Table of Contents - mspire-0.10.8.0 Documentation
Classes and Modules
- Array
- Bio
- Bio::FastaFormat
- Bio::FlatFile
- CV
- CV::Param
- CV::ReferenceableParamGroupRef
- Enumerable
- Hash
- IO
- Merge
- Mspire
- Mspire::Bin
- Mspire::CV
- Mspire::CV::Obo
- Mspire::CV::Param
- Mspire::CV::Paramable
- Mspire::Commandline
- Mspire::Digester
- Mspire::ErrorRate
- Mspire::ErrorRate::Decoy
- Mspire::ErrorRate::Qvalue
- Mspire::Fasta
- Mspire::Ident
- Mspire::Ident::Peptide
- Mspire::Ident::Peptide::Db
- Mspire::Ident::Peptide::Db::Creator
- Mspire::Ident::Peptide::Db::IO
- Mspire::Ident::PeptideHit
- Mspire::Ident::PeptideHit::Qvalue
- Mspire::Ident::PeptideHitLike
- Mspire::Ident::Pepxml
- Mspire::Ident::Pepxml::AminoacidModification
- Mspire::Ident::Pepxml::EnzymaticSearchConstraint
- Mspire::Ident::Pepxml::MsmsPipelineAnalysis
- Mspire::Ident::Pepxml::MsmsRunSummary
- Mspire::Ident::Pepxml::Mspire
- Mspire::Ident::Pepxml::Mspire::Ident
- Mspire::Ident::Pepxml::Mspire::Ident::Pepxml
- Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire
- Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident
- Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml
- Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- Mspire::Ident::Pepxml::Parameters
- Mspire::Ident::Pepxml::SampleEnzyme
- Mspire::Ident::Pepxml::SearchDatabase
- Mspire::Ident::Pepxml::SearchHit
- Mspire::Ident::Pepxml::SearchHit::ModificationInfo
- Mspire::Ident::Pepxml::SearchResult
- Mspire::Ident::Pepxml::SearchSummary
- Mspire::Ident::Pepxml::SpectrumQuery
- Mspire::Ident::Pepxml::TerminalModification
- Mspire::Ident::Protein
- Mspire::Ident::ProteinGroup
- Mspire::Ident::ProteinLike
- Mspire::Ident::Search
- Mspire::Ident::SearchGroup
- Mspire::Ident::SearchLike
- Mspire::Identml
- Mspire::Identml::SearchModification
- Mspire::Imzml
- Mspire::Imzml::Writer
- Mspire::Imzml::Writer::Commandline
- Mspire::Isotope
- Mspire::Isotope::AA
- Mspire::Isotope::Distribution
- Mspire::Isotope::NIST
- Mspire::Isotope::NIST::Updater
- Mspire::Isotope::Neese
- Mspire::Mascot
- Mspire::Mass
- Mspire::Mass::AA
- Mspire::Mass::All
- Mspire::Mass::Common
- Mspire::Mass::Element
- Mspire::Mass::Subatomic
- Mspire::Mass::Util
- Mspire::MolecularFormula
- Mspire::Mzid
- Mspire::Mzid::Modification
- Mspire::Mzml
- Mspire::Mzml::Activation
- Mspire::Mzml::Analyzer
- Mspire::Mzml::CV
- Mspire::Mzml::Chromatogram
- Mspire::Mzml::ChromatogramList
- Mspire::Mzml::Component
- Mspire::Mzml::Contact
- Mspire::Mzml::Convenience
- Mspire::Mzml::DataArray
- Mspire::Mzml::DataArrayContainerLike
- Mspire::Mzml::DataProcessing
- Mspire::Mzml::Default
- Mspire::Mzml::Detector
- Mspire::Mzml::FileContent
- Mspire::Mzml::FileDescription
- Mspire::Mzml::IOIndex
- Mspire::Mzml::IOIndexableList
- Mspire::Mzml::Index
- Mspire::Mzml::IndexList
- Mspire::Mzml::InstrumentConfiguration
- Mspire::Mzml::IsolationWindow
- Mspire::Mzml::List
- Mspire::Mzml::Parser
- Mspire::Mzml::Precursor
- Mspire::Mzml::ProcessingMethod
- Mspire::Mzml::Product
