RubyGems - msf - Versions diffs - 0.1.0 - Mend

msf 0.1.0

Files changed (80) hide show

data/.document +5 -0
data/.rspec +1 -0
data/Gemfile +24 -0
data/Gemfile.lock +67 -0
data/LICENSE.txt +20 -0
data/README.md +45 -0
data/Rakefile +43 -0
data/VERSION +1 -0
data/bin/ibspectra +43 -0
data/erd/config.png +0 -0
data/erd/empty.png +0 -0
data/erd/erd.png +0 -0
data/erd/msf.xcdatamodeld/.xccurrentversion +8 -0
data/erd/msf.xcdatamodeld/msf.xcdatamodel/contents +330 -0
data/erd/schema.txt +666 -0
data/lib/msf.rb +2 -0
data/lib/msf/models.rb +4 -0
data/lib/msf/models/amino_acid.rb +50 -0
data/lib/msf/models/amino_acid_modification.rb +55 -0
data/lib/msf/models/amino_acid_modification_neutral_loss.rb +31 -0
data/lib/msf/models/amino_acid_modifications_amino_acid_nls.rb +23 -0
data/lib/msf/models/amino_acid_modifications_amino_acids.rb +27 -0
data/lib/msf/models/annotation_data_version.rb +20 -0
data/lib/msf/models/annotation_dataset.rb +29 -0
data/lib/msf/models/annotation_group.rb +38 -0
data/lib/msf/models/annotation_type.rb +23 -0
data/lib/msf/models/chromatogram.rb +26 -0
data/lib/msf/models/custom_data_field.rb +56 -0
data/lib/msf/models/custom_data_peptide.rb +25 -0
data/lib/msf/models/custom_data_processing_node.rb +25 -0
data/lib/msf/models/custom_data_protein.rb +25 -0
data/lib/msf/models/custom_data_spectrum.rb +25 -0
data/lib/msf/models/enzyme.rb +32 -0
data/lib/msf/models/fasta_file.rb +50 -0
data/lib/msf/models/file_info.rb +41 -0
data/lib/msf/models/mass_peak.rb +36 -0
data/lib/msf/models/peptide.rb +118 -0
data/lib/msf/models/peptide_score.rb +34 -0
data/lib/msf/models/peptide_score_decoy.rb +34 -0
data/lib/msf/models/peptide_terminal_modification.rb +29 -0
data/lib/msf/models/peptides_amino_acid_modifications.rb +32 -0
data/lib/msf/models/peptides_proteins.rb +27 -0
data/lib/msf/models/processing_node.rb +65 -0
data/lib/msf/models/processing_node_score.rb +45 -0
data/lib/msf/models/protein.rb +38 -0
data/lib/msf/models/protein_annotation.rb +35 -0
data/lib/msf/models/protein_identification_group.rb +19 -0
data/lib/msf/models/protein_score.rb +34 -0
data/lib/msf/models/reporter_ion_quan_result.rb +31 -0
data/lib/msf/models/reporter_ion_quan_result_search_spectrum.rb +29 -0
data/lib/msf/models/scan_event.rb +37 -0
data/lib/msf/models/schema_info.rb +29 -0
data/lib/msf/models/spectrum.rb +34 -0
data/lib/msf/models/spectrum_header.rb +63 -0
data/lib/msf/models/spectrum_score.rb +24 -0
data/lib/msf/models/taxonomy_name.rb +26 -0
data/lib/msf/models/workflow_info.rb +46 -0
data/lib/msf/models/workflow_message.rb +31 -0
data/lib/msf/msf.rb +32 -0
data/lib/msf/sql/enzyme_cleavage_specificity.rb +16 -0
data/lib/msf/sql/false_discovery_rate.rb +24 -0
data/lib/msf/sql/fasta_file_protein_annotation.rb +17 -0
data/lib/msf/sql/mass_peak_relation.rb +17 -0
data/lib/msf/sql/peptide_amino_acid_modification_decoy.rb +23 -0
data/lib/msf/sql/peptide_decoy.rb +32 -0
data/lib/msf/sql/peptide_terminal_modification_decoy.rb +20 -0
data/lib/msf/sql/precursor_ion_quan_result.rb +29 -0
data/lib/msf/sql/precursor_ion_quan_result_event_spectrum.rb +17 -0
data/lib/msf/sql/precursor_ion_quan_result_search_spectrum.rb +20 -0
data/lib/msf/sql/processing_node_filter_parameter.rb +29 -0
data/lib/msf/sql/processing_node_interface.rb +19 -0
data/lib/msf/sql/processing_node_parameter.rb +46 -0
data/lib/msf/sql/processing_node_spectrum.rb +16 -0
data/lib/msf/sql/quan_result.rb +40 -0
data/lib/msf/sql/result_filter_set.rb +12 -0
data/lib/msf/sql/taxonomy_node.rb +26 -0
data/msf.gemspec +143 -0
data/spec/msf_spec.rb +7 -0
data/spec/spec_helper.rb +14 -0
metadata +275 -0

