Index

A

add_fixed_modifications() (psm_utils.Peptidoform method) (psm_utils.peptidoform.Peptidoform method) (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) AlphaDIAReader (class in psm_utils.io.alphadia) AmbiguousResidueException

append() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) apply_fixed_modifications() (psm_utils.Peptidoform method) (psm_utils.peptidoform.Peptidoform method) (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

C

calculate_qvalues() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) collections (psm_utils.psm_list.PSMList property) (psm_utils.PSMList property)

composition (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

E

extend() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

F

find_decoys() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

format_number_as_string() (in module psm_utils.peptidoform) from_dataframe() (psm_utils.io.alphadia.AlphaDIAReader class method)

G

get_precursor_charge() (psm_utils.PSM method) (psm_utils.psm.PSM method) get_psm_dict() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

get_rank1_psms() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) get_usi() (psm_utils.PSM method) (psm_utils.psm.PSM method)

I

is_modified (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

M

mass_to_mz() (in module psm_utils.utils) model_config (psm_utils.PSM attribute) (psm_utils.psm.PSM attribute) (psm_utils.psm_list.PSMList attribute) (psm_utils.PSMList attribute) ModificationException modified_sequence (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

module psm_utils psm_utils.io.alphadia psm_utils.peptidoform psm_utils.psm psm_utils.psm_list psm_utils.utils mz_to_mass() (in module psm_utils.utils)

P

parsed_sequence (psm_utils.Peptidoform attribute) (psm_utils.peptidoform.Peptidoform attribute) Peptidoform (class in psm_utils) (class in psm_utils.peptidoform) PeptidoformException PeptidoformProperties (class in psm_utils.peptidoform) precursor_charge (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) precursor_mz_error (psm_utils.PSM property) (psm_utils.psm.PSM property) proforma (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) properties (psm_utils.Peptidoform attribute) (psm_utils.peptidoform.Peptidoform attribute) PSM (class in psm_utils) (class in psm_utils.psm)

psm_utils module psm_utils.io.alphadia module psm_utils.peptidoform module psm_utils.psm module psm_utils.psm_list module psm_utils.utils module PSMList (class in psm_utils) (class in psm_utils.psm_list)

R

read_file() (psm_utils.io.alphadia.AlphaDIAReader method) rename_modifications() (psm_utils.Peptidoform method) (psm_utils.peptidoform.Peptidoform method) (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

runs (psm_utils.psm_list.PSMList property) (psm_utils.PSMList property)

S

sequence (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) sequential_composition (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

sequential_theoretical_mass (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) set_ranks() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

T

theoretical_mass (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) theoretical_mz (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

to_dataframe() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method)

V

validate_peptidoform() (psm_utils.PSM class method) (psm_utils.psm.PSM class method)