- Mspire::Mzml::Reader
- Mspire::Mzml::ReferenceableParamGroup
- Mspire::Mzml::Run
- Mspire::Mzml::Sample
- Mspire::Mzml::Scan
- Mspire::Mzml::ScanList
- Mspire::Mzml::ScanNumbersNotFound
- Mspire::Mzml::ScanNumbersNotUnique
- Mspire::Mzml::ScanSettings
- Mspire::Mzml::ScanWindow
- Mspire::Mzml::SelectedIon
- Mspire::Mzml::Software
- Mspire::Mzml::Source
- Mspire::Mzml::SourceFile
- Mspire::Mzml::Spectrum
- Mspire::Mzml::SpectrumList
- Mspire::OBO
- Mspire::Paramable
- Mspire::Peak
- Mspire::Peaklist
- Mspire::Plms1
- Mspire::Quant
- Mspire::Quant::Cmdline
- Mspire::Quant::ProteinGroupComparison
- Mspire::Quant::ProteinGroupComparison::Qspec
- Mspire::Quant::ProteinGroupComparison::SpectralCounts
- Mspire::Quant::ProteinGroupComparison::UniqAAzCounts
- Mspire::Quant::Qspec
- Mspire::Quant::SpectralCounts
- Mspire::Quant::SpectralCounts::Counts
- Mspire::Spectrum
- Mspire::Spectrum::Centroid
- Mspire::Spectrum::Centroidish
- Mspire::SpectrumLike
- Mspire::TaggedPeak
- Mspire::UserParam
- Numeric
- Object
- Obo
- Obo::Ontology
- Obo::Stanza
Methods
- ::[] — Mspire::Digester
- ::[] — Mspire::MolecularFormula
- ::[] — Mspire::Mzml::DataArray
- ::[] — Mspire::Mzml::SourceFile
- ::[] — Mspire::Peaklist
- ::[] — Mspire::CV::Param
- ::[] — Mspire::Mass::AA
- ::[] — Mspire::Mass::All
- ::[] — Mspire::Mass::Common
- ::[] — Mspire::Mass::Element
- ::[] — Mspire::Mass::Subatomic
- ::aa — Mspire::Mass
- ::aa_to_exact_mass — Mspire::Mass
- ::args_to_hashes — Mspire::Quant::Cmdline
- ::bin — Mspire::Bin
- ::calc_precursor_neutral_mass — Mspire::Ident::Pepxml::SpectrumQuery
- ::calculate — Mspire::Isotope::Distribution
- ::cmdline — Mspire::Ident::Peptide::Db::Creator
- ::conditions_to_ints — Mspire::Quant::Qspec
- ::counts — Mspire::Quant::SpectralCounts
- ::create_bins — Mspire::Peaklist
- ::create_index_list — Mspire::Mzml::IndexList
- ::data_arrays_from_xml — Mspire::Mzml::DataArray
- ::downcase_keys — Mspire::Mass::All
- ::empty_data_arrays — Mspire::Mzml::DataArray
- ::filetype — Mspire::Ident
- ::foreach — Mspire::Mzml
- ::foreach — Mspire::Fasta
- ::formula — Mspire::Mass
- ::formula_to_exact_mass — Mspire::Mass
- ::from_aaseq — Mspire::MolecularFormula
- ::from_any — Mspire::MolecularFormula
- ::from_arrays — Mspire::Mzml::DataArray
- ::from_arrays — Mspire::Mzml::Spectrum
- ::from_file — Mspire::Ident::PeptideHit::Qvalue
- ::from_io — Mspire::Mzml::IndexList
- ::from_peaklist — Mspire::Spectrum
- ::from_pepxml_node — Mspire::Ident::Pepxml::MsmsRunSummary
- ::from_pepxml_node — Mspire::Ident::Pepxml::SampleEnzyme
- ::from_pepxml_node — Mspire::Ident::Pepxml::SearchSummary
- ::from_pepxml_node — Mspire::Ident::Pepxml::SpectrumQuery
- ::from_phq — Mspire::Ident::PeptideHit::Qvalue
- ::from_string — Mspire::MolecularFormula
- ::from_xml — Mspire::Mzml::Chromatogram
- ::from_xml — Mspire::Mzml::CV
- ::from_xml — Mspire::Mzml::DataArray
- ::from_xml — Mspire::Mzml::DataProcessing
- ::from_xml — Mspire::Mzml::FileDescription
- ::from_xml — Mspire::Mzml::InstrumentConfiguration
