Index

_

__init__ (pyteomics.auxiliary.structures.Charge attribute) (pyteomics.auxiliary.structures.CVQueryEngine attribute) (pyteomics.auxiliary.utils.BinaryDataArrayTransformer attribute) (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzmlb.chunk_interval_cache_record attribute) (pyteomics.mzmlb.external_array_slice attribute) (pyteomics.mztab.Group attribute) (pyteomics.mztab.MetadataPropertyAnnotator attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.usi.USI attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute) __init__() (pyteomics.auxiliary.file_helpers.ChainBase method) (pyteomics.auxiliary.file_helpers.FileReader method) (pyteomics.auxiliary.file_helpers.FileReadingProcess method) (pyteomics.auxiliary.file_helpers.IndexSavingMixin method) (pyteomics.auxiliary.file_helpers.IndexSavingTextReader method) (pyteomics.auxiliary.file_helpers.IndexedReaderMixin method) (pyteomics.auxiliary.file_helpers.IndexedTextReader method) (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.file_helpers.TableJoiner method) (pyteomics.auxiliary.file_helpers.TimeOrderedIndexedReaderMixin method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.auxiliary.structures.Ion method) (pyteomics.auxiliary.structures.PyteomicsError method) (pyteomics.fasta.FASTA method) (pyteomics.fasta.FASTABase method) (pyteomics.fasta.FlavoredMixin method) (pyteomics.fasta.IndexedFASTA method) (pyteomics.fasta.IndexedNCBI method) (pyteomics.fasta.IndexedRefSeq method) (pyteomics.fasta.IndexedSPD method) (pyteomics.fasta.IndexedUniMes method) (pyteomics.fasta.IndexedUniParc method) (pyteomics.fasta.IndexedUniProt method) (pyteomics.fasta.IndexedUniRef method) (pyteomics.fasta.NCBI method) (pyteomics.fasta.NCBIMixin method) (pyteomics.fasta.RefSeq method) (pyteomics.fasta.RefSeqMixin method) (pyteomics.fasta.SPD method) (pyteomics.fasta.SPDMixin method) (pyteomics.fasta.TwoLayerIndexedFASTA method) (pyteomics.fasta.UniMes method) (pyteomics.fasta.UniMesMixin method) (pyteomics.fasta.UniParc method) (pyteomics.fasta.UniParcMixin method) (pyteomics.fasta.UniProt method) (pyteomics.fasta.UniProtMixin method) (pyteomics.fasta.UniRef method) (pyteomics.fasta.UniRefMixin method) (pyteomics.mass.mass.Composition method) (pyteomics.mass.mass.Unimod method) (pyteomics.mass.unimod.Unimod method) (pyteomics.mgf.IndexedMGF method) (pyteomics.mgf.MGF method) (pyteomics.mgf.MGFBase method) (pyteomics.ms1.IndexedMS1 method) (pyteomics.ms1.MS1 method) (pyteomics.ms1.MS1Base method) (pyteomics.ms2.IndexedMS2 method) (pyteomics.ms2.MS2 method) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalArrayRegistry method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzmlb.HDF5ByteBuffer method) (pyteomics.mzmlb.MzMLb method) (pyteomics.mztab.MetadataBackedCollection method) (pyteomics.mztab.MetadataBackedProperty method) (pyteomics.mztab.MzTab method) (pyteomics.mztab._MzTabTable method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.peff.Header method) (pyteomics.peff.IndexedPEFF method) (pyteomics.pepxml.PepXML method) (pyteomics.proforma.ChargeState method) (pyteomics.proforma.FormulaModification method) (pyteomics.proforma.GNOResolver method) (pyteomics.proforma.GNOmeModification method) (pyteomics.proforma.GenericModification method) (pyteomics.proforma.GenericResolver method) (pyteomics.proforma.GlycanModification method) (pyteomics.proforma.InformationTag method) (pyteomics.proforma.LocalizationMarker method) (pyteomics.proforma.MassModification method) (pyteomics.proforma.ModificationBase method) (pyteomics.proforma.ModificationResolver method) (pyteomics.proforma.ModificationRule method) (pyteomics.proforma.ModificationToken method) (pyteomics.proforma.PSIModModification method) (pyteomics.proforma.PSIModResolver method) (pyteomics.proforma.PositionLabelTag method) (pyteomics.proforma.ProForma method) (pyteomics.proforma.StableIsotope method) (pyteomics.proforma.TagBase method) (pyteomics.proforma.TaggedInterval method) (pyteomics.proforma.UnimodModification method) (pyteomics.proforma.UnimodResolver method) (pyteomics.proforma.XLMODModification method) (pyteomics.proforma.XLMODResolver method) (pyteomics.protxml.ProtXML method) (pyteomics.pylab_aux.SpectrumUtilsColorScheme method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.usi.JPOSTBackend method) (pyteomics.usi.MassIVEBackend method) (pyteomics.usi.PRIDEBackend method) (pyteomics.usi.PROXIAggregator method) (pyteomics.usi.PeptideAtlasBackend method) (pyteomics.usi.ProteomeExchangeBackend method) (pyteomics.xml.ArrayConversionMixin method) (pyteomics.xml.ByteCountingXMLScanner method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.TagSpecificXMLByteIndex method) (pyteomics.xml.XML method)

_MzTabTable (class in pyteomics.mztab)

A

accession (pyteomics.auxiliary.structures.cvstr attribute) add_metaclass() (in module pyteomics.auxiliary.utils) adducts (pyteomics.proforma.ChargeState attribute) AlternativeName (class in pyteomics.mass.unimod) ambiguous (pyteomics.proforma.TaggedInterval attribute) amino_acid_composition() (in module pyteomics.parser) AminoAcid (class in pyteomics.mass.unimod)

annotate_spectrum() (in module pyteomics.pylab_aux) append() (pyteomics.auxiliary.structures.ChargeList method) array (pyteomics.mzmlb.chunk_interval_cache_record attribute) array_name (pyteomics.mzmlb.external_array_slice attribute) ArrayConversionMixin (class in pyteomics.xml) ArrayConversionMixin.binary_array_record (class in pyteomics.xml) as_df() (pyteomics.mztab._MzTabTable method) assays (pyteomics.mztab.MzTab attribute)