data/.document ADDED

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+-
+features/**/*.feature
+LICENSE.txt

data/.rspec ADDED

	@@ -0,0 +1 @@
1	+ --color

data/Gemfile ADDED

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+gem "bundler", "~> 1.2.1"
+group :development, :test do
+  gem "rspec", "~> 2.8.0"
+  gem "simplecov", "~> 0.7.1", :require => false
+end
+group :development do
+  gem "jeweler", "~> 1.8.4"
+  gem "debugger", ">= 1.2.0"
+  gem "yard", "~> 0.7"
+  gem "redcarpet", "~> 2.2.2"
+end
+gem "activerecord", "~> 3.2.0"
+gem "sqlite3", "~> 1.3.0"
+# gem "composite_primary_keys", "~> 5.0.9"

data/Gemfile.lock ADDED

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    activemodel (3.2.8)
+      activesupport (= 3.2.8)
+      builder (~> 3.0.0)
+    activerecord (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
+      arel (~> 3.0.2)
+      tzinfo (~> 0.3.29)
+    activesupport (3.2.8)
+      i18n (~> 0.6)
+      multi_json (~> 1.0)
+    arel (3.0.2)
+    builder (3.0.4)
+    columnize (0.3.6)
+    debugger (1.2.1)
+      columnize (>= 0.3.1)
+      debugger-linecache (~> 1.1.1)
+      debugger-ruby_core_source (~> 1.1.4)
+    debugger-linecache (1.1.2)
+      debugger-ruby_core_source (>= 1.1.1)
+    debugger-ruby_core_source (1.1.4)
+    diff-lcs (1.1.3)
+    git (1.2.5)
+    i18n (0.6.1)
+    jeweler (1.8.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+      rdoc
+    json (1.7.5)
+    multi_json (1.3.6)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
+    redcarpet (2.2.2)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.8.0)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    sqlite3 (1.3.6)
+    tzinfo (0.3.34)
+    yard (0.8.3)
+PLATFORMS
+  ruby
+DEPENDENCIES
+  activerecord (~> 3.2.0)
+  bundler (~> 1.2.1)
+  debugger (>= 1.2.0)
+  jeweler (~> 1.8.4)
+  redcarpet (~> 2.2.2)
+  rspec (~> 2.8.0)
+  simplecov (~> 0.7.1)
+  sqlite3 (~> 1.3.0)
+  yard (~> 0.7)

data/LICENSE.txt ADDED

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+Copyright (c) 2012 William Van Etten
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md ADDED

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+# MSF Parser #
+A library for accessing Thermo’s ProteomeDiscoverer’s MSF result file format.
+MSF files are SQLite3-based, so the this interface represents a simple API using ActiveRecord that is directly translatable to the database’s schema.
+This gem takes heavily from Angel Pizzaro's thermo_msf gem.
+https://github.com/itmat/thermo_msf
+## WARNING ##
+This gem has not been developed to completion,
+taken only sufficiently far to serve my present needs.
+It has not been tested on MSF files other than those generated by my instrument
+operating my version of Thermo's Proteome Discoverer.
+## Installation ##
+    gem install msf
+## Usage ##
+    msf = MSF.new({:path => msf_file})
+    Peptides.all do |peptide|
+      <whatever>
+    end
+    ibspectra msf_file >> msf_file/msf_file.ibspectra.csv
+## Contributing to msf ##
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+## Copyright ##
+Copyright (c) 2012 William Van Etten. See LICENSE.txt for
+further details.

data/Rakefile ADDED

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+# encoding: utf-8
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "msf"
+  gem.homepage = "http://github.com/vanetten/msf"
+  gem.license = "MIT"
+  gem.summary = "ActiveRecord access to MSF file (sqlite3 database)."
+  gem.description = "An MSF file is sqlite3 dtabase. ActiveRecord is a great ORM for accessing the data. Much taken from Angel Pizarro's thermo_msf."
+  gem.email = "bill@bioteam.net"
+  gem.authors = ["William Van Etten"]
+  gem.files.include 'bin/ibspectra'
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+task :default => :spec
+require 'yard'
+YARD::Rake::YardocTask.new