- ::from_xml — Mspire::Mzml::Precursor
- ::from_xml — Mspire::Mzml::Product
- ::from_xml — Mspire::Mzml::ReferenceableParamGroup
- ::from_xml — Mspire::Mzml::Run
- ::from_xml — Mspire::Mzml::Sample
- ::from_xml — Mspire::Mzml::Scan
- ::from_xml — Mspire::Mzml::ScanList
- ::from_xml — Mspire::Mzml::Software
- ::from_xml — Mspire::Mzml::SourceFile
- ::from_xml — Mspire::Mzml::Spectrum
- ::index_offset — Mspire::Mzml::IndexList
- ::isotope_from_nist_line — Mspire::Isotope::NIST::Updater
- ::isotopes_from_nist_site — Mspire::Isotope::NIST::Updater
- ::list_xml — Mspire::Mzml::CV
- ::list_xml — Mspire::Mzml::DataArray
- ::list_xml — Mspire::Mzml::ReferenceableParamGroup
- ::list_xml — Mspire::Mzml::Component
- ::match — Mspire::Isotope::NIST::Updater
- ::members — Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- ::members — Mspire::Ident::Pepxml::SpectrumQuery
- ::merge — Mspire::Peaklist
- ::merge_and_deconvolve — Mspire::Peaklist
- ::merge_centroids — Mspire::Peaklist
- ::min_max_x — Mspire::Peaklist
- ::new — CV::Param
- ::new — CV::ReferenceableParamGroupRef
- ::new — Mspire::Bin
- ::new — Mspire::Digester
- ::new — Mspire::Ident::Peptide::Db
- ::new — Mspire::Ident::Peptide::Db::IO
- ::new — Mspire::Ident::PeptideHit
- ::new — Mspire::Ident::Pepxml
- ::new — Mspire::Ident::Pepxml::AminoacidModification
- ::new — Mspire::Ident::Pepxml::TerminalModification
- ::new — Mspire::Ident::Pepxml::MsmsPipelineAnalysis
- ::new — Mspire::Ident::Pepxml::MsmsRunSummary
- ::new — Mspire::Ident::Pepxml::SampleEnzyme
- ::new — Mspire::Ident::Pepxml::SearchDatabase
- ::new — Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- ::new — Mspire::Ident::Pepxml::SearchResult
- ::new — Mspire::Ident::Pepxml::SearchSummary
- ::new — Mspire::Ident::Pepxml::SpectrumQuery
- ::new — Mspire::Ident::Protein
- ::new — Mspire::Ident::Search
- ::new — Mspire::Isotope
- ::new — Mspire::MolecularFormula
- ::new — Mspire::Mzml
- ::new — Mspire::Mzml::Chromatogram
- ::new — Mspire::Mzml::CV
- ::new — Mspire::Mzml::DataArray
- ::new — Mspire::Mzml::DataProcessing
- ::new — Mspire::Mzml::FileDescription
- ::new — Mspire::Mzml::InstrumentConfiguration
- ::new — Mspire::Mzml::IOIndex
- ::new — Mspire::Mzml::IOIndexableList
- ::new — Mspire::Mzml::Precursor
- ::new — Mspire::Mzml::ProcessingMethod
- ::new — Mspire::Mzml::Product
- ::new — Mspire::Mzml::ReferenceableParamGroup
- ::new — Mspire::Mzml::Run
- ::new — Mspire::Mzml::Sample
- ::new — Mspire::Mzml::Scan
- ::new — Mspire::Mzml::ScanList
- ::new — Mspire::Mzml::ScanSettings
- ::new — Mspire::Mzml::Software
- ::new — Mspire::Mzml::SourceFile
- ::new — Mspire::Mzml::Spectrum
- ::new — Mspire::OBO
- ::new — Mspire::Plms1
- ::new — Mspire::Quant::Qspec
- ::new — Mspire::Quant::ProteinGroupComparison::Qspec
- ::new — Mspire::Quant::SpectralCounts::Counts
- ::new — Mspire::TaggedPeak
- ::new — Mspire::UserParam
- ::new — Obo::Ontology
- ::new — Mspire::CV::Paramable
- ::new — Mspire::Fasta
- ::new — Mspire::Ident::SearchGroup
- ::new — Mspire::Mzml::Component
