm_reader_yaml[‘maxquant’][‘column_mapping’] (alphabase.psm_reader.psm_reader_yaml).

  • modification_mapping (dict, optional) – By default None. If None, use psm_reader_yaml[‘maxquant’][‘modification_mapping’] (alphabase.psm_reader.psm_reader_yaml).

  • fdr (float, optional) – Load PSMs with FDR < this fdr, by default 0.01

  • keep_decoy (bool, optional) – If keep decoy PSMs, by default False

  • fixed_C57 (bool, optional) – If true, the search engine will not show Carbamidomethyl in the modified sequences. by default True

  • mod_seq_columns (list, optional) – The columns to find modified sequences, by default [‘Modified sequence’]

class alphabase.psm_reader.dia_psm_reader.SpectronautReportReader(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, rt_unit='minute', **kwargs)[source][source]#

Bases: MaxQuantReader

Reader for Spectronaut’s report TSV/CSV.

Other parameters, please see MaxQuantReader in alphabase.psm_reader.maxquant_reader

Parameters:

csv_sep (str, optional) – Delimiter for TSV/CSV, by default ‘,’

Methods:

__init__(*[, column_mapping, ...])

Reader for MaxQuant msms.txt and evidence.txt
__init__(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, rt_unit='minute', **kwargs)[source][source]#

Reader for MaxQuant msms.txt and evidence.txt

Parameters:

  • column_mapping (dict, optional) – By default None. If None, use psm_reader_yaml[‘maxquant’][‘column_mapping’] (alphabase.psm_reader.psm_reader_yaml).

  • modification_mapping (dict, optional) – By default None. If None, use psm_reader_yaml[‘maxquant’][‘modification_mapping’] (alphabase.psm_reader.psm_reader_yaml).

  • fdr (float, optional) – Load PSMs with FDR < this fdr, by default 0.01

  • keep_decoy (bool, optional) – If keep decoy PSMs, by default False

  • fixed_C57 (bool, optional) – If true, the search engine will not show Carbamidomethyl in the modified sequences. by default True

  • mod_seq_columns (list, optional) – The columns to find modified sequences, by default [‘Modified sequence’]

class alphabase.psm_reader.dia_psm_reader.SwathReader(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, mod_seq_columns=['ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'ModifiedPeptideSequence', 'LabeledSequence', 'FullUniModPeptideName'], **kwargs)[source][source]#

Bases: SpectronautReader

Methods:

__init__(*[, column_mapping, ...])

SWATH or OpenSWATH library, similar to SpectronautReader
__init__(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=False, mod_seq_columns=['ModifiedPeptide', 'ModifiedSequence', 'FullUniModPeptideName', 'ModifiedPeptideSequence', 'LabeledSequence', 'FullUniModPeptideName'], **kwargs)[source][source]#

SWATH or OpenSWATH library, similar to SpectronautReader