B

backends (pyteomics.usi.PROXIAggregator attribute) BasicComposition (class in pyteomics.auxiliary.structures) BinaryDataArrayTransformer (class in pyteomics.auxiliary.utils) BinaryDataArrayTransformer.binary_array_record (class in pyteomics.auxiliary.utils) bit_length() (pyteomics.auxiliary.structures.Charge method) build_byte_index() (pyteomics.xml.ByteCountingXMLScanner method) build_id_cache() (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method) build_index() (pyteomics.xml.TagSpecificXMLByteIndex method) build_second_index() (pyteomics.fasta.IndexedNCBI method) (pyteomics.fasta.IndexedRefSeq method) (pyteomics.fasta.IndexedSPD method) (pyteomics.fasta.IndexedUniMes method) (pyteomics.fasta.IndexedUniParc method) (pyteomics.fasta.IndexedUniProt method) (pyteomics.fasta.IndexedUniRef method) (pyteomics.fasta.TwoLayerIndexedFASTA method) (pyteomics.peff.IndexedPEFF method)

build_tree() (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method) by_id() (pyteomics.mass.mass.Unimod method) by_name() (pyteomics.mass.mass.Unimod method) (pyteomics.mass.unimod.Unimod method) by_title() (pyteomics.mass.mass.Unimod method) (pyteomics.mass.unimod.Unimod method) ByteCountingXMLScanner (class in pyteomics.xml)

C

c_term (pyteomics.proforma.ProForma attribute) calculate_mass() (in module pyteomics.mass.mass) calculate_RT() (in module pyteomics.achrom) capitalize() (pyteomics.auxiliary.structures.Ion method) casefold() (pyteomics.auxiliary.structures.Ion method) center() (pyteomics.auxiliary.structures.Ion method) chain() (in module pyteomics.fasta) (in module pyteomics.mgf) (in module pyteomics.ms1) (in module pyteomics.ms2) (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzxml) (in module pyteomics.openms.featurexml) (in module pyteomics.openms.idxml) (in module pyteomics.openms.trafoxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) (in module pyteomics.traml) chain.from_iterable() (in module pyteomics.fasta) (in module pyteomics.mgf) (in module pyteomics.ms1) (in module pyteomics.ms2) (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzxml) (in module pyteomics.openms.featurexml) (in module pyteomics.openms.idxml) (in module pyteomics.openms.trafoxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) (in module pyteomics.traml) ChainBase (class in pyteomics.auxiliary.file_helpers) Charge (class in pyteomics.auxiliary.structures) charge (pyteomics.proforma.ChargeState attribute) charge() (in module pyteomics.electrochem) charge_state (pyteomics.proforma.ProForma attribute) ChargeList (class in pyteomics.auxiliary.structures) ChargeState (class in pyteomics.proforma) chunk_cache (pyteomics.mzmlb.ExternalArrayRegistry attribute) chunk_interval_cache_record (class in pyteomics.mzmlb) chunk_size (pyteomics.mzmlb.ExternalArrayRegistry attribute) Classification (class in pyteomics.mass.unimod) clear() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.mztab.Group method) clear_id_cache() (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method) clear_tree() (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method)

clear_unit_cv_table() (in module pyteomics.auxiliary.structures) cleave() (in module pyteomics.parser) close() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) (pyteomics.mzmlb.HDF5ByteBuffer method) coalesce() (pyteomics.usi.PROXIAggregator method) collapse_properties() (pyteomics.mztab._MzTabTable method) (pyteomics.mztab.MzTab method) colunit_peptide (pyteomics.mztab.MzTab attribute) colunit_protein (pyteomics.mztab.MzTab attribute) colunit_psm (pyteomics.mztab.MzTab attribute) colunit_small_molecule (pyteomics.mztab.MzTab attribute) colunit_small_molecule_evidence (pyteomics.mztab.MzTab attribute) colunit_small_molecule_feature (pyteomics.mztab.MzTab attribute) comments (pyteomics.mztab.MzTab attribute) composition (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) compression (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute) compression_type_map (pyteomics.auxiliary.utils.BinaryDataArrayTransformer attribute) conjugate() (pyteomics.auxiliary.structures.Charge method) contacts (pyteomics.mztab.MzTab attribute) copy() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.mztab.Group method) count() (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.auxiliary.structures.Ion method) (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record method) (pyteomics.mzml.MzML.binary_array_record method) (pyteomics.mzml.PreIndexedMzML.binary_array_record method) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record method) (pyteomics.mzmlb.chunk_interval_cache_record method) (pyteomics.mzmlb.external_array_slice method) (pyteomics.mzxml.MzXML.binary_array_record method) (pyteomics.usi.USI method) (pyteomics.xml.ArrayConversionMixin.binary_array_record method) coverage() (in module pyteomics.parser) Crossreference (class in pyteomics.mass.unimod) custom (pyteomics.mztab.MzTab attribute) cvquery() (in module pyteomics.auxiliary.structures) CVQueryEngine (class in pyteomics.auxiliary.structures) cvs (pyteomics.mztab.MzTab attribute) cvstr (class in pyteomics.auxiliary.structures)

