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#[] Ms::Ident::Peptide::Db::IO
#[] Ms::Ident::Peptide::Db
#_parse_for_prot_groups Proph::ProtSummary::Parser
#aaseq Ms::Ident::Pepxml::SearchHit::Simple
#aaseq Proph::Prot::Pep
#aaseq Ms::Ident::PeptideHit
#add_stylesheet Ms::Ident::Pepxml
#aminoacid Ms::Ident::Pepxml::AminoacidModification
#base_name Ms::Ident::Pepxml::MsmsRunSummary
#base_name Ms::Ident::Pepxml::SearchSummary
#binary Ms::Ident::Pepxml::AminoacidModification
#block_arg Ms::Ident::Pepxml::SearchSummary
#block_arg Ms::Ident::Pepxml::MsmsRunSummary
#block_arg Ms::Ident::Pepxml::MsmsPipelineAnalysis
#calc_neutral_pep_mass Ms::Ident::Pepxml::SearchHit
#calc_pI Ms::Ident::Pepxml::SearchHit
calc_precursor_neutral_mass Ms::Ident::Pepxml::SpectrumQuery
#charge Ms::Ident::Pepxml::SearchHit::Simple
#charge Ms::Ident::PeptideHit
cmdline Ms::Ident::Peptide::Db
#cut Ms::Ident::Pepxml::SampleEnzyme
#database_name Ms::Ident::Pepxml::SearchDatabase
#database_release_date Ms::Ident::Pepxml::SearchDatabase
#database_release_identifier Ms::Ident::Pepxml::SearchDatabase
#date Ms::Ident::Pepxml::MsmsPipelineAnalysis
#description Ms::Ident::Pepxml::TerminalModification
#description Ms::Ident::Protein
#each Ms::Ident::Peptide::Db::IO
#enzymatic_search_constraint Ms::Ident::Pepxml::SearchSummary
expand_peptides Ms::Ident::Peptide::Db
#extension Ms::Ident::SearchGroup
filetype Ms::Ident
#first_entry Proph::Prot
#first_entry Proph::PepSummary::Prot
#fragment_mass_type Ms::Ident::Pepxml::SearchSummary
#from_file Ms::Ident::SearchGroup
from_file Ms::Ident::PeptideHit::Qvalue
#from_filenames Ms::Ident::SearchGroup
#from_pepxml_node Ms::Ident::Pepxml::SearchSummary
#from_pepxml_node Ms::Ident::Pepxml::MsmsRunSummary
#from_pepxml_node Ms::Ident::Pepxml::SampleEnzyme
from_pepxml_node Ms::Ident::Pepxml::SearchSummary
from_pepxml_node Ms::Ident::Pepxml::SpectrumQuery
#from_pepxml_node Proph::PepSummary::Pep
#from_pepxml_node Ms::Ident::Pepxml::SearchHit
from_pepxml_node Ms::Ident::Pepxml::SampleEnzyme
from_pepxml_node Ms::Ident::Pepxml::MsmsRunSummary
#from_pepxml_node Ms::Ident::Pepxml::SpectrumQuery
#gene_id Ms::Ident::ProteinHit
#get_version Proph::ProtSummary
#get_version Proph::PepSummary
#group_number Proph::ProtGroup
#hi_prob_best Proph::ProtSummary
#hi_prob_best Proph::PepSummary
#hit_rank Ms::Ident::Pepxml::SearchHit
#id Ms::Ident::Protein
#id Ms::Ident::Pepxml::SearchHit::Simple
#id Ms::Ident::Search
#id Ms::Ident::PeptideHit
#index Ms::Ident::Peptide::Db::IO
#initialize Ms::Ident::ProteinHit
#initialize Proph::ProtGroup
#initialize Ms::Ident::Pepxml::MsmsPipelineAnalysis
#initialize Ms::Ident::Pepxml::SampleEnzyme
#initialize Ms::Ident::Pepxml::AminoacidModification
#initialize Proph::PepSummary
#initialize Ms::Ident::Peptide::Db::IO
#initialize Ms::Ident::Pepxml::SearchSummary
#initialize Ms::Ident::Peptide::Db
#initialize Ms::Ident::Protein
