mspire-lipid 0.2.0

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Files changed (38) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitignore +53 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +4 -0
  6. data/LICENSE +21 -0
  7. data/README.md +11 -0
  8. data/Rakefile +24 -0
  9. data/bin/lipidomic-search.rb +203 -0
  10. data/lib/mspire/lipid.rb +19 -0
  11. data/lib/mspire/lipid/ion.rb +71 -0
  12. data/lib/mspire/lipid/ion/fragment.rb +68 -0
  13. data/lib/mspire/lipid/modification.rb +120 -0
  14. data/lib/mspire/lipid/search.rb +205 -0
  15. data/lib/mspire/lipid/search/bin.rb +79 -0
  16. data/lib/mspire/lipid/search/db_isobar_group.rb +20 -0
  17. data/lib/mspire/lipid/search/hit.rb +79 -0
  18. data/lib/mspire/lipid/search/probability_distribution.rb +50 -0
  19. data/lib/mspire/lipid/search/query.rb +23 -0
  20. data/lib/mspire/lipid/version.rb +6 -0
  21. data/lib/mspire/lipid_maps.rb +110 -0
  22. data/mspire-lipid.gemspec +38 -0
  23. data/scratch/OBConversion_methods.txt +47 -0
  24. data/scratch/atom_methods.txt +145 -0
  25. data/scratch/bond_methods.txt +867 -0
  26. data/scratch/mol_methods.txt +183 -0
  27. data/scratch/split_molecules.rb +93 -0
  28. data/script/find_nearest_lipid.rb +134 -0
  29. data/spec/mspire/lipid/ion_spec.rb +96 -0
  30. data/spec/mspire/lipid/modification_spec.rb +70 -0
  31. data/spec/mspire/lipid/search_spec.rb +82 -0
  32. data/spec/mspire/lipid_maps_spec.rb +64 -0
  33. data/spec/mspire/lipid_spec.rb +16 -0
  34. data/spec/spec_helper.rb +13 -0
  35. data/spec/testfiles/lipidmaps_download.tsv +11 -0
  36. data/spec/testfiles/lipidmaps_programmatic_short.tsv +32 -0
  37. data/spec/testfiles/lipidmaps_sd_download.tsv +11 -0
  38. metadata +202 -0
data/spec/mspire/lipid/modification_spec.rb ADDED
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+ require 'spec_helper'
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+
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+ require 'mspire/lipid/modification'
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+ require 'mspire/lipid'
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+ require 'mspire/lipid/ion'
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+
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+ describe Mspire::Lipid::Modification do
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+ Mod = Mspire::Lipid::Modification
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+
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+ describe 'creates common mods easily' do
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+
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+ it 'water loss' do
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+ water_loss = Mod.new(:water, :loss => true)
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+ water_loss.loss?.should be_true
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+ water_loss.massdiff.<(0).should be_true
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+ water_loss.charge.should == 0
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+ water_loss.charged_formula_string.should == 'H2O'
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+ end
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+
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+ it 'proton gain' do
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+ prot = Mod.new(:proton)
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+ prot.gain?.should be_true
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+ prot.massdiff.>(0).should be_true
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+ prot.charge.should == 1
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+ prot.charged_formula_string.should == 'H+'
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+ end
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+
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+ it 'proton loss' do
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+ prot_loss = Mod.new(:proton, :loss => true)
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+ prot_loss.gain?.should be_false
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+ prot_loss.loss?.should be_true
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+ prot_loss.massdiff.<(0).should be_true
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+ prot_loss.charge.should == -1
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+ prot_loss.charged_formula_string.should == 'H-'
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+ end
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+
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+ it 'ammonium gain' do
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+ ammon = Mod.new(:ammonium)
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+ ammon.gain?.should be_true
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+ ammon.massdiff.>(0).should be_true
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+ ammon.charge.should == 1
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+ ammon.charged_formula_string.should == 'H4N+'
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+ end
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+ end
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+
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+ it 'can create custom mods' do
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+ mymod = Mod.new(:super_snazzy)
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+ mymod.formula.should be_nil
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+ mymod.massdiff.should be_nil
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+ mymod.charge.should be_nil
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+
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+ mymod.formula = 'CH4'
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+ mymod.charge = 2
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+ mymod.massdiff = Mspire::Lipid::Modification.massdiff(mymod.formula, mymod.charge)
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+ mymod.massdiff.should be_within(1e4).of(16.030202)
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+
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+ mymod.formula = 'CH4'