data/VERSION ADDED

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1	+ 0.1.0

data/bin/ibspectra ADDED

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+#!/usr/bin/env ruby
+#
+require 'msf'
+msf_file = ARGV.shift
+if msf_file.nil? || !File.readable?(msf_file)
+  puts "Usage: #{File.basename($0)} file.msf\n\n"
+  exit 0
+end
+msf = MSF.new({:path => msf_file})
+header = %w{"accession" "start.pos" "peptide" "modif" "charge" "theo.mass" "exp.mass" "parent.intens" "retention.time" "spectrum" "score.mascot" "score.phenyx" "use.for.quant" "file" "X113_mass" "X114_mass" "X115_mass" "X116_mass" "X117_mass" "X118_mass" "X119_mass" "X121_mass" "X113_ions" "X114_ions" "X115_ions" "X116_ions" "X117_ions" "X118_ions" "X119_ions" "X121_ions"}
+puts header.join("\t") + "\n"
+Peptide.all.each do |peptide|
+  next unless peptide.confidence_level == 3
+  next if peptide.terminal_modification.nil?
+  next unless peptide.spectrum.search_spectrum
+  peptide.proteins.each do |protein|
+    row = []
+    row << '"' + protein.protein_annotation.accession + '"'
+    row << protein.sequence.index(peptide.sequence) + 1
+    row << '"' + peptide.sequence + '"'
+    row << '"' + peptide.isobar_sequence + '"'
+    row << peptide.spectrum.spectrum_header.charge
+    row << peptide.theoretical_mass
+    row << peptide.spectrum.spectrum_header.mass_peak.mass
+    row << peptide.spectrum.spectrum_header.mass_peak.intensity
+    row << peptide.spectrum.spectrum_header.retention_time
+    row << '"' + peptide.spectrum.spectrum_header.title + '"'
+    row << peptide.peptide_score.score_value
+    row << 0
+    row << 'TRUE'
+    row << '"' + File.basename(msf_file) + '"'
+    peptide.spectrum.search_spectrum.reporter_ion_quan_results.each do |result|
+      row << result.mass
+    end
+    peptide.spectrum.search_spectrum.reporter_ion_quan_results.each do |result|
+      row << result.height
+    end
+    puts row.join("\t") + "\n"
+  end
+end

data/erd/config.png ADDED

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data/erd/empty.png ADDED

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data/erd/erd.png ADDED

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data/erd/msf.xcdatamodeld/.xccurrentversion ADDED

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>_XCCurrentVersionName</key>
+	<string>msf.xcdatamodel</string>
+</dict>
+</plist>