#initialize Proph::ProtSummary
#initialize Ms::Ident::SearchGroup
#initialize Ms::Ident::Pepxml::SearchDatabase
#initialize Ms::Ident::Pepxml::TerminalModification
#initialize Ms::Ident::Search
#initialize Proph::ProtSummary::Parser
#initialize Ms::Ident::Pepxml
#initialize Ms::Ident::Pepxml::MsmsRunSummary
#initialize Ms::Ident::Pepxml::SpectrumQuery
#initialize Ms::Ident::Pepxml::SearchHit
#initialize Ms::Ident::Pepxml::SearchResult
#io Ms::Ident::Peptide::Db::IO
#is_rejected Ms::Ident::Pepxml::SearchHit
#keys Ms::Ident::Peptide::Db::IO
#local_path Ms::Ident::Pepxml::SearchDatabase
#mass Ms::Ident::Pepxml::TerminalModification
#mass Ms::Ident::Pepxml::AminoacidModification
#massdiff Ms::Ident::Pepxml::SearchHit
#massdiff Ms::Ident::Pepxml::TerminalModification
#massdiff Ms::Ident::Pepxml::AminoacidModification
members Ms::Ident::Pepxml::SearchHit
#members Ms::Ident::Pepxml::SpectrumQuery
#members Ms::Ident::Pepxml::SearchHit
members Ms::Ident::Pepxml::SpectrumQuery
#merge! Ms::Ident::Search
#merge! Merge
#missed_cleavages Ms::Ident::PeptideHit
#modification_info Ms::Ident::Pepxml::SearchHit
#modifications Ms::Ident::Pepxml::SearchSummary
#ms_detector Ms::Ident::Pepxml::MsmsRunSummary
#ms_ionization Ms::Ident::Pepxml::MsmsRunSummary
#ms_manufacturer Ms::Ident::Pepxml::MsmsRunSummary
#ms_mass_analyzer Ms::Ident::Pepxml::MsmsRunSummary
#ms_model Ms::Ident::Pepxml::MsmsRunSummary
#msms_pipeline_analysis Ms::Ident::Pepxml
#msms_run_summaries Proph::PepSummary
#msms_run_summary Ms::Ident::Pepxml::MsmsPipelineAnalysis
#name Ms::Ident::Pepxml::SampleEnzyme
#name Proph::Prot
#no_cut Ms::Ident::Pepxml::SampleEnzyme
#num_matched_ions Ms::Ident::Pepxml::SearchHit
#num_missed_cleavages Ms::Ident::Pepxml::SampleEnzyme
#num_missed_cleavages Ms::Ident::Pepxml::SearchHit
#num_tol_term Ms::Ident::Pepxml::SearchHit
#num_tol_term Ms::Ident::Pepxml::SampleEnzyme
#num_tot_proteins Ms::Ident::Pepxml::SearchHit
open Ms::Ident::Peptide::Db::IO
#orig_database_url Ms::Ident::Pepxml::SearchDatabase
#out_data Ms::Ident::Pepxml::SearchSummary
#out_data_type Ms::Ident::Pepxml::SearchSummary
#parameters Ms::Ident::Pepxml::SearchSummary
#parse_file Proph::ProtSummary::Parser
#peptide Ms::Ident::Pepxml::SearchHit
peptide_centric_db Ms::Ident::Peptide::Db
#peptide_hits Ms::Ident::ProteinGroup
#peptide_hits Ms::Ident::ProteinHit
#peptide_hits Ms::Ident::Search
peptide_hits_to_protein_groups Ms::Ident::ProteinGroup
#peptide_next_aa Ms::Ident::Pepxml::SearchHit
#peptide_prev_aa Ms::Ident::Pepxml::SearchHit
#peptide_terminus Ms::Ident::Pepxml::AminoacidModification
#peptideprophet_summary Proph::PepSummary
#pepxml_version Ms::Ident::Pepxml::MsmsPipelineAnalysis
#pepxml_version Ms::Ident::Pepxml::MsmsRunSummary
#pepxml_version Ms::Ident::Pepxml
#precursor_mass_type Ms::Ident::Pepxml::SearchSummary
prepare_sequence Ms::Ident::Peptide
#probability Proph::Prot::Pep
#probability Proph::ProtGroup