D

daemon (pyteomics.auxiliary.file_helpers.FileReadingProcess attribute) data (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute) databases (pyteomics.mztab.MzTab attribute) datafile (pyteomics.usi.USI attribute), [1] DataFrame() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) dataset (pyteomics.usi.USI attribute), [1] decode() (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record method) (pyteomics.mzml.MzML.binary_array_record method) (pyteomics.mzml.PreIndexedMzML.binary_array_record method) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record method) (pyteomics.mzmlb.external_array_slice method) (pyteomics.mzxml.MzXML.binary_array_record method) (pyteomics.xml.ArrayConversionMixin.binary_array_record method) decode_data_array() (pyteomics.auxiliary.utils.BinaryDataArrayTransformer method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.xml.ArrayConversionMixin method)

decoy_chain() (in module pyteomics.fasta) decoy_chain.from_iterable() (in module pyteomics.fasta) decoy_db() (in module pyteomics.fasta) decoy_entries() (in module pyteomics.fasta) decoy_sequence() (in module pyteomics.fasta) default_factory (pyteomics.auxiliary.structures.BasicComposition attribute) definition (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) delta_predict() (in module pyteomics.mzmlb) denominator (pyteomics.auxiliary.structures.Charge attribute) derivatization_agents (pyteomics.mztab.MzTab attribute) description (pyteomics.mztab.MzTab attribute) dtype (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzmlb.external_array_slice attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute)

E

elements() (pyteomics.auxiliary.structures.BasicComposition method) encode() (pyteomics.auxiliary.structures.Ion method) end (pyteomics.mzmlb.chunk_interval_cache_record attribute) (pyteomics.proforma.TaggedInterval attribute) endswith() (pyteomics.auxiliary.structures.Ion method) ephemeral_pool (pyteomics.usi.PROXIAggregator attribute) execute() (pyteomics.mass.unimod.Unimod method) exitcode (pyteomics.auxiliary.file_helpers.FileReadingProcess attribute) expandtabs() (pyteomics.auxiliary.structures.Ion method)

expasy_rules (in module pyteomics.parser) extend() (pyteomics.auxiliary.structures.ChargeList method) external_array_slice (class in pyteomics.mzmlb) external_study_uris (pyteomics.mztab.MzTab attribute) ExternalArrayRegistry (class in pyteomics.mzmlb) ExternalDataMzML (class in pyteomics.mzmlb) ExternalDataMzML.binary_array_record (class in pyteomics.mzmlb) extra (pyteomics.proforma.TagBase attribute) extract_path() (in module pyteomics.mztab)

F

false_discovery_rate (pyteomics.mztab.MzTab attribute) fast_mass() (in module pyteomics.mass.mass) fast_mass2() (in module pyteomics.mass.mass) fast_valid() (in module pyteomics.parser) FASTA (class in pyteomics.fasta) FASTABase (class in pyteomics.fasta) fdr() (in module pyteomics.auxiliary.target_decoy) (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) FeatureXML (class in pyteomics.openms.featurexml) file (pyteomics.mztab.MzTab attribute) fileno() (pyteomics.mzmlb.HDF5ByteBuffer method) FileReader (class in pyteomics.auxiliary.file_helpers) FileReadingProcess (class in pyteomics.auxiliary.file_helpers) filter() (in module pyteomics.auxiliary.target_decoy) (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) filter.chain() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) filter.chain.from_iterable() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) filter_df() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem)

find() (pyteomics.auxiliary.structures.Ion method) find_tag_type() (pyteomics.proforma.FormulaModification method) (pyteomics.proforma.GNOmeModification method) (pyteomics.proforma.GenericModification method) (pyteomics.proforma.GlycanModification method) (pyteomics.proforma.InformationTag method) (pyteomics.proforma.LocalizationMarker method) (pyteomics.proforma.MassModification method) (pyteomics.proforma.ModificationBase method) (pyteomics.proforma.PSIModModification method) (pyteomics.proforma.PositionLabelTag method) (pyteomics.proforma.TagBase method) (pyteomics.proforma.UnimodModification method) (pyteomics.proforma.XLMODModification method) find_tags_by_id() (pyteomics.proforma.ProForma method) fixed_mods (pyteomics.mztab.MzTab attribute) FlavoredMixin (class in pyteomics.fasta) flush() (pyteomics.mzmlb.HDF5ByteBuffer method) format() (pyteomics.auxiliary.structures.Ion method) format_map() (pyteomics.auxiliary.structures.Ion method) FormulaModification (class in pyteomics.proforma) Fragment (class in pyteomics.mass.unimod) fragments() (pyteomics.proforma.ProForma method) from_bytes() (pyteomics.auxiliary.structures.Charge method) from_index() (pyteomics.auxiliary.file_helpers.OffsetIndex method) from_slice() (pyteomics.auxiliary.file_helpers.OffsetIndex method) fromkeys() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition class method) (pyteomics.mztab.Group method) fused_decoy() (in module pyteomics.fasta)

G

gather() (pyteomics.mztab._MzTabTable method) (pyteomics.mztab.MzTab method) GenericModification (class in pyteomics.proforma) GenericResolver (class in pyteomics.proforma) get() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mass.unimod.Unimod method) (pyteomics.mztab.Group method) (pyteomics.peff.Header method) (pyteomics.usi.JPOSTBackend method) (pyteomics.usi.MassIVEBackend method) (pyteomics.usi.PRIDEBackend method) (pyteomics.usi.PROXIAggregator method) (pyteomics.usi.PeptideAtlasBackend method) (pyteomics.usi.ProteomeExchangeBackend method) get_by_id() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (pyteomics.fasta.IndexedNCBI method) (pyteomics.fasta.IndexedRefSeq method) (pyteomics.fasta.IndexedSPD method) (pyteomics.fasta.IndexedUniMes method) (pyteomics.fasta.IndexedUniParc method) (pyteomics.fasta.IndexedUniProt method) (pyteomics.fasta.IndexedUniRef method) (pyteomics.fasta.TwoLayerIndexedFASTA method) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzmlb.MzMLb method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.peff.IndexedPEFF method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method)

get_dataset() (pyteomics.mzmlb.MzMLb method) get_mass_from_glycan_composition() (pyteomics.proforma.GNOResolver method) get_mass_from_term() (pyteomics.proforma.GNOResolver method) get_path() (pyteomics.mztab.Group method) get_RCs() (in module pyteomics.achrom) get_RCs_vary_lcp() (in module pyteomics.achrom) get_spectrum() (in module pyteomics.mgf) GlycanModification (class in pyteomics.proforma) GNOmeModification (class in pyteomics.proforma) GNOResolver (class in pyteomics.proforma) gravy() (in module pyteomics.electrochem) Group (class in pyteomics.mztab) group_id (pyteomics.proforma.TagBase attribute) group_ids (pyteomics.proforma.ProForma attribute)