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+ mymod.charge = 2
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+ mymod.massdiff = Mspire::Lipid::Modification.massdiff(mymod.formula, mymod.charge)
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+ mymod.massdiff.should be_within(1e4).of(16.030202)
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+ end
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+
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+ it 'handles mods with negative charges' do
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+ mod = Mod.new(:acetate)
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+ p mod.formula
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+ p mod.massdiff
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+ p mod.massdiff
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+ p mod.charge
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+ end
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+ end
data/spec/mspire/lipid/search_spec.rb ADDED
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+
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+ =begin
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+ require 'spec_helper'
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+
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+ require 'mspire/lipid_maps'
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+ require 'mspire/lipid/search'
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+ require 'mspire/lipid/search/query'
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+ require 'mspire/lipid/modification'
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+
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+ describe Mspire::Lipid::Search do
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+ before do
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+ @proton = Mspire::Lipid::Modification.new(:proton)
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+ @h2o_loss = Mspire::Lipid::Modification.new(:water, :loss => true)
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+ end
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+ describe 'searching a section of lipid maps' do
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+ before do
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+ @lipids = Mspire::LipidMaps.parse_file(TESTFILES + '/lipidmaps_programmatic_short.tsv')
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+ @ions = @lipids.map do |lipid|
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+ [[@proton], [@proton, @h2o_loss]].map do |mods|
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+ Mspire::Lipid::Ion.new(lipid, mods)
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+ end
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+ end.flatten(1)
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+ @samples = Hash[ {
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+ :sample1 => [[187.1633, 244.22, 616.51, 717.50],
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+ [100, 200, 100, 200]],
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+ :sample2 => [[187.164, 396.15, 244.24, 347.28, 618.502],
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+ [110, 210, 110, 210, 110]],
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+ :sample3 => [[187.160, 396.28, 244.24, 347.263, 618.511],
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+ [120, 220, 120, 220, 120]],
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+ :sample4 => [[187.157, 396.20, 244.30, 618.22, 933.01],
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+ [30, 33, 38, 99, 22]],
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+ }.map {|key,data| [key, Mspire::Spectrum.new(data)] } ]
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+ @pretend_search_mzs = [187.157, 396.20, 244.30, 618.22, 933.01]
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+ end
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+
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+ xit 'creates a query search spectrum' do
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+ #spec = .create_query_search_spectrum(@ions)
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+ #spec.mzs.any? {|mz| mz.nil? }.should be_false
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+ #spec.mzs.size.should == 56
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+ #spec.intensities.map(&:size).count(2).should == 4
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+ #spec.intensities.map(&:size).count(1).should == 52
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+ end
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+
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+ xit 'creates a probability function' do
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+ #subject.create_search_function(@ions, :prob_min_bincnt => 20)
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+ end
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+
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+ xit 'searches mz values' do
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+ searcher = Mspire::Lipid::Search.new(@ions, :query_min_count_per_bin => 8, :num_rand_samples_per_bin => 1000, :ppm => false)
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+ num_nearest_hits = 3
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+ (hit_groups, qvals) = searcher.search(@pretend_search_mzs, 3)
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+ p hit_groups.map(&:first).map(&:pvalue)
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+ end
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+ end
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+
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+ describe 'searching a full lipid maps' do
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+
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+ before do
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+ # this will be specific to your install since it's not part of install
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+ path_to_lipidmaps_db = "#{ENV['HOME']}/tmp/tamil/lipidmaps_20120103_classes_1_2_3_4_5_6_7_8.exact_mass.tsv"