- ::new — Mspire::Paramable
- ::new — Mspire::Quant::ProteinGroupComparison
- ::new — Mspire::SpectrumLike
- ::open — Mspire::Ident::Peptide::Db::IO
- ::open — Mspire::Mzml
- ::open — Mspire::Fasta
- ::parser — Mspire::Imzml::Writer::Commandline
- ::peptide_hits_to_protein_groups — Mspire::Ident::ProteinGroup
- ::prepare_sequence — Mspire::Ident::Peptide
- ::read_index_list — Mspire::Mzml::IndexList
- ::remove_non_amino_acids — Mspire::Ident::Peptide
- ::results_array — Mspire::Quant::Qspec
- ::run — Mspire::Commandline
- ::run — Mspire::Imzml::Writer::Commandline
- ::sequence_to_aaseq — Mspire::Ident::Peptide
- ::simple_search_hits — Mspire::Ident::Pepxml
- ::spectrum — Mspire::Isotope::Distribution
- ::split_sequence — Mspire::Ident::Peptide
- ::symbol_keys — Mspire::Mass::Util
- ::to_file — Mspire::Ident::PeptideHit::Qvalue
- ::to_mf — Mspire::Isotope::Distribution
- ::to_phq — Mspire::Ident::PeptideHit::Qvalue
- ::uniprot_id — Mspire::Fasta
- ::uri_basename_and_path — Mspire::Mzml::SourceFile
- ::write_nist_info — Mspire::Isotope::NIST::Updater
- #'[]' — Mspire::Mzml::Convenience
- #* — Mspire::MolecularFormula
- #+ — Mspire::MolecularFormula
- #- — Mspire::MolecularFormula
- #/ — Mspire::MolecularFormula
- #<< — Mspire::Bin
- #== — CV::Param
- #== — Mspire::MolecularFormula
- #== — Mspire::SpectrumLike
- #[] — Mspire::Ident::Peptide::Db
- #[] — Mspire::Ident::Peptide::Db::IO
- #[] — Mspire::Mzml::IndexList
- #[] — Mspire::Mzml::IOIndex
- #[] — Mspire::Mzml::IOIndexableList
- #[] — Mspire::SpectrumLike
- #accession — Mspire::UserParam
- #accessionable_params — Mspire::Paramable
- #add! — Mspire::MolecularFormula
- #add_stylesheet — Mspire::Ident::Pepxml
- #array_init — Mspire::Mzml::DataArray
- #avg_mass — Mspire::MolecularFormula
- #block_arg — Mspire::Ident::Pepxml::MsmsPipelineAnalysis
- #block_arg — Mspire::Ident::Pepxml::MsmsRunSummary
- #block_arg — Mspire::Ident::Pepxml::SearchSummary
- #bookmark — IO
- #build_hash — Mspire::OBO
- #build_hash — Obo::Ontology
- #cast — Obo::Stanza
- #cast_method — Obo::Stanza
- #centroided? — Mspire::Mzml::Spectrum
- #centroided? — Mspire::SpectrumLike
- #chromatogram — Mspire::Mzml::Convenience
- #cleavage_sites — Mspire::Digester
- #conditions — Mspire::Quant::Qspec
- #create — Mspire::Ident::Peptide::Db::Creator
- #create_digestion_file — Mspire::Ident::Peptide::Db::Creator
- #create_file_description — Mspire::Imzml::Writer
- #create_id_to_index! — Mspire::Mzml::IOIndexableList
- #create_referenceable_params_by_id_hash — Mspire::Imzml::Writer
- #create_scan_to_index — Mspire::Mzml::Index
- #data_array_xml_atts — Mspire::Mzml::DataArrayContainerLike
- #date — Mspire::Ident::Pepxml::MsmsPipelineAnalysis
- #db_from_fasta_digestion_file — Mspire::Ident::Peptide::Db::Creator
- #default_array_length — Mspire::Mzml::DataArrayContainerLike
- #describe! — Mspire::CV::Paramable
- #describe! — Mspire::Paramable
- #describe_from_xml! — Mspire::CV::Paramable
- #describe_from_xml! — Mspire::Paramable
- #describe_many! — Mspire::CV::Paramable