H

handle (pyteomics.mzmlb.MzMLb attribute) HDF5ByteBuffer (class in pyteomics.mzmlb) Header (class in pyteomics.peff) header (pyteomics.mgf.IndexedMGF attribute) (pyteomics.mgf.MGF attribute) (pyteomics.ms1.IndexedMS1 attribute) (pyteomics.ms1.MS1 attribute) (pyteomics.ms2.IndexedMS2 attribute) (pyteomics.ms2.MS2 attribute) (pyteomics.mztab._MzTabTable attribute)

hydropathicity_KD (in module pyteomics.electrochem)

I

icleave() (in module pyteomics.parser) id (pyteomics.mztab.MzTab attribute) (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.ModificationToken attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) id_confidence_measures (pyteomics.mztab.MzTab attribute) ident (pyteomics.auxiliary.file_helpers.FileReadingProcess attribute) IDXML (class in pyteomics.openms.idxml) imag (pyteomics.auxiliary.structures.Charge attribute) index() (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.auxiliary.structures.CVQueryEngine method) (pyteomics.auxiliary.structures.Ion method) (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record method) (pyteomics.mzml.MzML.binary_array_record method) (pyteomics.mzml.PreIndexedMzML.binary_array_record method) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record method) (pyteomics.mzmlb.chunk_interval_cache_record method) (pyteomics.mzmlb.external_array_slice method) (pyteomics.mzxml.MzXML.binary_array_record method) (pyteomics.usi.USI method) (pyteomics.xml.ArrayConversionMixin.binary_array_record method) index_sequence (pyteomics.auxiliary.file_helpers.OffsetIndex attribute) indexed_tag_keys (pyteomics.xml.TagSpecificXMLByteIndex attribute) indexed_tags (pyteomics.xml.TagSpecificXMLByteIndex attribute) IndexedFASTA (class in pyteomics.fasta) IndexedMGF (class in pyteomics.mgf) IndexedMS1 (class in pyteomics.ms1) IndexedMS2 (class in pyteomics.ms2) IndexedNCBI (class in pyteomics.fasta) IndexedPEFF (class in pyteomics.peff) IndexedReaderMixin (class in pyteomics.auxiliary.file_helpers) IndexedRefSeq (class in pyteomics.fasta) IndexedSPD (class in pyteomics.fasta) IndexedTextReader (class in pyteomics.auxiliary.file_helpers) IndexedUniMes (class in pyteomics.fasta) IndexedUniParc (class in pyteomics.fasta) IndexedUniProt (class in pyteomics.fasta) IndexedUniRef (class in pyteomics.fasta) IndexedXML (class in pyteomics.xml) IndexSavingMixin (class in pyteomics.auxiliary.file_helpers) IndexSavingTextReader (class in pyteomics.auxiliary.file_helpers) IndexSavingXML (class in pyteomics.xml) InformationTag (class in pyteomics.proforma) insert() (pyteomics.auxiliary.structures.ChargeList method) instruments (pyteomics.mztab.MzTab attribute) interpretation (pyteomics.usi.USI attribute), [1] intervals (pyteomics.proforma.ProForma attribute)

Ion (class in pyteomics.auxiliary.structures) is_alive() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) is_decoy() (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) is_modX() (in module pyteomics.parser) is_term_mod() (in module pyteomics.parser) isalnum() (pyteomics.auxiliary.structures.Ion method) isalpha() (pyteomics.auxiliary.structures.Ion method) isascii() (pyteomics.auxiliary.structures.Ion method) isatty() (pyteomics.mzmlb.HDF5ByteBuffer method) isdecimal() (pyteomics.auxiliary.structures.Ion method) isdigit() (pyteomics.auxiliary.structures.Ion method) isidentifier() (pyteomics.auxiliary.structures.Ion method) islower() (pyteomics.auxiliary.structures.Ion method) isnumeric() (pyteomics.auxiliary.structures.Ion method) isoforms() (in module pyteomics.parser) isotope (pyteomics.proforma.StableIsotope attribute) isotopes (pyteomics.proforma.ProForma attribute) isotopic_composition_abundance() (in module pyteomics.mass.mass) isotopologues() (in module pyteomics.mass.mass) isprintable() (pyteomics.auxiliary.structures.Ion method) isspace() (pyteomics.auxiliary.structures.Ion method) istitle() (pyteomics.auxiliary.structures.Ion method) isupper() (pyteomics.auxiliary.structures.Ion method) items() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) (pyteomics.peff.Header method) iterfind() (in module pyteomics.mzid) (in module pyteomics.mzml), [1] (in module pyteomics.mzxml), [1] (in module pyteomics.openms.idxml) (in module pyteomics.pepxml), [1] (in module pyteomics.tandem), [1] (in module pyteomics.traml) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method)

J

join() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) (pyteomics.auxiliary.structures.Ion method)

JPOSTBackend (class in pyteomics.usi)

K

key (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzmlb.external_array_slice attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute)

keys() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) (pyteomics.peff.Header method) kill() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) kwargs (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzxml) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) (in module pyteomics.traml) (pyteomics.auxiliary.file_helpers.ChainBase attribute)