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+ @lipids = Mspire::LipidMaps.parse_file(path_to_lipidmaps_db)
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+ @ions = @lipids.map do |lipid|
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+ [[@proton], [@proton, @proton], [@proton, @h2o_loss]].map do |mods|
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+ Mspire::Lipid::Search::Query.new(lipid, mods)
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+ end
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+ end.flatten(1)
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+ @pretend_search_mzs = [187.157, 396.20, 244.30, 618.22, 933.01]
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+ end
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+
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+ xit 'returns hit groups parallel with input m/zs' do
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+ searcher = Mspire::Lipid::Search.new(@ions, :query_min_count_per_bin => 1000, :ppm => false)
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+ hit_groups = searcher.search(@pretend_search_mzs, 3)
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+ best_hits = hit_groups.map(&:best_hit)
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+ best_hits.map {|hit| hit.observed_mz }.should == @pretend_search_mzs
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+ end
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+
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+ it 'works with :ppm => true'
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+
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+ end
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+
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+ end
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+ =end
data/spec/mspire/lipid_maps_spec.rb ADDED
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+ require 'spec_helper'
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+
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+ require 'mspire/lipid_maps'
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+ require 'mspire/molecular_formula'
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+ HAVE_RUBABEL =
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+ begin
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+ require 'rubabel' ; true
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+ rescue ; false
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+ end
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+
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+ describe Mspire::LipidMaps do
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+ describe 'parsing programmatically downloaded files' do
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+
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+ before do
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+ @tfile = TESTFILES + '/lipidmaps_programmatic_short.tsv'
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+ end
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+
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+ it 'parses lipid maps files' do
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+ lipids = Mspire::LipidMaps.parse_file(@tfile)
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+ lipids.size.should == 30 # one is rejected for no formula
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+ ll = lipids.last
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+ ll.sub_class.should == 'Isoflavonoids [PK1205]'
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+ ll.lm_id.should == "LMPK12050388"
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+ ll.formula.should be_a(Mspire::MolecularFormula)
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+ # ensures a high res mass by default
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+ ll.mass.should be_within(0.000000001).of(314.07903816634)
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+ end
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+ end
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+
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+ describe 'parsing lipidmaps downloaded files' do
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+
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+ before do
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+ @tfile = TESTFILES + '/lipidmaps_download.tsv'
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+ @tfile_sd = TESTFILES + '/lipidmaps_sd_download.tsv'
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+ end
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+
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+ it 'parses lipid maps files' do
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+
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+ [@tfile, @tfile_sd].each do |file|
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+
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+ lipids = Mspire::LipidMaps.parse_file(file)
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+ lipids.size.should == 10
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+ ll = lipids.last
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+ ll.sub_class.should == '[pretend subclass]'
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+ ll.lm_id.should == 'LMFA00000014'
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+ ll.mass.should == 347.282416
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+ ll.formula.should be_a(Mspire::MolecularFormula)
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+ ll.formula[:C].should == 22 # <- frozen
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+ if file =~ /_sd_/
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+ ll.structure.include?('25 24 0 0 0 0 0 0 0 0999 V2000').should be_true
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+ if HAVE_RUBABEL
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+ lipids = Mspire::LipidMaps.parse_file(file, :rubabel_molecules => true)
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+ lipids.last.structure.should be_a(Rubabel::Molecule)