data/erd/msf.xcdatamodeld/msf.xcdatamodel/contents ADDED

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+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<model name="" userDefinedModelVersionIdentifier="" type="com.apple.IDECoreDataModeler.DataModel" documentVersion="1.0" lastSavedToolsVersion="1487" systemVersion="12C54" minimumToolsVersion="Automatic" macOSVersion="Automatic" iOSVersion="Automatic">
+    <entity name="AminoAcid" syncable="YES">
+        <attribute name="aminoAcidID" optional="YES" syncable="YES"/>
+        <attribute name="aminoAcidName" optional="YES" syncable="YES"/>
+        <attribute name="averageMass" optional="YES" syncable="YES"/>
+        <attribute name="monoisotopicMass" optional="YES" syncable="YES"/>
+        <attribute name="oneLetterCode" optional="YES" syncable="YES"/>
+        <attribute name="sumFormula" optional="YES" syncable="YES"/>
+        <attribute name="threeLetterCode" optional="YES" syncable="YES"/>
+        <relationship name="aminoAcidModifications" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="AminoAcidsModificationsAminoAcids" inverseName="aminoAcid" inverseEntity="AminoAcidsModificationsAminoAcids" syncable="YES"/>
+    </entity>
+    <entity name="AminoAcidModification" syncable="YES">
+        <attribute name="abbreviation" optional="YES" syncable="YES"/>
+        <attribute name="aminoAcidModificationID" optional="YES" syncable="YES"/>
+        <attribute name="deltaAverageMass" optional="YES" syncable="YES"/>
+        <attribute name="deltaMass" optional="YES" syncable="YES"/>
+        <attribute name="isActive" optional="YES" syncable="YES"/>
+        <attribute name="isSubstitution" optional="YES" syncable="YES"/>
+        <attribute name="leavingGroup" optional="YES" syncable="YES"/>
+        <attribute name="modificationName" optional="YES" syncable="YES"/>
+        <attribute name="positionType" optional="YES" syncable="YES"/>
+        <attribute name="substitution" optional="YES" syncable="YES"/>
+        <attribute name="unimodAccession" optional="YES" syncable="YES"/>
+        <relationship name="aminoAcid" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidsModificationsAminoAcids" inverseName="aminoAcidModification" inverseEntity="AminoAcidsModificationsAminoAcids" syncable="YES"/>
+        <relationship name="internalPeptides" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="PeptidesAminoAcidModifications" inverseName="internalModification" inverseEntity="PeptidesAminoAcidModifications" syncable="YES"/>
+        <relationship name="neutralLoss" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModificationsAminoAcidsNL" inverseName="aminoAcidModification" inverseEntity="AminoAcidModificationsAminoAcidsNL" syncable="YES"/>
+        <relationship name="terminalPeptides" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="PeptideTerminalModifications" inverseName="terminalModification" inverseEntity="PeptideTerminalModifications" syncable="YES"/>
+    </entity>
+    <entity name="AminoAcidModificationsAminoAcidsNL" syncable="YES">
+        <attribute name="aminoAcidID" optional="YES" syncable="YES"/>
+        <attribute name="aminoAcidModificationID" optional="YES" syncable="YES"/>
+        <attribute name="neutralLossID" optional="YES" syncable="YES"/>
+        <relationship name="aminoAcidModification" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModification" inverseName="neutralLoss" inverseEntity="AminoAcidModification" syncable="YES"/>
+        <relationship name="neutralLoss" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModificationsNeutralLoss" inverseName="aminoAcidModifications" inverseEntity="AminoAcidModificationsNeutralLoss" syncable="YES"/>
+    </entity>
+    <entity name="AminoAcidModificationsNeutralLoss" syncable="YES">
+        <attribute name="averageMass" optional="YES" syncable="YES"/>
+        <attribute name="monoisotopicMass" optional="YES" syncable="YES"/>
+        <attribute name="name" optional="YES" syncable="YES"/>
+        <attribute name="neutralLossID" optional="YES" syncable="YES"/>
+        <relationship name="aminoAcidModifications" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="AminoAcidModificationsAminoAcidsNL" inverseName="neutralLoss" inverseEntity="AminoAcidModificationsAminoAcidsNL" syncable="YES"/>
+    </entity>
+    <entity name="AminoAcidsModificationsAminoAcids" syncable="YES">
+        <attribute name="aminoAcidID" optional="YES" syncable="YES"/>
+        <attribute name="aminoAcidModificationID" optional="YES" syncable="YES"/>
+        <attribute name="classification" optional="YES" syncable="YES"/>
+        <relationship name="aminoAcid" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcid" inverseName="aminoAcidModifications" inverseEntity="AminoAcid" syncable="YES"/>
+        <relationship name="aminoAcidModification" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModification" inverseName="aminoAcid" inverseEntity="AminoAcidModification" syncable="YES"/>
+    </entity>
+    <entity name="AnnotationDataset" syncable="YES"/>
+    <entity name="AnnotationDataVersion" syncable="YES"/>
+    <entity name="AnnotationGroups" syncable="YES"/>
+    <entity name="Annotations" syncable="YES"/>
+    <entity name="AnnotationsAnnotationGroups" syncable="YES"/>
+    <entity name="AnnotationsProteins" syncable="YES"/>
+    <entity name="AnnotationTypes" syncable="YES"/>
+    <entity name="Chromatograms" syncable="YES">
+        <attribute name="chromatogram" optional="YES" syncable="YES"/>
+        <attribute name="fileID" optional="YES" syncable="YES"/>
+        <attribute name="traceType" optional="YES" syncable="YES"/>
