Index

A

add_fixed_modifications() (psm_utils.Peptidoform method) (psm_utils.peptidoform.Peptidoform method) (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) add_note() (psm_utils.io.idxml.IdXMLException method) (psm_utils.io.idxml.IdXMLReaderEmptyListException method) (psm_utils.io.ionbot.InvalidIonbotModificationError method) (psm_utils.io.maxquant.MSMSParsingError method) (psm_utils.io.msamanda.MSAmandaParsingError method) (psm_utils.io.mzid.UnknownMzidScore method) (psm_utils.io.peptide_record.InvalidPeprecError method) (psm_utils.io.peptide_record.InvalidPeprecModificationError method) (psm_utils.io.percolator.PercolatorIOException method) (psm_utils.io.xtandem.XTandemException method) (psm_utils.io.xtandem.XTandemModificationException 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) CBORReader (class in psm_utils.io.cbor) CBORWriter (class in psm_utils.io.cbor)

collections (psm_utils.psm_list.PSMList property) (psm_utils.PSMList property) composition (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property) convert() (in module psm_utils.io)

D

DIANNTSVReader (class in psm_utils.io.diann)

E

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

F

FileType (class in psm_utils.io) find_decoys() (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) FlashLFQReader (class in psm_utils.io.flashlfq) FlashLFQWriter (class in psm_utils.io.flashlfq) format_number_as_string() (in module psm_utils.peptidoform) FragPipeReader (class in psm_utils.io.fragpipe)

from_dataframe() (in module psm_utils.io.peptide_record) (psm_utils.io.alphadia.AlphaDIAReader class method) (psm_utils.io.diann.DIANNTSVReader class method) (psm_utils.io.fragpipe.FragPipeReader class method) (psm_utils.io.proteoscape.ProteoScapeReader static method) (psm_utils.io.sage.SageParquetReader class method) (psm_utils.io.sage.SageTSVReader 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

IdXMLException IdXMLReader (class in psm_utils.io.idxml) IdXMLReaderEmptyListException IdXMLWriter (class in psm_utils.io.idxml) InvalidIonbotModificationError

InvalidPeprecError InvalidPeprecModificationError IonbotReader (class in psm_utils.io.ionbot) is_modified (psm_utils.Peptidoform property) (psm_utils.peptidoform.Peptidoform property)

J

join_pout_files() (in module psm_utils.io.percolator)

JSONReader (class in psm_utils.io.json) JSONWriter (class in psm_utils.io.json)

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.__main__ psm_utils.io psm_utils.io.alphadia psm_utils.io.cbor psm_utils.io.diann psm_utils.io.flashlfq psm_utils.io.fragpipe psm_utils.io.idxml psm_utils.io.ionbot psm_utils.io.json psm_utils.io.maxquant psm_utils.io.msamanda psm_utils.io.mzid psm_utils.io.parquet psm_utils.io.peptide_record psm_utils.io.pepxml psm_utils.io.percolator psm_utils.io.proteome_discoverer psm_utils.io.proteoscape psm_utils.io.sage psm_utils.io.tsv psm_utils.io.xtandem psm_utils.peptidoform psm_utils.psm psm_utils.psm_list psm_utils.utils

MSAmandaParsingError MSAmandaReader (class in psm_utils.io.msamanda) MSFReader (class in psm_utils.io.proteome_discoverer) MSMSParsingError MSMSReader (class in psm_utils.io.maxquant) mz_to_mass() (in module psm_utils.utils) MzidReader (class in psm_utils.io.mzid) MzidWriter (class in psm_utils.io.mzid)

P

ParquetReader (class in psm_utils.io.parquet) ParquetWriter (class in psm_utils.io.parquet) parsed_sequence (psm_utils.Peptidoform attribute) (psm_utils.peptidoform.Peptidoform attribute) peprec_to_proforma() (in module psm_utils.io.peptide_record) PeptideRecordReader (class in psm_utils.io.peptide_record) PeptideRecordWriter (class in psm_utils.io.peptide_record) Peptidoform (class in psm_utils) (class in psm_utils.peptidoform) PeptidoformException PeptidoformProperties (class in psm_utils.peptidoform) PepXMLReader (class in psm_utils.io.pepxml) PercolatorIOException PercolatorTabReader (class in psm_utils.io.percolator) PercolatorTabWriter (class in psm_utils.io.percolator) 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) proforma_to_peprec() (in module psm_utils.io.peptide_record) properties (psm_utils.Peptidoform attribute) (psm_utils.peptidoform.Peptidoform attribute) ProteoScapeReader (class in psm_utils.io.proteoscape) PSM (class in psm_utils) (class in psm_utils.psm) psm_utils module psm_utils.__main__ module psm_utils.io module psm_utils.io.alphadia module psm_utils.io.cbor module psm_utils.io.diann module psm_utils.io.flashlfq module

