alphabase.psm_reader.maxquant_reader#

Classes:

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

Functions:

parse_mod_seq(modseq[, mod_sep, fixed_C57])

Extract modifications and sites from the modified sequence (modseq)

replace_parentheses_with_brackets(modseq)

class alphabase.psm_reader.maxquant_reader.MaxQuantReader(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=True, mod_seq_columns=['Modified sequence'], **kwargs)[source][source]#

Bases: PSMReaderBase

Methods:

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

Reader for MaxQuant msms.txt and evidence.txt

set_modification_mapping(modification_mapping)

__init__(*, column_mapping: dict = None, modification_mapping: dict = None, fdr=0.01, keep_decoy=False, fixed_C57=True, mod_seq_columns=['Modified sequence'], **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’]

set_modification_mapping(modification_mapping: dict)[source][source]#
alphabase.psm_reader.maxquant_reader.parse_mod_seq(modseq: str, mod_sep: str = '()', fixed_C57: bool = True) → tuple[source]#

Extract modifications and sites from the modified sequence (modseq)

Parameters:

  • modseq (str) – modified sequence to extract modifications.

  • mod_sep (str, optional) – separator to indicate the modification section. Defaults to ‘()’

  • fixed_C (bool) – If Carbamidomethyl@C is a fixed modification and not displayed in the sequence. Defaults to True for MaxQuant.

Returns:

str: naked peptide sequence

str: modification names, separated by ‘;’

str: modification sites, separated by ‘;’. 0 for N-term; -1 for C-term; 1 to N for normal modifications.

Return type:

tuple

alphabase.psm_reader.maxquant_reader.replace_parentheses_with_brackets(modseq: str)[source]#