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+ end
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+ else
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+ ll.structure.should be_nil
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+ end
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+
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+ end
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+ end
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+ end
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+
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+ end
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+
data/spec/mspire/lipid_spec.rb ADDED
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+ require 'spec_helper'
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+
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+ require 'mspire/lipid'
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+
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+ describe Mspire::Lipid do
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+
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+ before do
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+ @data = ['LMFA00000007', 'n-decanohydroxamic acid', 'N-hydroxydecanamide', 'C10H21NO2', 187.16, 'Fatty Acyls [FA]', 'Other Fatty Acyls [FA00]']
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+ end
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+
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+ it 'can be initialized with an array' do
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+ lipid = Mspire::Lipid.new(*@data)
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+ lipid.mass.should == @data[4]
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+ lipid.sub_class.should == nil
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+ end
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+ end
data/spec/spec_helper.rb ADDED
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'rspec'
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+
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+ # Requires supporting files with custom matchers and macros, etc,
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+ # in ./support/ and its subdirectories.
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+ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
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+
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+ RSpec.configure do |config|
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+ config.formatter = :documentation
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+ end
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+
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+ TESTFILES = File.expand_path(File.join(File.dirname(__FILE__), "testfiles"))
data/spec/testfiles/lipidmaps_download.tsv ADDED
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+ LM_ID SYSTEMATIC_NAME SYNONYMS CATEGORY MAIN_CLASS EXACT_MASS FORMULA PUBCHEM_SID INCHI_KEY LIPID_MAPS_CMPD_URL PUBCHEM_SUBSTANCE_URL COMMON_NAME KEGG_ID CHEBI_ID SUB_CLASS HMDBID LIPIDBANK_ID LIPIDAT_ID METABOLOMICS_ID CLASS_LEVEL4
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+ LMFA00000001 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride Acetylenic acids Fatty Acyls [FA] Other Fatty Acyls [FA00] 626.491002 C40H66O5 74380251 VOGBKCAANIAXCI-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000001 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380251
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+ LMFA00000002 N-(3S-hydroxydecanoyl)-L-serine Fatty Acyls [FA] Other Fatty Acyls [FA00] 275.173247 C13H25NO5 74380252 NDDJIMSGSZNACM-QWRGUYRKSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000002 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380252 Serratamic acid
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+ LMFA00000003 N-(3-(hexadecanoyloxy)-heptadecanoyl)-L-ornithine Fatty Acyls [FA] Other Fatty Acyls [FA00] 638.559742 C38H74N2O5 74380253 GSCCUVDKVJUMTG-HTIIIDOHSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000003 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380253
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+ LMFA00000004 N-(9Z,12Z,15Z-octadecatrienoyl)-glutamine Fatty Acyls [FA] Other Fatty Acyls [FA00] 406.283131 C23H38N2O4 74380254 FEFAAEYMDHYUFL-IWFQAGGASA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000004 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380254 N-linolenoyl-glutamine
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+ LMFA00000005 N-(3-(15-methyl-hexadecanoyloxy)-13-methyl-tetradecanoyl)-L-serine Fatty Acyls [FA] Other Fatty Acyls [FA00] 625.528108 C37H71NO6 74380255 WTGXHHUORCSXNB-DNKZHYAASA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000005 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380255
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+ LMFA00000006 2-((2S)-6-amino-2-(3-hydroxy-14-methylpentadecanamido)hexanoyloxy)ethyl 2-hydroxy-13-methyltetradecanoate Fatty Acyls [FA] Other Fatty Acyls [FA00] 684.565213 C39H76N2O7 74380256 RAKAWZJMWJKWRH-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000006 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380256 Lysine-containing siolipin
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+ LMFA00000007 N-hydroxydecanamide Decanohydroxamic acid; caprinohydroxamic acid; n-Decanohydroxamic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 187.157216 C10H21NO2 85291220 QZXOLBPUAUOQFB-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000007 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291220 n-decanohydroxamic acid C12889 32350
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+ LMFA00000008 (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid (9S,10S)-10-hydroxy-9-(phosphonooxy)stearic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 396.227658 C18H37O7P 85291221 UELBXEKQONEDKM-IRXDYDNUSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000008 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291221 (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid C15989 49253