L

labile_modifications (pyteomics.proforma.ProForma attribute) length (pyteomics.mzmlb.external_array_slice attribute) length() (in module pyteomics.parser) linear_predict() (in module pyteomics.mzmlb) linear_regression() (in module pyteomics.auxiliary.math)

linear_regression_perpendicular() (in module pyteomics.auxiliary.math) linear_regression_vertical() (in module pyteomics.auxiliary.math) ljust() (pyteomics.auxiliary.structures.Ion method) LocalizationMarker (class in pyteomics.proforma) lower() (pyteomics.auxiliary.structures.Ion method) lstrip() (pyteomics.auxiliary.structures.Ion method)

M

maketrans() (pyteomics.auxiliary.structures.Ion static method) map() (pyteomics.auxiliary.file_helpers.ChainBase method) (pyteomics.auxiliary.file_helpers.TableJoiner method) (pyteomics.fasta.IndexedFASTA method) (pyteomics.fasta.IndexedNCBI method) (pyteomics.fasta.IndexedRefSeq method) (pyteomics.fasta.IndexedSPD method) (pyteomics.fasta.IndexedUniMes method) (pyteomics.fasta.IndexedUniParc method) (pyteomics.fasta.IndexedUniProt method) (pyteomics.fasta.IndexedUniRef method) (pyteomics.fasta.TwoLayerIndexedFASTA method) (pyteomics.mgf.IndexedMGF method) (pyteomics.ms1.IndexedMS1 method) (pyteomics.ms2.IndexedMS2 method) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzmlb.MzMLb method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.peff.IndexedPEFF method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.traml.TraML method) (pyteomics.xml.MultiProcessingXML method) mass (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.ProForma attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) mass() (pyteomics.mass.mass.Composition method) mass_data (pyteomics.mass.mass.Unimod attribute)

MassIVEBackend (class in pyteomics.usi) MassModification (class in pyteomics.proforma) match_modX() (in module pyteomics.parser) memoize() (in module pyteomics.auxiliary.utils) message (pyteomics.auxiliary.structures.PyteomicsError attribute) metadata (pyteomics.mztab.MzTab attribute) MetadataBackedCollection (class in pyteomics.mztab) MetadataBackedProperty (class in pyteomics.mztab) MetadataPropertyAnnotator (class in pyteomics.mztab) MGF (class in pyteomics.mgf) MGFBase (class in pyteomics.mgf) mirror() (in module pyteomics.pylab_aux) mode (pyteomics.mztab.MzTab attribute) Modification (class in pyteomics.mass.unimod) modification_tag (pyteomics.proforma.ModificationRule attribute) ModificationBase (class in pyteomics.proforma) ModificationResolver (class in pyteomics.proforma) ModificationRule (class in pyteomics.proforma) ModificationToken (class in pyteomics.proforma) mods (pyteomics.mass.mass.Unimod attribute) most_common() (pyteomics.auxiliary.structures.BasicComposition method) most_probable_isotopic_composition() (in module pyteomics.mass.mass) move_to_end() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.mztab.Group method) mro() (pyteomics.mztab.MetadataPropertyAnnotator method) MS1 (class in pyteomics.ms1) MS1Base (class in pyteomics.ms1) MS2 (class in pyteomics.ms2) ms_runs (pyteomics.mztab.MzTab attribute) MultiProcessingXML (class in pyteomics.xml) MzIdentML (class in pyteomics.mzid) MzML (class in pyteomics.mzml) MzML.binary_array_record (class in pyteomics.mzml) mzml_parser (pyteomics.mzmlb.MzMLb attribute) MzMLb (class in pyteomics.mzmlb) MzTab (class in pyteomics.mztab) MzXML (class in pyteomics.mzxml) MzXML.binary_array_record (class in pyteomics.mzxml)

N

n_term (pyteomics.proforma.ProForma attribute) n_threads (pyteomics.usi.PROXIAggregator attribute) name (pyteomics.mztab._MzTabTable attribute) (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.ModificationToken attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute)

NCBI (class in pyteomics.fasta) NCBIMixin (class in pyteomics.fasta) nist_mass (in module pyteomics.mass.mass) num_sites() (in module pyteomics.parser) numerator (pyteomics.auxiliary.structures.Charge attribute)

O

offset (pyteomics.mzmlb.external_array_slice attribute)

OffsetIndex (class in pyteomics.auxiliary.file_helpers) offsets (pyteomics.xml.TagSpecificXMLByteIndex attribute)

P

parse() (in module pyteomics.fasta) (in module pyteomics.parser) (in module pyteomics.proforma) (pyteomics.proforma.ProForma class method) (pyteomics.usi.USI class method) parse_identifier() (pyteomics.proforma.GenericResolver method) (pyteomics.proforma.GNOResolver method) (pyteomics.proforma.ModificationResolver method) (pyteomics.proforma.PSIModResolver method) (pyteomics.proforma.UnimodResolver method) (pyteomics.proforma.XLMODResolver method) partition() (pyteomics.auxiliary.structures.Ion method) path (pyteomics.mzmlb.MzMLb attribute) peptide_table (pyteomics.mztab.MzTab attribute) PeptideAtlasBackend (class in pyteomics.usi) PepXML (class in pyteomics.pepxml) pI() (in module pyteomics.electrochem) pid (pyteomics.auxiliary.file_helpers.FileReadingProcess attribute) pK_bjellqvist (in module pyteomics.electrochem) pK_cterm_bjellqvist (in module pyteomics.electrochem) pK_dawson (in module pyteomics.electrochem) pK_lehninger (in module pyteomics.electrochem) pK_nterm_bjellqvist (in module pyteomics.electrochem) pK_rodwell (in module pyteomics.electrochem) pK_sillero (in module pyteomics.electrochem) plot_function_3d() (in module pyteomics.pylab_aux) plot_function_contour() (in module pyteomics.pylab_aux) plot_line() (in module pyteomics.pylab_aux) plot_qvalue_curve() (in module pyteomics.pylab_aux) plot_spectrum() (in module pyteomics.pylab_aux) pop() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.auxiliary.structures.ChargeList method) (pyteomics.mztab.Group method) popitem() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) Position (class in pyteomics.mass.unimod) PositionLabelTag (class in pyteomics.proforma) prebuild_byte_offset_file() (pyteomics.auxiliary.file_helpers.IndexSavingMixin class method) (pyteomics.auxiliary.file_helpers.IndexSavingTextReader class method) (pyteomics.mgf.IndexedMGF class method) (pyteomics.mzid.MzIdentML class method) (pyteomics.mzml.MzML class method) (pyteomics.mzml.PreIndexedMzML class method) (pyteomics.mzmlb.ExternalDataMzML class method) (pyteomics.mzxml.MzXML class method) (pyteomics.pepxml.PepXML class method) (pyteomics.traml.TraML class method) (pyteomics.xml.IndexSavingXML class method) PreIndexedMzML (class in pyteomics.mzml) PreIndexedMzML.binary_array_record (class in pyteomics.mzml) PRIDEBackend (class in pyteomics.usi) print_tree() (in module pyteomics.auxiliary.utils)