- #describe_many! — Mspire::Paramable
- #describe_self_from_xml! — Mspire::CV::Paramable
- #describe_self_from_xml! — Mspire::Paramable
- #digest — Mspire::Digester
- #div! — Mspire::MolecularFormula
- #each — Mspire::Ident::Peptide::Db::IO
- #each — Mspire::Mzml::IOIndex
- #each — Mspire::Mzml::Convenience
- #each — Mspire::SpectrumLike
- #each_accessionable_param — Mspire::Paramable
- #each_chromatogram — Mspire::Mzml::Convenience
- #each_pair — Mspire::Mzml::IndexList
- #each_param — Mspire::CV::Paramable
- #each_param — Mspire::Paramable
- #each_peak — Mspire::SpectrumLike
- #each_spectrum — Mspire::Mzml::Convenience
- #executable — Mspire::Quant::Qspec
- #expand_peptides — Mspire::Ident::Peptide::Db::Creator
- #experiment_hash_to_cvs — Mspire::Imzml::Writer
- #extension — Mspire::Ident::SearchGroup
- #fetch — Mspire::CV::Paramable
- #fetch — Mspire::Paramable
- #fetch_by_acc — Mspire::CV::Paramable
- #fetch_by_acc — Mspire::Paramable
- #fetch_by_accession — Mspire::CV::Paramable
- #fetch_by_accession — Mspire::Paramable
- #fetch_by_scan_num — Mspire::Mzml::SpectrumList
- #fetch_xml_node — Mspire::Mzml::IOIndex
- #find_all_nearest — Mspire::SpectrumLike
- #find_all_nearest_index — Mspire::SpectrumLike
- #find_nearest — Mspire::SpectrumLike
- #find_nearest_index — Mspire::SpectrumLike
- #fppr — Mspire::ErrorRate::Decoy
- #from_file — Mspire::Ident::SearchGroup
- #from_filenames — Mspire::Ident::SearchGroup
- #from_pepxml_node — Mspire::Ident::Pepxml::MsmsRunSummary
- #from_pepxml_node — Mspire::Ident::Pepxml::SampleEnzyme
- #from_pepxml_node — Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- #from_pepxml_node — Mspire::Ident::Pepxml::SearchSummary
- #from_pepxml_node — Mspire::Ident::Pepxml::SpectrumQuery
- #gene_id — Mspire::Ident::ProteinLike
- #get_a_trie — Mspire::Ident::Peptide::Db::Creator
- #get_default_data_processing_ids — Mspire::Mzml::Reader
- #get_header_string — Mspire::Mzml::Reader
- #get_xml_string — Mspire::Mzml::IOIndex
- #hash_like_from_digestion_file — Mspire::Ident::Peptide::Db::Creator
- #hi_x — Mspire::Peaklist
- #id_to_cast — Obo::Ontology
- #id_to_element — Mspire::OBO
- #id_to_element — Obo::Ontology
- #id_to_name — Mspire::OBO
- #id_to_name — Obo::Ontology
- #image_hash_to_cvs — Mspire::Imzml::Writer
- #in_groups — Array
- #index_by — Enumerable
- #inspect — Mspire::Bin
- #intensities — Mspire::Mzml::Chromatogram
- #intensities — Mspire::SpectrumLike
- #intensities= — Mspire::SpectrumLike
- #intensity — Mspire::Spectrum::Centroidish
- #inverse — Hash
- #isotope_distribution — Mspire::MolecularFormula
- #isotope_distribution_spectrum — Mspire::MolecularFormula
- #key? — Mspire::Ident::Peptide::Db::IO
- #keys — Mspire::Ident::Peptide::Db
- #keys — Mspire::Ident::Peptide::Db::IO
- #keys — Mspire::Mzml::IndexList
- #length — Mspire::Ident::Peptide::Db::IO
- #length — Mspire::Mzml::IOIndex
- #length — Mspire::Mzml::Convenience
- #list_type — Mspire::Mzml::IOIndexableList
- #list_xml — Mspire::Mzml::ScanList
- #list_xml — Mspire::Mzml::List