+        <relationship name="fileInfo" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="FileInfo" inverseName="chromatograms" inverseEntity="FileInfo" syncable="YES"/>
+    </entity>
+    <entity name="CustomDataFields" syncable="YES"/>
+    <entity name="CustomDataPeptides" syncable="YES"/>
+    <entity name="CustomDataProcessinNodes" syncable="YES"/>
+    <entity name="CustomDataProteins" syncable="YES"/>
+    <entity name="CustomDataSpectra" syncable="YES"/>
+    <entity name="Enzymes" syncable="YES"/>
+    <entity name="EnzymesCleavageSpecificities" syncable="YES"/>
+    <entity name="EventAnnotations" syncable="YES"/>
+    <entity name="EventAreaAnnotations" syncable="YES"/>
+    <entity name="Events" syncable="YES"/>
+    <entity name="FastaFiles" syncable="YES"/>
+    <entity name="FastaFilesProteinAnnotations" syncable="YES"/>
+    <entity name="FileInfo" syncable="YES">
+        <attribute name="fileID" optional="YES" syncable="YES"/>
+        <attribute name="fileName" optional="YES" syncable="YES"/>
+        <attribute name="fileSize" optional="YES" syncable="YES"/>
+        <attribute name="fileTime" optional="YES" syncable="YES"/>
+        <attribute name="fileType" optional="YES" syncable="YES"/>
+        <attribute name="physicalFileName" optional="YES" syncable="YES"/>
+        <relationship name="chromatograms" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="Chromatograms" inverseName="fileInfo" inverseEntity="Chromatograms" syncable="YES"/>
+        <relationship name="massPeaks" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="MassPeak" inverseName="fileInfo" inverseEntity="MassPeak" syncable="YES"/>
+    </entity>
+    <entity name="MassPeak" syncable="YES">
+        <attribute name="charge" optional="YES" syncable="YES"/>
+        <attribute name="fileID" optional="YES" syncable="YES"/>
+        <attribute name="intensity" optional="YES" syncable="YES"/>
+        <attribute name="ionInjectTime" optional="YES" syncable="YES"/>
+        <attribute name="mass" optional="YES" syncable="YES"/>
+        <attribute name="massPeakID" optional="YES" syncable="YES"/>
+        <attribute name="percentIsolationInterference" optional="YES" syncable="YES"/>
+        <attribute name="scanNumbers" optional="YES" syncable="YES"/>
+        <relationship name="fileInfo" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="FileInfo" inverseName="massPeaks" inverseEntity="FileInfo" syncable="YES"/>
+        <relationship name="spectrumHeader" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="SpectrumHeader" inverseName="massPeak" inverseEntity="SpectrumHeader" syncable="YES"/>
+    </entity>
+    <entity name="MassPeakRelations" syncable="YES"/>
+    <entity name="Peptide">
+        <attribute name="annotation" optional="YES" syncable="YES"/>
+        <attribute name="confidenceLevel" optional="YES" syncable="YES"/>
+        <attribute name="hidden" optional="YES" syncable="YES"/>
+        <attribute name="matchedIonsCount" optional="YES" syncable="YES"/>
+        <attribute name="missedCleavages" optional="YES" syncable="YES"/>
+        <attribute name="peptideID" optional="YES" attributeType="Date">
+            <userInfo/>
+        </attribute>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="searchEngneRank" optional="YES" syncable="YES"/>
+        <attribute name="sequence" optional="YES" syncable="YES"/>
+        <attribute name="spectrumID" optional="YES" syncable="YES"/>
+        <attribute name="totalIonsCount" optional="YES" syncable="YES"/>
+        <attribute name="uniquePeptideSeqeunceID" optional="YES" syncable="YES"/>
+        <relationship name="internalModifications" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="PeptidesAminoAcidModifications" inverseName="peptide" inverseEntity="PeptidesAminoAcidModifications" syncable="YES"/>
+        <relationship name="peptideScore" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="PeptideScores" inverseName="peptide" inverseEntity="PeptideScores" syncable="YES"/>
+        <relationship name="proteins" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="PeptidesProteins" inverseName="peptide" inverseEntity="PeptidesProteins" syncable="YES"/>
+        <relationship name="spectrum" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Spectrum" inverseName="peptides" inverseEntity="Spectrum" syncable="YES"/>
+        <relationship name="terminalModification" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="PeptideTerminalModifications" inverseName="peptide" inverseEntity="PeptideTerminalModifications" syncable="YES"/>
+        <userInfo/>
+    </entity>
+    <entity name="PeptideDecoy" syncable="YES"/>
+    <entity name="PeptidesAminoAcidModifications" syncable="YES">
+        <attribute name="aminoAcidModificationID" optional="YES" syncable="YES"/>
+        <attribute name="peptideID" optional="YES" syncable="YES"/>
+        <attribute name="position" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <relationship name="internalModification" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModification" inverseName="internalPeptides" inverseEntity="AminoAcidModification" syncable="YES"/>
+        <relationship name="peptide" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Peptide" inverseName="internalModifications" inverseEntity="Peptide" syncable="YES"/>
+    </entity>
+    <entity name="PeptidesAminoAcidModificationsDecoy" syncable="YES"/>
+    <entity name="PeptideScoreDecoy" syncable="YES"/>
+    <entity name="PeptideScores" syncable="YES">
+        <attribute name="peptideID" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeID" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="scoreID" optional="YES" syncable="YES"/>