ProForma (class in pyteomics.proforma) protein_search_engine_scores (pyteomics.mztab.MzTab attribute) protein_table (pyteomics.mztab.MzTab attribute) ProteomeExchangeBackend (class in pyteomics.usi) protocol (pyteomics.usi.USI attribute), [1] ProtXML (class in pyteomics.protxml) provider (pyteomics.proforma.FormulaModification attribute) (pyteomics.proforma.GNOmeModification attribute) (pyteomics.proforma.GenericModification attribute) (pyteomics.proforma.GlycanModification attribute) (pyteomics.proforma.ModificationBase attribute) (pyteomics.proforma.ModificationToken attribute) (pyteomics.proforma.PSIModModification attribute) (pyteomics.proforma.UnimodModification attribute) (pyteomics.proforma.XLMODModification attribute) proxi() (in module pyteomics.usi) PROXIAggregator (class in pyteomics.usi) PSIModModification (class in pyteomics.proforma) PSIModResolver (class in pyteomics.proforma) psims_rules (in module pyteomics.parser) psm_search_engine_scores (pyteomics.mztab.MzTab attribute) publications (pyteomics.mztab.MzTab attribute) pyteomics.achrom (module) pyteomics.auxiliary.file_helpers (module) pyteomics.auxiliary.math (module) pyteomics.auxiliary.structures (module) pyteomics.auxiliary.target_decoy (module) pyteomics.auxiliary.utils (module) pyteomics.electrochem (module) pyteomics.fasta (module) pyteomics.mass.mass (module) pyteomics.mass.unimod (module) pyteomics.mgf (module) pyteomics.ms1 (module) pyteomics.ms2 (module) pyteomics.mzid (module) pyteomics.mzml (module) pyteomics.mzmlb (module) pyteomics.mztab (module) pyteomics.mzxml (module) pyteomics.openms.featurexml (module) pyteomics.openms.idxml (module) pyteomics.openms.trafoxml (module) pyteomics.parser (module) pyteomics.peff (module) pyteomics.pepxml (module) pyteomics.proforma (module) pyteomics.protxml (module) pyteomics.pylab_aux (module) pyteomics.tandem (module) pyteomics.traml (module) pyteomics.usi (module) pyteomics.version (module) pyteomics.xml (module) PyteomicsError

Q

quantification_method (pyteomics.mztab.MzTab attribute) query() (pyteomics.auxiliary.structures.CVQueryEngine method) (pyteomics.mass.unimod.Unimod method) qvalues() (in module pyteomics.auxiliary.target_decoy) (in module pyteomics.mzid) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem)