- #list_xml_element — Mspire::Mzml::List
- #lo_x — Mspire::Peaklist
- #mass — Mspire::MolecularFormula
- #members — Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- #members — Mspire::Ident::Pepxml::SpectrumQuery
- #merge! — Merge
- #mixed_target_decoy — Mspire::ErrorRate::Qvalue
- #ms_level — Mspire::Mzml::Spectrum
- #mul! — Mspire::MolecularFormula
- #mz — Mspire::MolecularFormula
- #mz — Mspire::Spectrum::Centroidish
- #mzs — Mspire::SpectrumLike
- #mzs= — Mspire::SpectrumLike
- #mzs_and_intensities — Mspire::SpectrumLike
- #name — Mspire::Mzml::IOIndex
- #name_to_id — Mspire::OBO
- #name_to_id — Obo::Ontology
- #normalize — Mspire::SpectrumLike
- #num_chromatograms — Mspire::Mzml::Convenience
- #num_missed_cleavages — Mspire::Ident::Pepxml::SampleEnzyme
- #num_tol_term — Mspire::Ident::Pepxml::SampleEnzyme
- #old_equal — Mspire::MolecularFormula
- #openany — Object
- #order — Mspire::Mzml::DataProcessing
- #param? — Mspire::CV::Paramable
- #param? — Mspire::Paramable
- #param_by_acc — Mspire::CV::Paramable
- #param_by_acc — Mspire::Paramable
- #param_by_accession — Mspire::CV::Paramable
- #param_by_accession — Mspire::Paramable
- #params — Mspire::Paramable
- #params? — Mspire::CV::Paramable
- #params? — Mspire::Paramable
- #params_initialize — Mspire::Mzml::Chromatogram
- #params_initialize — Mspire::Mzml::Spectrum
- #peak_boundaries — Mspire::Peaklist
- #peaks — Mspire::SpectrumLike
- #pepxml_version — Mspire::Ident::Pepxml
- #precision — Mspire::ErrorRate::Decoy
- #precursor_charge — Mspire::Mzml::Spectrum
- #precursor_mz — Mspire::Mzml::Spectrum
- #profile? — Mspire::Mzml::Spectrum
- #raw_isotope_distribution — Mspire::MolecularFormula
- #read — Mspire::Plms1
- #read_float64 — Mspire::Plms1
- #read_header! — Mspire::Mzml::Reader
- #read_uint32 — Mspire::Plms1
- #reject! — Mspire::CV::Paramable
- #reject! — Mspire::Paramable
- #replace! — Mspire::CV::Paramable
- #replace! — Mspire::Paramable
- #replace_many! — Mspire::CV::Paramable
- #replace_many! — Mspire::Paramable
- #retention_time — Mspire::Mzml::Spectrum
- #run — Mspire::Quant::Qspec
- #sample_id — Mspire::TaggedPeak
- #sample_id= — Mspire::TaggedPeak
- #scan — Mspire::Mzml::Spectrum
- #scan_window — Mspire::Mzml::Scan
- #scan_window_limits — Mspire::Mzml::Scan
- #search_class — Mspire::Ident::SearchGroup
- #select_indices — Mspire::SpectrumLike
- #set_from_xml_io! — Mspire::Mzml::Reader
- #set_size_of_residues! — Mspire::Ident::Pepxml::SearchDatabase
- #set_trypsin — Mspire::Ident::Pepxml::SampleEnzyme
- #site_digest — Mspire::Digester
- #size — Mspire::Ident::Peptide::Db
- #size — Mspire::Ident::Peptide::Db::IO
- #size — Mspire::Mzml::IOIndex
- #size — Mspire::Mzml::Convenience
- #size — Mspire::SpectrumLike
- #sort! — Mspire::SpectrumLike
- #spectrum — Mspire::Mzml::Precursor
- #spectrum — Mspire::Mzml::Convenience
- #spectrum_from_scan_num — Mspire::Mzml::Convenience
- #spectrum_queries — Mspire::Ident::Pepxml
- #split — Mspire::Peaklist
- #split_contiguous — Mspire::Peaklist
