alphabase.psm_reader.msfragger_reader

MSFragger reader.

Classes:

MSFraggerModificationTranslator(...)

Translate MSFragger PSM.TSV modifications to alphabase format.

MSFraggerPepXML(*args, **kwargs)

Deprecated.

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

Reader for MSFragger's pep.xml file.

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

Reader for MSFragger's psm.tsv file.

Functions:

register_readers()

Register MSFragger readers.
class alphabase.psm_reader.msfragger_reader.MSFraggerModificationTranslator(mass_mapped_mods: List[str], mod_mass_tol: float, rev_mod_mapping: Dict[str, str])[source][source]

Bases: object

Translate MSFragger PSM.TSV modifications to alphabase format.

Methods:

__init__(mass_mapped_mods, mod_mass_tol, ...)

Initialize MSFragger modification translator.

translate(psm_df)

Translate modifications from MSFragger assigned modifications.
__init__(mass_mapped_mods: List[str], mod_mass_tol: float, rev_mod_mapping: Dict[str, str])[source][source]

Initialize MSFragger modification translator.

Parameters:

  • mass_mapped_mods (List[str]) – List of modification names to match against (e.g., [‘Phospho@S’, ‘Oxidation@M’])

  • mod_mass_tol (float) – Mass tolerance for matching modifications in Daltons.

  • rev_mod_mapping (Dict[str, str]) – Reverse mapping from MSFragger format to alphabase format. Keys use MSFragger’s native format: ‘AA(mass)’ or ‘N-term(mass)’. Values use alphabase format: ‘Mod@AA’.

translate(psm_df: DataFrame) → DataFrame[source][source]

Translate modifications from MSFragger assigned modifications.

Parameters:

psm_df (pd.DataFrame) – DataFrame with PsmDfCols.TMP_MODS column containing raw assigned modifications strings

Returns:

The input DataFrame with ‘mods’ and ‘mod_sites’ columns added

Return type:

pd.DataFrame

class alphabase.psm_reader.msfragger_reader.MSFraggerPepXML(*args, **kwargs)[source][source]

Bases: MSFraggerPepXMLReader

Deprecated.

Methods:

__init__(*args, **kwargs)

Deprecated.
__init__(*args, **kwargs)[source][source]

Deprecated.

class alphabase.psm_reader.msfragger_reader.MSFraggerPepXMLReader(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.001, keep_decoy: bool = False, rt_unit: str | None = None, keep_unknown_aa_mass_diffs: bool = False, **kwargs)[source][source]

Bases: PSMReaderBase

Reader for MSFragger’s pep.xml file.

Methods:

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

Initialize the MSFraggerreader.
__init__(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.001, keep_decoy: bool = False, rt_unit: str | None = None, keep_unknown_aa_mass_diffs: bool = False, **kwargs)[source][source]

Initialize the MSFraggerreader.

See documentation of PSMReaderBase for more information.

MSFragger is not fully supported as we can only access the pepxml file.

Parameters:

keep_unknown_aa_mass_diffs – whether to keep PSMs with unknown amino acid mass differences, default: False

See documentation of PSMReaderBase for the rest of parameters.

class alphabase.psm_reader.msfragger_reader.MSFraggerPsmTsvReader(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, **kwargs)[source][source]

Bases: PSMReaderBase

Reader for MSFragger’s psm.tsv file.

Methods:

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

Initialize MSFragger PSM TSV reader.
__init__(*, column_mapping: dict | None = None, modification_mapping: dict | None = None, fdr: float = 0.01, keep_decoy: bool = False, rt_unit: str | None = None, **kwargs)[source][source]

Initialize MSFragger PSM TSV reader.

Parameters:

  • column_mapping (Optional[dict]) – Custom column name mapping.

  • modification_mapping (Optional[dict]) – Custom modification mapping from alphabase format to MSFragger format. Keys use alphabase format: ‘Mod@AA’. Values use MSFragger’s native format: ‘AA(mass)’ or ‘N-term(mass)’ or ‘C-term(mass)’. Example: {‘Phospho@S’: ‘S(79.9663)’, ‘TMTpro@Any_N-term’: ‘N-term(304.2071)’}

  • fdr (float) – False discovery rate threshold. Default: 0.01

  • keep_decoy (bool) – Whether to keep decoy hits. Default: False

  • rt_unit (Optional[str]) – Retention time unit.

  • **kwargs – Additional arguments passed to PSMReaderBase.

alphabase.psm_reader.msfragger_reader.register_readers() → None[source][source]

Register MSFragger readers.