R

RCs_browne_hfba (in module pyteomics.achrom) RCs_browne_tfa (in module pyteomics.achrom) RCs_gilar_atlantis_ph10_0 (in module pyteomics.achrom) RCs_gilar_atlantis_ph3_0 (in module pyteomics.achrom) RCs_gilar_atlantis_ph4_5 (in module pyteomics.achrom) RCs_gilar_beh (in module pyteomics.achrom) RCs_gilar_beh_amide (in module pyteomics.achrom) RCs_gilar_rp (in module pyteomics.achrom) RCs_guo_ph2_0 (in module pyteomics.achrom) RCs_guo_ph7_0 (in module pyteomics.achrom) RCs_krokhin_100A_fa (in module pyteomics.achrom) RCs_krokhin_100A_tfa (in module pyteomics.achrom) RCs_meek_ph2_1 (in module pyteomics.achrom) RCs_meek_ph7_4 (in module pyteomics.achrom) RCs_palmblad (in module pyteomics.achrom) RCs_yoshida (in module pyteomics.achrom) RCs_yoshida_lc (in module pyteomics.achrom) RCs_zubarev (in module pyteomics.achrom) read() (in module pyteomics.fasta) (in module pyteomics.mgf) (in module pyteomics.ms1) (in module pyteomics.ms2) (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzmlb) (in module pyteomics.mzxml) (in module pyteomics.openms.featurexml) (in module pyteomics.openms.idxml) (in module pyteomics.openms.trafoxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) (in module pyteomics.traml) read_header() (in module pyteomics.mgf) (in module pyteomics.ms1) (in module pyteomics.ms2) readable() (pyteomics.mzmlb.HDF5ByteBuffer method) readall() (pyteomics.mzmlb.HDF5ByteBuffer method) readline() (pyteomics.mzmlb.HDF5ByteBuffer method) readlines() (pyteomics.mzmlb.HDF5ByteBuffer method) real (pyteomics.auxiliary.structures.Charge attribute) RefSeq (class in pyteomics.fasta) RefSeqMixin (class in pyteomics.fasta) registry (pyteomics.mzmlb.ExternalArrayRegistry attribute) remove() (pyteomics.auxiliary.structures.ChargeList method) replace() (pyteomics.auxiliary.structures.Ion method) replace_entities() (pyteomics.xml.ByteCountingXMLScanner method) reset() (pyteomics.auxiliary.file_helpers.FileReader method) (pyteomics.auxiliary.file_helpers.IndexSavingTextReader method) (pyteomics.auxiliary.file_helpers.IndexedTextReader method) (pyteomics.fasta.FASTA method) (pyteomics.fasta.IndexedFASTA method) (pyteomics.fasta.IndexedNCBI method) (pyteomics.fasta.IndexedRefSeq method) (pyteomics.fasta.IndexedSPD method) (pyteomics.fasta.IndexedUniMes method) (pyteomics.fasta.IndexedUniParc method) (pyteomics.fasta.IndexedUniProt method) (pyteomics.fasta.IndexedUniRef method) (pyteomics.fasta.NCBI method) (pyteomics.fasta.RefSeq method) (pyteomics.fasta.SPD method) (pyteomics.fasta.TwoLayerIndexedFASTA method) (pyteomics.fasta.UniMes method) (pyteomics.fasta.UniParc method) (pyteomics.fasta.UniProt method) (pyteomics.fasta.UniRef method) (pyteomics.mgf.IndexedMGF method) (pyteomics.mgf.MGF method) (pyteomics.ms1.IndexedMS1 method) (pyteomics.ms1.MS1 method) (pyteomics.ms2.IndexedMS2 method) (pyteomics.ms2.MS2 method) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.openms.featurexml.FeatureXML method) (pyteomics.openms.idxml.IDXML method) (pyteomics.openms.trafoxml.TrafoXML method) (pyteomics.peff.IndexedPEFF method) (pyteomics.pepxml.PepXML method) (pyteomics.protxml.ProtXML method) (pyteomics.tandem.TandemXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method) (pyteomics.xml.IndexedXML method) (pyteomics.xml.MultiProcessingXML method) (pyteomics.xml.XML method)

resolve() (pyteomics.proforma.FormulaModification method) (pyteomics.proforma.GNOmeModification method) (pyteomics.proforma.GenericModification method) (pyteomics.proforma.GlycanModification method) (pyteomics.proforma.ModificationBase method) (pyteomics.proforma.PSIModModification method) (pyteomics.proforma.UnimodModification method) (pyteomics.proforma.XLMODModification method) reverse() (in module pyteomics.fasta) (pyteomics.auxiliary.structures.ChargeList method) rfind() (pyteomics.auxiliary.structures.Ion method) rindex() (pyteomics.auxiliary.structures.Ion method) rjust() (pyteomics.auxiliary.structures.Ion method) roc_curve() (in module pyteomics.pepxml) rows (pyteomics.mztab._MzTabTable attribute) rpartition() (pyteomics.auxiliary.structures.Ion method) rsplit() (pyteomics.auxiliary.structures.Ion method) rstrip() (pyteomics.auxiliary.structures.Ion method) run() (pyteomics.auxiliary.file_helpers.FileReadingProcess method)

S

sample_processing (pyteomics.mztab.MzTab attribute) samples (pyteomics.mztab.MzTab attribute) scan_identifier (pyteomics.usi.USI attribute), [1] scan_identifier_type (pyteomics.usi.USI attribute), [1] scatter_trend() (in module pyteomics.pylab_aux) schema_version (pyteomics.mzmlb.MzMLb attribute) seek() (pyteomics.mzmlb.HDF5ByteBuffer method) seekable() (pyteomics.mzmlb.HDF5ByteBuffer method) sentinel (pyteomics.auxiliary.file_helpers.FileReadingProcess attribute) sequence (pyteomics.proforma.ProForma attribute) set_unimod_path() (in module pyteomics.proforma) setdefault() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) shuffle() (in module pyteomics.fasta) sigma_fdr() (in module pyteomics.auxiliary.target_decoy) sigma_T() (in module pyteomics.auxiliary.target_decoy) small_molecule_feature_quantification_unit (pyteomics.mztab.MzTab attribute) small_molecule_identification_reliability (pyteomics.mztab.MzTab attribute) small_molecule_quantification_unit (pyteomics.mztab.MzTab attribute) small_molecule_table (pyteomics.mztab.MzTab attribute) software (pyteomics.mztab.MzTab attribute) sort() (pyteomics.auxiliary.structures.ChargeList method) source (pyteomics.auxiliary.utils.BinaryDataArrayTransformer.binary_array_record attribute) (pyteomics.mzml.MzML.binary_array_record attribute) (pyteomics.mzml.PreIndexedMzML.binary_array_record attribute) (pyteomics.mzmlb.ExternalDataMzML.binary_array_record attribute) (pyteomics.mzmlb.external_array_slice attribute) (pyteomics.mzxml.MzXML.binary_array_record attribute) (pyteomics.xml.ArrayConversionMixin.binary_array_record attribute) source_cls (pyteomics.proforma.ModificationToken attribute) sources (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzxml) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml) (in module pyteomics.protxml) (in module pyteomics.tandem) (in module pyteomics.traml) (pyteomics.auxiliary.file_helpers.ChainBase attribute)