- #split_on_zeros — Mspire::Peaklist
- #start_byte — Mspire::Mzml::Index
- #sub! — Mspire::MolecularFormula
- #target_decoy_qvalues — Mspire::ErrorRate::Qvalue
- #tic — Mspire::SpectrumLike
- #times — Mspire::Mzml::Chromatogram
- #to_binary — Mspire::Mzml::DataArray
- #to_hash — Mspire::MolecularFormula
- #to_paths — Mspire::Ident::SearchGroup
- #to_peaklist — Mspire::SpectrumLike
- #to_plms1 — Mspire::Mzml
- #to_plus_minus_string — Numeric
- #to_s — Mspire::MolecularFormula
- #to_spectrum — Mspire::Peaklist
- #to_xml — CV::Param
- #to_xml — CV::ReferenceableParamGroupRef
- #to_xml — Mspire::Ident::Pepxml
- #to_xml — Mspire::Ident::Pepxml::AminoacidModification
- #to_xml — Mspire::Ident::Pepxml::TerminalModification
- #to_xml — Mspire::Ident::Pepxml::MsmsPipelineAnalysis
- #to_xml — Mspire::Ident::Pepxml::MsmsRunSummary
- #to_xml — Mspire::Ident::Pepxml::Parameters
- #to_xml — Mspire::Ident::Pepxml::SampleEnzyme
- #to_xml — Mspire::Ident::Pepxml::SearchDatabase
- #to_xml — Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::Mspire::Ident::Pepxml::SearchHit
- #to_xml — Mspire::Ident::Pepxml::SearchResult
- #to_xml — Mspire::Ident::Pepxml::SearchSummary
- #to_xml — Mspire::Ident::Pepxml::SpectrumQuery
- #to_xml — Mspire::Mzml
- #to_xml — Mspire::Mzml::Activation
- #to_xml — Mspire::Mzml::Chromatogram
- #to_xml — Mspire::Mzml::Contact
- #to_xml — Mspire::Mzml::CV
- #to_xml — Mspire::Mzml::DataArray
- #to_xml — Mspire::Mzml::DataProcessing
- #to_xml — Mspire::Mzml::FileContent
- #to_xml — Mspire::Mzml::FileDescription
- #to_xml — Mspire::Mzml::InstrumentConfiguration
- #to_xml — Mspire::Mzml::IOIndexableList
- #to_xml — Mspire::Mzml::IsolationWindow
- #to_xml — Mspire::Mzml::Precursor
- #to_xml — Mspire::Mzml::ProcessingMethod
- #to_xml — Mspire::Mzml::Product
- #to_xml — Mspire::Mzml::ReferenceableParamGroup
- #to_xml — Mspire::Mzml::Run
- #to_xml — Mspire::Mzml::Sample
- #to_xml — Mspire::Mzml::Scan
- #to_xml — Mspire::Mzml::ScanList
- #to_xml — Mspire::Mzml::ScanSettings
- #to_xml — Mspire::Mzml::ScanWindow
- #to_xml — Mspire::Mzml::SelectedIon
- #to_xml — Mspire::Mzml::Software
- #to_xml — Mspire::Mzml::SourceFile
- #to_xml — Mspire::Mzml::Spectrum
- #to_xml — Mspire::UserParam
- #to_xml — Mspire::CV::Paramable
- #to_xml — Mspire::Mzml::Component
- #to_xml — Mspire::Paramable
- #to_xml_definition — Mspire::Mzml::ReferenceableParamGroup
- #uniq_by — Enumerable
- #values — Mspire::Ident::Peptide::Db
- #values — Mspire::Ident::Peptide::Db::IO
- #weighted_x — Mspire::Peaklist
- #write — Mspire::Imzml::Writer
- #write — Mspire::Mzml
- #write — Mspire::Plms1
- #write — Mspire::Quant::Qspec
- #write_ascii — Mspire::Plms1
- #write_binary — Mspire::Imzml::Writer
- #write_data_array — Mspire::Imzml::Writer
- #write_file_or_string — Object
- #write_float64 — Mspire::Plms1
- #write_uint32 — Mspire::Plms1
- #x= — Mspire::Peak
- #x= — Mspire::TaggedPeak
- #x_y_positions — Mspire::Imzml::Writer
- #xml_node_from_start_byte — Mspire::Mzml::IOIndex
- #y= — Mspire::Peak
- #y= — Mspire::TaggedPeak