+        <attribute name="scoreValue" optional="YES" syncable="YES"/>
+        <relationship name="peptide" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Peptide" inverseName="peptideScore" inverseEntity="Peptide" syncable="YES"/>
+    </entity>
+    <entity name="PeptidesProteins" syncable="YES">
+        <attribute name="peptideID" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="proteinID" optional="YES" syncable="YES"/>
+        <relationship name="peptide" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Peptide" inverseName="proteins" inverseEntity="Peptide" syncable="YES"/>
+        <relationship name="protein" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Protein" inverseName="peptides" inverseEntity="Protein" syncable="YES"/>
+    </entity>
+    <entity name="PeptidesProteinsDecoy" syncable="YES"/>
+    <entity name="PeptideTerminalModifications" syncable="YES">
+        <attribute name="peptideID" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="terminalModificationID" optional="YES" syncable="YES"/>
+        <relationship name="peptide" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Peptide" inverseName="terminalModification" inverseEntity="Peptide" syncable="YES"/>
+        <relationship name="terminalModification" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="AminoAcidModification" inverseName="terminalPeptides" inverseEntity="AminoAcidModification" syncable="YES"/>
+    </entity>
+    <entity name="PeptideTerminalModificationsDecoy" syncable="YES"/>
+    <entity name="PrecursorIonAreaSearchSpectra" syncable="YES"/>
+    <entity name="PrecursorIonQuanResults" syncable="YES"/>
+    <entity name="PrecursorIonQuanResultsSearchSpectra" syncable="YES"/>
+    <entity name="ProcessingNodeConnectionPoints" syncable="YES"/>
+    <entity name="ProcessingNodeExtensions" syncable="YES"/>
+    <entity name="ProcessingNodeFilterParameters" syncable="YES"/>
+    <entity name="ProcessingNodeInterfaces" syncable="YES"/>
+    <entity name="ProcessingNodeParameters" syncable="YES"/>
+    <entity name="ProcessingNodes" syncable="YES"/>
+    <entity name="ProcessingNodeScores" syncable="YES"/>
+    <entity name="ProcessingNodesSpectra" syncable="YES"/>
+    <entity name="Protein" syncable="YES">
+        <attribute name="isMasterProtein" optional="YES" syncable="YES"/>
+        <attribute name="proteinID" optional="YES" syncable="YES"/>
+        <attribute name="seqeunceHashCode" optional="YES" syncable="YES"/>
+        <attribute name="sequence" optional="YES" syncable="YES"/>
+        <relationship name="peptides" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="PeptidesProteins" inverseName="protein" inverseEntity="PeptidesProteins" syncable="YES"/>
+        <relationship name="proteinAnnotation" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="ProteinAnnotations" inverseName="protein" inverseEntity="ProteinAnnotations" syncable="YES"/>
+        <relationship name="proteinScore" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="ProteinScores" inverseName="protein" inverseEntity="ProteinScores" syncable="YES"/>
+    </entity>
+    <entity name="ProteinAnnotations" syncable="YES">
+        <attribute name="decription" optional="YES" syncable="YES"/>
+        <attribute name="descriptionHash" optional="YES" syncable="YES"/>
+        <attribute name="proteinAnnotationID" optional="YES" syncable="YES"/>
+        <attribute name="proteinID" optional="YES" syncable="YES"/>
+        <attribute name="taxonomyID" optional="YES" syncable="YES"/>
+        <relationship name="protein" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Protein" inverseName="proteinAnnotation" inverseEntity="Protein" syncable="YES"/>
+    </entity>
+    <entity name="ProteinIdentificationGroups" syncable="YES"/>
+    <entity name="ProteinScores" syncable="YES">
+        <attribute name="coverage" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="proteinID" optional="YES" syncable="YES"/>
+        <attribute name="proteinIdentificationGroupID" optional="YES" syncable="YES"/>
+        <attribute name="proteinScore" optional="YES" syncable="YES"/>
+        <relationship name="protein" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Protein" inverseName="proteinScore" inverseEntity="Protein" syncable="YES"/>
+    </entity>
+    <entity name="ProteinScoresDecoy" syncable="YES"/>
+    <entity name="ProteinsProteinGroups" syncable="YES">
+        <attribute name="proteinGroupID" optional="YES" syncable="YES"/>
+        <attribute name="proteinID" optional="YES" syncable="YES"/>
+    </entity>
+    <entity name="PtmAnnotationData" syncable="YES"/>
+    <entity name="ReporterIonQuanResults" syncable="YES">
+        <attribute name="height" optional="YES" syncable="YES"/>
+        <attribute name="mass" optional="YES" syncable="YES"/>
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="quanChannelID" optional="YES" syncable="YES"/>
+        <attribute name="spectrumID" optional="YES" syncable="YES"/>
+        <relationship name="searchSpectrum" optional="YES" maxCount="1" deletionRule="Nullify" destinationEntity="ReporterIonQuanResultsSearchSpectra" inverseName="reporterIonQuanResults" inverseEntity="ReporterIonQuanResultsSearchSpectra" syncable="YES"/>
+    </entity>
+    <entity name="ReporterIonQuanResultsSearchSpectra" syncable="YES">
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="searchSpectrumID" optional="YES" syncable="YES"/>
+        <attribute name="spectrumID" optional="YES" syncable="YES"/>