#prot_groups Proph::ProtSummary::Parser
#prot_groups Proph::ProtSummary
#protein Ms::Ident::Pepxml::SearchHit
#protein_desc Ms::Ident::Pepxml::SearchHit
#protein_mw Ms::Ident::Pepxml::SearchHit
#protein_terminus Ms::Ident::Pepxml::TerminalModification
#proteins Ms::Ident::PeptideHit
#prots Proph::ProtGroup
#qvalue Ms::Ident::PeptideHit
#raw_data Ms::Ident::Pepxml::MsmsRunSummary
#raw_data_type Ms::Ident::Pepxml::MsmsRunSummary
#reference Proph::PepSummary::Prot
#reference Proph::Prot
remove_non_amino_acids Ms::Ident::Peptide
#sample_enzyme Ms::Ident::Pepxml::MsmsRunSummary
#search Ms::Ident::Pepxml::SearchHit::Simple
#search Ms::Ident::PeptideHit
#search_class Ms::Ident::SearchGroup
#search_database Ms::Ident::Pepxml::SearchSummary
#search_engine Ms::Ident::Pepxml::SearchSummary
#search_hit_class Proph::PepSummary
#search_hits Ms::Ident::Pepxml::SearchResult
#search_id Ms::Ident::Pepxml::SearchSummary
#search_scores Ms::Ident::Pepxml::SearchHit::Simple
#search_scores Ms::Ident::Pepxml::SearchHit
#search_summary Ms::Ident::Pepxml::MsmsRunSummary
#searches Ms::Ident::SearchGroup
#sense Ms::Ident::Pepxml::SampleEnzyme
#seq Ms::Ident::Protein
#seq_type Ms::Ident::Pepxml::SearchDatabase
sequence_to_aaseq Ms::Ident::Peptide
#set_size_of_residues! Ms::Ident::Pepxml::SearchDatabase
#set_trypsin Ms::Ident::Pepxml::SampleEnzyme
simple_search_hits Ms::Ident::Pepxml
#size Ms::Ident::Peptide::Db::IO
#size_of_residues Ms::Ident::Pepxml::SearchDatabase
#spectrum_queries Ms::Ident::Pepxml::MsmsRunSummary
#spectrum_queries Ms::Ident::Pepxml
#spectrum_query Ms::Ident::Pepxml::SearchHit
split_sequence Ms::Ident::Peptide
#summary_xml Ms::Ident::Pepxml::MsmsPipelineAnalysis
#symbol Ms::Ident::Pepxml::TerminalModification
#symbol Ms::Ident::Pepxml::AminoacidModification
#terminus Ms::Ident::Pepxml::TerminalModification
to_file Ms::Ident::PeptideHit::Qvalue
#to_paths Ms::Ident::SearchGroup
to_phq Ms::Ident::PeptideHit::Qvalue
#to_plus_minus_string Numeric
#to_xml Ms::Ident::Pepxml::SpectrumQuery
#to_xml Ms::Ident::Pepxml::SearchSummary
#to_xml Ms::Ident::Pepxml::SampleEnzyme
#to_xml Ms::Ident::Pepxml::TerminalModification
#to_xml Ms::Ident::Pepxml::SearchResult
#to_xml Ms::Ident::Pepxml::AminoacidModification
#to_xml Ms::Ident::Pepxml::SearchHit
#to_xml Ms::Ident::Pepxml::Parameters
#to_xml Ms::Ident::Pepxml::MsmsPipelineAnalysis
#to_xml Ms::Ident::Pepxml
#to_xml Ms::Ident::Pepxml::SearchDatabase
#to_xml Ms::Ident::Pepxml::MsmsRunSummary
#tot_num_ions Ms::Ident::Pepxml::SearchHit
#unique_prots Proph::ProtSummary
#values Ms::Ident::Peptide::Db::IO
#variable Ms::Ident::Pepxml::TerminalModification
#variable Ms::Ident::Pepxml::AminoacidModification
#version Proph::ProtSummary
#version Proph::PepSummary
#xmlns Ms::Ident::Pepxml::MsmsPipelineAnalysis
#xmlns_xsi Ms::Ident::Pepxml::MsmsPipelineAnalysis
#xsi_schema_location Ms::Ident::Pepxml::MsmsPipelineAnalysis