psm_utils.io.fragpipe module psm_utils.io.idxml module psm_utils.io.ionbot module psm_utils.io.json module psm_utils.io.maxquant module psm_utils.io.msamanda module psm_utils.io.mzid module psm_utils.io.parquet module psm_utils.io.peptide_record module psm_utils.io.pepxml module psm_utils.io.percolator module psm_utils.io.proteome_discoverer module psm_utils.io.proteoscape module psm_utils.io.sage module psm_utils.io.tsv module psm_utils.io.xtandem 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() (in module psm_utils.io) (psm_utils.io.alphadia.AlphaDIAReader method) (psm_utils.io.cbor.CBORReader method) (psm_utils.io.diann.DIANNTSVReader method) (psm_utils.io.flashlfq.FlashLFQReader method) (psm_utils.io.fragpipe.FragPipeReader method) (psm_utils.io.idxml.IdXMLReader method) (psm_utils.io.ionbot.IonbotReader method) (psm_utils.io.json.JSONReader method) (psm_utils.io.maxquant.MSMSReader method) (psm_utils.io.msamanda.MSAmandaReader method) (psm_utils.io.mzid.MzidReader method) (psm_utils.io.parquet.ParquetReader method) (psm_utils.io.peptide_record.PeptideRecordReader method) (psm_utils.io.pepxml.PepXMLReader method) (psm_utils.io.percolator.PercolatorTabReader method) (psm_utils.io.proteome_discoverer.MSFReader method) (psm_utils.io.proteoscape.ProteoScapeReader method) (psm_utils.io.sage.SageParquetReader method) (psm_utils.io.sage.SageTSVReader method) (psm_utils.io.tsv.TSVReader method) (psm_utils.io.xtandem.XTandemReader 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

SageParquetReader (class in psm_utils.io.sage) SageReader (in module psm_utils.io.sage) SageTSVReader (class in psm_utils.io.sage) 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() (in module psm_utils.io.peptide_record) (psm_utils.psm_list.PSMList method) (psm_utils.PSMList method) TSVReader (class in psm_utils.io.tsv) TSVWriter (class in psm_utils.io.tsv)

U

UnknownMzidScore

V

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

W

with_traceback() (psm_utils.io.idxml.IdXMLException method) (psm_utils.io.idxml.IdXMLReaderEmptyListException method) (psm_utils.io.ionbot.InvalidIonbotModificationError method) (psm_utils.io.maxquant.MSMSParsingError method) (psm_utils.io.msamanda.MSAmandaParsingError method) (psm_utils.io.mzid.UnknownMzidScore method) (psm_utils.io.peptide_record.InvalidPeprecError method) (psm_utils.io.peptide_record.InvalidPeprecModificationError method) (psm_utils.io.percolator.PercolatorIOException method) (psm_utils.io.xtandem.XTandemException method) (psm_utils.io.xtandem.XTandemModificationException method) write_file() (in module psm_utils.io) (psm_utils.io.cbor.CBORWriter method) (psm_utils.io.flashlfq.FlashLFQWriter method) (psm_utils.io.idxml.IdXMLWriter method) (psm_utils.io.json.JSONWriter method) (psm_utils.io.mzid.MzidWriter method) (psm_utils.io.parquet.ParquetWriter method) (psm_utils.io.peptide_record.PeptideRecordWriter method) (psm_utils.io.percolator.PercolatorTabWriter method) (psm_utils.io.tsv.TSVWriter method)

write_psm() (psm_utils.io.cbor.CBORWriter method) (psm_utils.io.flashlfq.FlashLFQWriter method) (psm_utils.io.idxml.IdXMLWriter method) (psm_utils.io.json.JSONWriter method) (psm_utils.io.mzid.MzidWriter method) (psm_utils.io.parquet.ParquetWriter method) (psm_utils.io.peptide_record.PeptideRecordWriter method) (psm_utils.io.percolator.PercolatorTabWriter method) (psm_utils.io.tsv.TSVWriter method)

X

XTandemException

XTandemModificationException XTandemReader (class in psm_utils.io.xtandem)