+        <relationship name="reporterIonQuanResults" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="ReporterIonQuanResults" inverseName="searchSpectrum" inverseEntity="ReporterIonQuanResults" syncable="YES"/>
+        <relationship name="spectrum" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Spectrum" inverseName="searchSpectrum" inverseEntity="Spectrum" syncable="YES"/>
+    </entity>
+    <entity name="ScanEvent" syncable="YES">
+        <attribute name="activationType" optional="YES" syncable="YES"/>
+        <attribute name="ionization" optional="YES" syncable="YES"/>
+        <attribute name="massAnalyzer" optional="YES" syncable="YES"/>
+        <attribute name="msLevel" optional="YES" syncable="YES"/>
+        <attribute name="polarity" optional="YES" syncable="YES"/>
+        <attribute name="scanEventID" optional="YES" syncable="YES"/>
+        <attribute name="scanType" optional="YES" syncable="YES"/>
+        <relationship name="spectrumHeaders" optional="YES" toMany="YES" deletionRule="Nullify" syncable="YES"/>
+    </entity>
+    <entity name="SchemaInfo" syncable="YES"/>
+    <entity name="Spectrum" syncable="YES">
+        <attribute name="spectrum" optional="YES" syncable="YES"/>
+        <attribute name="spectrumHashCode" optional="YES" syncable="YES"/>
+        <attribute name="uniqueSpectrumID" optional="YES" syncable="YES"/>
+        <relationship name="peptides" optional="YES" toMany="YES" deletionRule="Nullify" destinationEntity="Peptide" inverseName="spectrum" inverseEntity="Peptide" syncable="YES"/>
+        <relationship name="searchSpectrum" optional="YES" maxCount="1" deletionRule="Nullify" destinationEntity="ReporterIonQuanResultsSearchSpectra" inverseName="spectrum" inverseEntity="ReporterIonQuanResultsSearchSpectra" syncable="YES"/>
+        <relationship name="spectrumHeader" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="SpectrumHeader" inverseName="spectrum" inverseEntity="SpectrumHeader" syncable="YES"/>
+        <relationship name="spectrumScore" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="SpectrumScores" inverseName="spectrum" inverseEntity="SpectrumScores" syncable="YES"/>
+    </entity>
+    <entity name="SpectrumHeader" syncable="YES">
+        <attribute name="charge" optional="YES" syncable="YES"/>
+        <attribute name="creatingProcessingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="firstScan" optional="YES" syncable="YES"/>
+        <attribute name="hidden" optional="YES" syncable="YES"/>
+        <attribute name="lastScan" optional="YES" syncable="YES"/>
+        <attribute name="mass" optional="YES" syncable="YES"/>
+        <attribute name="massPeakID" optional="YES" syncable="YES"/>
+        <attribute name="retentionTime" optional="YES" syncable="YES"/>
+        <attribute name="scanEventID" optional="YES" syncable="YES"/>
+        <attribute name="scanNumbers" optional="YES" syncable="YES"/>
+        <attribute name="spectrumID" optional="YES" syncable="YES"/>
+        <attribute name="uniqueSpectrumID" optional="YES" syncable="YES"/>
+        <relationship name="massPeak" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="MassPeak" inverseName="spectrumHeader" inverseEntity="MassPeak" syncable="YES"/>
+        <relationship name="spectrum" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Spectrum" inverseName="spectrumHeader" inverseEntity="Spectrum" syncable="YES"/>
+        <relationship name="uniqueSpectrum" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="SpectrumHeader" syncable="YES"/>
+    </entity>
+    <entity name="SpectrumScores" syncable="YES">
+        <attribute name="processingNodeNumber" optional="YES" syncable="YES"/>
+        <attribute name="score" optional="YES" syncable="YES"/>
+        <attribute name="spectrumID" optional="YES" syncable="YES"/>
+        <relationship name="spectrum" optional="YES" minCount="1" maxCount="1" deletionRule="Nullify" destinationEntity="Spectrum" inverseName="spectrumScore" inverseEntity="Spectrum" syncable="YES"/>
+    </entity>
+    <entity name="TaxonomyNames" syncable="YES"/>
+    <entity name="TaxonomyNodes" syncable="YES"/>
+    <entity name="WorkflowInfo" syncable="YES"/>
+    <entity name="WorkflowMessages" syncable="YES"/>
+    <elements>
+        <element name="AminoAcid" positionX="-1647" positionY="-648" width="155" height="163"/>
+        <element name="AminoAcidModification" positionX="-2124" positionY="-655" width="144" height="268"/>
+        <element name="AminoAcidModificationsAminoAcidsNL" positionX="-1919" positionY="-504" width="227" height="118"/>
+        <element name="AminoAcidModificationsNeutralLoss" positionX="-1647" positionY="-450" width="234" height="118"/>
+        <element name="AminoAcidsModificationsAminoAcids" positionX="-1917" positionY="-631" width="218" height="118"/>
+        <element name="AnnotationDataset" positionX="-2430" positionY="497" width="128" height="43"/>
+        <element name="AnnotationDataVersion" positionX="-2430" positionY="450" width="128" height="43"/>
+        <element name="AnnotationGroups" positionX="-2430" positionY="587" width="128" height="43"/>
+        <element name="Annotations" positionX="-2430" positionY="360" width="128" height="43"/>
+        <element name="AnnotationsAnnotationGroups" positionX="-2430" positionY="630" width="173" height="43"/>
+        <element name="AnnotationsProteins" positionX="-2430" positionY="405" width="128" height="43"/>
+        <element name="AnnotationTypes" positionX="-2430" positionY="540" width="128" height="43"/>
+        <element name="Chromatograms" positionX="-1485" positionY="-238" width="128" height="103"/>
