peptdeep.protein.fasta#

Main entry APIs for predicting libraries from fasta (peptide list).

Check Tutorial: spectral library from fasta.

Classes:

PredictSpecLibFasta([model_manager, ...])

Predicted spec lib from fasta files or other peptide files.
class peptdeep.protein.fasta.PredictSpecLibFasta(model_manager: ModelManager = None, *, charged_frag_types: list = ['b_z1', 'b_z2', 'y_z1', 'y_z2'], protease: str = 'trypsin', max_missed_cleavages: int = 2, peptide_length_min: int = 7, peptide_length_max: int = 35, precursor_charge_min: int = 2, precursor_charge_max: int = 4, precursor_mz_min: float = 400.0, precursor_mz_max: float = 1800.0, var_mods: list = ['Acetyl@Protein N-term', 'Oxidation@M'], min_var_mod_num: int = 0, max_var_mod_num: int = 2, fix_mods: list = ['Carbamidomethyl@C'], labeling_channels: dict = None, special_mods: list = [], min_special_mod_num: int = 0, max_special_mod_num: int = 1, special_mods_cannot_modify_pep_n_term: bool = False, special_mods_cannot_modify_pep_c_term: bool = False, decoy: str = None, include_contaminants: bool = False, I_to_L=False, generate_precursor_isotope: bool = False, rt_to_irt: bool = False)[source][source]#

Bases: SpecLibFasta, PredictSpecLib

Predicted spec lib from fasta files or other peptide files.

Methods:

__init__([model_manager, ...])

param model_manager:

ModelManager of MS2/RT/CCS... models, by default None

add_charge()

Add charge states
__init__(model_manager: ModelManager = None, *, charged_frag_types: list = ['b_z1', 'b_z2', 'y_z1', 'y_z2'], protease: str = 'trypsin', max_missed_cleavages: int = 2, peptide_length_min: int = 7, peptide_length_max: int = 35, precursor_charge_min: int = 2, precursor_charge_max: int = 4, precursor_mz_min: float = 400.0, precursor_mz_max: float = 1800.0, var_mods: list = ['Acetyl@Protein N-term', 'Oxidation@M'], min_var_mod_num: int = 0, max_var_mod_num: int = 2, fix_mods: list = ['Carbamidomethyl@C'], labeling_channels: dict = None, special_mods: list = [], min_special_mod_num: int = 0, max_special_mod_num: int = 1, special_mods_cannot_modify_pep_n_term: bool = False, special_mods_cannot_modify_pep_c_term: bool = False, decoy: str = None, include_contaminants: bool = False, I_to_L=False, generate_precursor_isotope: bool = False, rt_to_irt: bool = False)[source][source]#
Parameters:

  • model_manager (ModelManager, optional) – ModelManager of MS2/RT/CCS… models, by default None

  • charged_frag_types (list, optional) – Fragment types with charge, by default [ ‘b_z1’,’b_z2’,’y_z1’, ‘y_z2’ ]

  • protease (str, optional) – Could be pre-defined protease name defined in protease_dict, or a regular expression. By default ‘trypsin’

  • max_missed_cleavages (int, optional) – Maximal missed cleavages, by default 2

  • peptide_length_min (int, optional) – Minimal cleaved peptide length, by default 7

  • peptide_length_max (int, optional) – Maximal cleaved peptide length, by default 35

  • precursor_charge_min (int, optional) – Minimal precursor charge, by default 2

  • precursor_charge_max (int, optional) – Maximal precursor charge, by default 4

  • precursor_mz_min (float, optional) – Minimal precursor mz, by default 200.0

  • precursor_mz_max (float, optional) – Maximal precursor mz, by default 2000.0

  • var_mods (list, optional) – list of variable modifications, by default [‘Acetyl@Protein N-term’,’Oxidation@M’]

  • max_var_mod_num (int, optional) – Minimal number of variable modifications on a peptide sequence, by default 0

  • max_var_mod_num – Maximal number of variable modifications on a peptide sequence, by default 2

  • fix_mods (list, optional) – list of fixed modifications, by default [‘Carbamidomethyl@C’]

  • labeling_channels (dict, optional) – Add isotope labeling with different channels, see add_peptide_labeling(). Defaults to None

  • special_mods (list, optional) – Special modifications. It is useful for modificaitons like Phospho which may largely explode the number of candidate modified peptides. The number of special_mods per peptide is controlled by max_append_mod_num. Defaults to [].

  • min_special_mod_num (int, optional) – Control the min number of special_mods per peptide, by default 0.

  • max_special_mod_num (int, optional) – Control the max number of special_mods per peptide, by default 1.

  • special_mods_cannot_modify_pep_c_term (bool, optional) – Some modifications cannot modify the peptide C-term, this will be useful for GlyGly@K as if C-term is di-Glyed, it cannot be cleaved/digested. Defaults to False.

  • special_mods_cannot_modify_pep_n_term (bool, optional) – Similar to special_mods_cannot_modify_pep_c_term, but at N-term. Defaults to False.

  • decoy (str, optional) – Decoy type, see alphabase.spectral_library.decoy_library, by default None

  • include_contaminants (bool, optional) – If include contaminants.fasta, by default False

  • generate_precursor_isotope (bool, optional) – If peptdeep.spec_lib.predict_lib.PredictSpecLib.predict_all() includes peptdeep.spec_lib.predict_lib.PredictSpecLib.calc_precursor_isotope(). Defaults to False

  • rt_to_irt (bool, optional) – If convert predicted RT to iRT values, by default False

add_charge()[source][source]#

Add charge states