SPD (class in pyteomics.fasta) SPDMixin (class in pyteomics.fasta) Specificity (class in pyteomics.mass.unimod) spectrum_match_table (pyteomics.mztab.MzTab attribute) SpectrumUtilsColorScheme (class in pyteomics.pylab_aux) split() (pyteomics.auxiliary.structures.Ion method) splitlines() (pyteomics.auxiliary.structures.Ion method) StableIsotope (class in pyteomics.proforma) start (pyteomics.mzmlb.chunk_interval_cache_record attribute) (pyteomics.proforma.TaggedInterval attribute) start() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) startswith() (pyteomics.auxiliary.structures.Ion method) std_aa_comp (in module pyteomics.mass.mass) std_aa_mass (in module pyteomics.mass.mass) std_amino_acids (in module pyteomics.parser) std_cterm (in module pyteomics.parser) std_ion_comp (in module pyteomics.mass.mass) std_labels (in module pyteomics.parser) std_nterm (in module pyteomics.parser) std_parsers (in module pyteomics.fasta) strip() (pyteomics.auxiliary.structures.Ion method) study_variables (pyteomics.mztab.MzTab attribute) subtract() (pyteomics.auxiliary.structures.BasicComposition method) swapcase() (pyteomics.auxiliary.structures.Ion method)

T

table_format (pyteomics.mztab.MzTab attribute) TableJoiner (class in pyteomics.auxiliary.file_helpers) tag_with_source() (pyteomics.usi.PROXIAggregator method) TagBase (class in pyteomics.proforma) TaggedInterval (class in pyteomics.proforma) tags (pyteomics.proforma.TaggedInterval attribute) TagSpecificXMLByteIndex (class in pyteomics.xml) TagTypeEnum (class in pyteomics.proforma) TandemXML (class in pyteomics.tandem) targets (pyteomics.proforma.ModificationRule attribute) tell() (pyteomics.mzmlb.HDF5ByteBuffer method) terminate() (pyteomics.auxiliary.file_helpers.FileReadingProcess method) time (pyteomics.mgf.IndexedMGF attribute) (pyteomics.ms1.IndexedMS1 attribute) (pyteomics.ms2.IndexedMS2 attribute) TimeOrderedIndexedReaderMixin (class in pyteomics.auxiliary.file_helpers)

timeout (pyteomics.usi.PROXIAggregator attribute) title (pyteomics.mztab.MzTab attribute) title() (pyteomics.auxiliary.structures.Ion method) to_bytes() (pyteomics.auxiliary.structures.Charge method) to_proforma() (in module pyteomics.parser) (in module pyteomics.proforma) to_string() (in module pyteomics.parser) tostring() (in module pyteomics.parser) TrafoXML (class in pyteomics.openms.trafoxml) TraML (class in pyteomics.traml) transform (pyteomics.mzmlb.external_array_slice attribute) translate() (pyteomics.auxiliary.structures.Ion method) truncate() (pyteomics.mzmlb.HDF5ByteBuffer method) TwoLayerIndexedFASTA (class in pyteomics.fasta) type (pyteomics.mztab.MzTab attribute) (pyteomics.proforma.TagBase attribute)

U

UniMes (class in pyteomics.fasta) UniMesMixin (class in pyteomics.fasta) Unimod (class in pyteomics.mass.mass) (class in pyteomics.mass.unimod) UnimodModification (class in pyteomics.proforma) UnimodResolver (class in pyteomics.proforma) UniParc (class in pyteomics.fasta) UniParcMixin (class in pyteomics.fasta) UniProt (class in pyteomics.fasta) UniProtMixin (class in pyteomics.fasta) UniRef (class in pyteomics.fasta) UniRefMixin (class in pyteomics.fasta) unit_accession (pyteomics.auxiliary.structures.cvstr attribute)

unit_info (pyteomics.auxiliary.structures.unitfloat attribute) (pyteomics.auxiliary.structures.unitint attribute) (pyteomics.auxiliary.structures.unitstr attribute) unitfloat (class in pyteomics.auxiliary.structures) unitint (class in pyteomics.auxiliary.structures) unitstr (class in pyteomics.auxiliary.structures) unlocalized_modifications (pyteomics.proforma.ProForma attribute) update() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) upper() (pyteomics.auxiliary.structures.Ion method) uris (pyteomics.mztab.MzTab attribute) USI (class in pyteomics.usi)

V

valid() (in module pyteomics.parser) value (pyteomics.proforma.TagBase attribute) values() (pyteomics.auxiliary.file_helpers.OffsetIndex method) (pyteomics.auxiliary.structures.BasicComposition method) (pyteomics.mztab.Group method) (pyteomics.peff.Header method)

variable_mods (pyteomics.mztab.MzTab attribute) version (pyteomics.mztab.MzTab attribute) version_info() (in module pyteomics.mzid) (in module pyteomics.mzml) (in module pyteomics.mzxml) (in module pyteomics.openms.idxml) (in module pyteomics.pepxml)

W

with_traceback() (pyteomics.auxiliary.structures.PyteomicsError method) writable() (pyteomics.mzmlb.HDF5ByteBuffer method) write() (in module pyteomics.fasta) (in module pyteomics.mgf) write_byte_offsets() (pyteomics.auxiliary.file_helpers.IndexSavingMixin method) (pyteomics.auxiliary.file_helpers.IndexSavingTextReader method) (pyteomics.mgf.IndexedMGF method) (pyteomics.mzid.MzIdentML method) (pyteomics.mzml.MzML method) (pyteomics.mzml.PreIndexedMzML method) (pyteomics.mzmlb.ExternalDataMzML method) (pyteomics.mzxml.MzXML method) (pyteomics.pepxml.PepXML method) (pyteomics.traml.TraML method) (pyteomics.xml.IndexSavingXML method)

write_decoy_db() (in module pyteomics.fasta) writelines() (pyteomics.mzmlb.HDF5ByteBuffer method)

X

xcleave() (in module pyteomics.parser) XLMODModification (class in pyteomics.proforma) XLMODResolver (class in pyteomics.proforma)

XML (class in pyteomics.xml) xpath() (in module pyteomics.xml) xsd_parser() (in module pyteomics.xml)

Z

zfill() (pyteomics.auxiliary.structures.Ion method)