+        <element name="CustomDataFields" positionX="-1269" positionY="567" width="128" height="43"/>
+        <element name="CustomDataPeptides" positionX="-1269" positionY="659" width="128" height="43"/>
+        <element name="CustomDataProcessinNodes" positionX="-1449" positionY="495" width="171" height="43"/>
+        <element name="CustomDataProteins" positionX="-2160" positionY="540" width="128" height="43"/>
+        <element name="CustomDataSpectra" positionX="-1269" positionY="612" width="128" height="43"/>
+        <element name="Enzymes" positionX="-2025" positionY="360" width="128" height="43"/>
+        <element name="EnzymesCleavageSpecificities" positionX="-2025" positionY="405" width="171" height="43"/>
+        <element name="EventAnnotations" positionX="-2160" positionY="452" width="128" height="43"/>
+        <element name="EventAreaAnnotations" positionX="-2160" positionY="360" width="128" height="43"/>
+        <element name="Events" positionX="-2160" positionY="405" width="128" height="43"/>
+        <element name="FastaFiles" positionX="-1406" positionY="540" width="128" height="43"/>
+        <element name="FastaFilesProteinAnnotations" positionX="-1458" positionY="450" width="180" height="43"/>
+        <element name="FileInfo" positionX="-1458" positionY="-99" width="128" height="163"/>
+        <element name="MassPeak" positionX="-1431" positionY="99" width="128" height="193"/>
+        <element name="MassPeakRelations" positionX="-2295" positionY="542" width="128" height="43"/>
+        <element name="Peptide" positionX="-2124" positionY="-325" width="153" height="298"/>
+        <element name="PeptideDecoy" positionX="-2115" positionY="-378" width="128" height="43"/>
+        <element name="PeptidesAminoAcidModifications" positionX="-2439" positionY="-430" width="189" height="133"/>
+        <element name="PeptidesAminoAcidModificationsDecoy" positionX="-2439" positionY="-486" width="216" height="43"/>
+        <element name="PeptideScoreDecoy" positionX="-2367" positionY="-261" width="128" height="43"/>
+        <element name="PeptideScores" positionX="-2369" positionY="-205" width="128" height="133"/>
+        <element name="PeptidesProteins" positionX="-2108" positionY="36" width="128" height="118"/>
+        <element name="PeptidesProteinsDecoy" positionX="-2178" positionY="-16" width="128" height="43"/>
+        <element name="PeptideTerminalModifications" positionX="-1863" positionY="-306" width="171" height="118"/>
+        <element name="PeptideTerminalModificationsDecoy" positionX="-1890" positionY="-360" width="207" height="43"/>
+        <element name="PrecursorIonAreaSearchSpectra" positionX="-1899" positionY="542" width="198" height="43"/>
+        <element name="PrecursorIonQuanResults" positionX="-1890" positionY="360" width="189" height="43"/>
+        <element name="PrecursorIonQuanResultsSearchSpectra" positionX="-1953" positionY="495" width="252" height="43"/>
+        <element name="ProcessingNodeConnectionPoints" positionX="-1665" positionY="585" width="216" height="43"/>
+        <element name="ProcessingNodeExtensions" positionX="-1665" positionY="540" width="216" height="43"/>
+        <element name="ProcessingNodeFilterParameters" positionX="-1899" positionY="450" width="198" height="43"/>
+        <element name="ProcessingNodeInterfaces" positionX="-1667" positionY="497" width="164" height="43"/>
+        <element name="ProcessingNodeParameters" positionX="-1665" positionY="450" width="162" height="43"/>
+        <element name="ProcessingNodes" positionX="-1665" positionY="360" width="128" height="43"/>
+        <element name="ProcessingNodeScores" positionX="-1665" positionY="405" width="144" height="43"/>
+        <element name="ProcessingNodesSpectra" positionX="-1665" positionY="630" width="153" height="43"/>
+        <element name="Protein" positionX="-2115" positionY="189" width="128" height="148"/>
+        <element name="ProteinAnnotations" positionX="-2349" positionY="-54" width="128" height="133"/>
+        <element name="ProteinIdentificationGroups" positionX="-1449" positionY="405" width="171" height="43"/>
+        <element name="ProteinScores" positionX="-2412" positionY="162" width="171" height="133"/>
+        <element name="ProteinScoresDecoy" positionX="-2385" positionY="108" width="128" height="43"/>
+        <element name="ProteinsProteinGroups" positionX="-1404" positionY="585" width="128" height="73"/>
+        <element name="PtmAnnotationData" positionX="-1829" positionY="405" width="128" height="43"/>
+        <element name="ReporterIonQuanResults" positionX="-1890" positionY="-160" width="180" height="133"/>
+        <element name="ReporterIonQuanResultsSearchSpectra" positionX="-1890" positionY="9" width="234" height="118"/>
+        <element name="ScanEvent" positionX="-1269" positionY="360" width="128" height="163"/>
+        <element name="SchemaInfo" positionX="-1665" positionY="675" width="128" height="43"/>
+        <element name="Spectrum" positionX="-1863" positionY="176" width="128" height="148"/>
+        <element name="SpectrumHeader" positionX="-1629" positionY="-99" width="128" height="268"/>
+        <element name="SpectrumScores" positionX="-1622" positionY="216" width="128" height="103"/>
+        <element name="TaxonomyNames" positionX="-2295" positionY="360" width="128" height="43"/>
+        <element name="TaxonomyNodes" positionX="-2295" positionY="405" width="128" height="43"/>
+        <element name="WorkflowInfo" positionX="-1406" positionY="657" width="128" height="43"/>
+        <element name="WorkflowMessages" positionX="-1269" positionY="522" width="128" height="43"/>
+    </elements>
+</model>