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+ LMFA00000009 6-(6-aminohexanamido)hexanoic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 244.178671 C12H24N2O3 85291222 IWENLYKHSZCPRD-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000009 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291222 N-(6-aminohexanoyl)-6-aminohexanoic acid C01255 49255
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+ LMFA00000014 2-aminoethyl-5Z,8Z,11Z,14Z-eicosatetraenoate Fatty Acyls [FA] Other Fatty Acyls [FA00] 347.282416 C22H37NO2 123060035 DLHLOYYQQGSXCC-DOFZRALJSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000014 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=123060035 Virodhamine [pretend subclass]
data/spec/testfiles/lipidmaps_programmatic_short.tsv ADDED
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+ LM_ID COMMON_NAME SYSTEMATIC_NAME FORMULA MASS CATEGORY MAIN_CLASS SUB_CLASS
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+ LMFA00000007 n-decanohydroxamic acid N-hydroxydecanamide C10H21NO2 187.16 Fatty Acyls [FA] Other Fatty Acyls [FA00]
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+ LMFA00000008 (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid C18H37O7P 396.23 Fatty Acyls [FA] Other Fatty Acyls [FA00]
4
+ LMFA00000009 N-(6-aminohexanoyl)-6-aminohexanoic acid 6-(6-aminohexanamido)hexanoic acid C12H24N2O3 244.18 Fatty Acyls [FA] Other Fatty Acyls [FA00]
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+ LMFA00000014 Virodhamine 2-aminoethyl-5Z,8Z,11Z,14Z-eicosatetraenoate C22H37NO2 347.28 Fatty Acyls [FA] Other Fatty Acyls [FA00]
6
+ MGL02010062 DG(16:0/20:3(8Z,11Z,14Z)/0:0)[iso2] 1-hexadecanoyl-2-(8Z,11Z,14Z-eicosatrienoyl)-sn-glycerol C39H70O5 618.52 Glycerolipids [GL] Diradylglycerols [GL02] Diacylglycerols [GL0201]
7
+ LMGL02010063 DG(18:2(9Z,12Z)/18:2(9Z,12Z)/0:0) 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycerol C39H68O5 616.51 Glycerolipids [GL] Diradylglycerols [GL02] Diacylglycerols [GL0201]
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+ LMGL02010064 DG(18:1(9Z)/18:3(9Z,12Z,15Z)/0:0)[iso2] 1-(9Z-octadecenoyl)-2-(9Z,12Z,15Z-octadecatrienoyl)-sn-glycerol C39H68O5 616.51 Glycerolipids [GL] Diradylglycerols [GL02] Diacylglycerols [GL0201]
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+ LMGL02010065 DG(18:0/19:0/0:0)[iso2] 1-octadecanoyl-2-nonadecanoyl-sn-glycerol C40H78O5 638.58 Glycerolipids [GL] Diradylglycerols [GL02] Diacylglycerols [GL0201]
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+ MGP01011596 PC(18:1(9Z)/13:0) 1-(9Z-octadecenoyl)-2-tridecanoyl-glycero-3-phosphocholine C39H76NO8P 717.53 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
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+ LMGP01011597 PC(18:1(9Z)/14:1(9Z)) 1-(9Z-octadecenoyl)-2-(9Z-tetradecenoyl)-glycero-3-phosphocholine C40H76NO8P 729.53 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
12
+ LMGP01011598 PC(18:1(9Z)/15:0) 1-(9Z-octadecenoyl)-2-pentadecanoyl-glycero-3-phosphocholine C41H80NO8P 745.56 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
13
+ LMGP01011599 PC(18:1(9Z)/15:1(9Z)) 1-(9Z-octadecenoyl)-2-(9Z-pentadecenoyl)-glycero-3-phosphocholine C41H78NO8P 743.55 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
14
+ LMGP01011600 PC(18:1(9Z)/17:0) 1-(9Z-octadecenoyl)-2-heptadecanoyl-glycero-3-phosphocholine C43H84NO8P 773.59 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
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+ MSP0502AN07 - Galalpha1-3Galalpha1-3Galalpha1-3Galalpha1-4Galbeta1-4Glcbeta-Cer(d18:1/24:1(15Z)) C78H141NO33 1619.94 Sphingolipids [SP] Neutral glycosphingolipids [SP05] GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc- (Globo series) [SP0502]
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+ LMSP0502AN08 - Galalpha1-3Galalpha1-3Galalpha1-3Galalpha1-4Galbeta1-4Glcbeta-Cer(d18:1/26:1(17Z)) C80H145NO33 1647.97 Sphingolipids [SP] Neutral glycosphingolipids [SP05] GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc- (Globo series) [SP0502]
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+ LMSP0502AO00 - Galbeta1-3Galalpha1-4Galbeta1-4Glcbeta-Cer - - Sphingolipids [SP] Neutral glycosphingolipids [SP05] GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc- (Globo series) [SP0502]
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+ LMSP0502AO01 - Galbeta1-3Galalpha1-4Galbeta1-4Glcbeta-Cer(d18:1/16:0) C58H107NO23 1185.72 Sphingolipids [SP] Neutral glycosphingolipids [SP05] GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc- (Globo series) [SP0502]
19
+ MST02020021 Dehydroepiandrosterone 3beta-hydroxyandrost-5-en-17-one C19H28O2 288.21 Sterol Lipids [ST] Steroids [ST02] C19 steroids (androgens) and derivatives [ST0202]
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+ LMST02020023 Epiandrosterone 3beta-hydroxy-androstan-17-one C19H30O2 290.22 Sterol Lipids [ST] Steroids [ST02] C19 steroids (androgens) and derivatives [ST0202]
21
+ LMST02020025 Fluoxymesterone 9alpha-fluoro-11beta,17beta-dihydroxy-17-methylandrost-4-en-3-one C20H29FO3 336.21 Sterol Lipids [ST] Steroids [ST02] C19 steroids (androgens) and derivatives [ST0202]
22
+ LMST02020026 Formyldienolone 11alpha,17beta-dihydroxy-17-methyl-3-oxoandrosta-1,4-diene-2-carboxaldehyde C21H28O4 344.20 Sterol Lipids [ST] Steroids [ST02] C19 steroids (androgens) and derivatives [ST0202]
23
+ LMST02020027 Mestanolone 17beta-hydroxy-17-methyl-androstan-3-one C20H32O2 304.24 Sterol Lipids [ST] Steroids [ST02] C19 steroids (androgens) and derivatives [ST0202]
24
+ MPR03010008 Decaprenol 3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38-decaen-1-ol C50H82O 698.64 Prenol Lipids [PR] Polyprenols [PR03] Bactoprenols [PR0301]
25
+ LMPR03020001 undecaprenyl phosphate 3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E,42-undecaen-1-yl phosphate C55H91O4P 846.67 Prenol Lipids [PR] Polyprenols [PR03] Bactoprenol monophosphates [PR0302]
26
+ LMPR03020002 Undecaprenyl phosphate mannose Alpha-mannosyl-undecaprenyl phosphate C61H101O9P 1008.72 Prenol Lipids [PR] Polyprenols [PR03] Bactoprenol monophosphates [PR0302]
27
+ LMPR03020004 Dodecaprenyl phosphate-galacturonic acid - C66H107O10P 1090.76 Prenol Lipids [PR] Polyprenols [PR03] Bactoprenol monophosphates [PR0302]
28
+ MPK12050384 Irisolidone 5,7-Dihydroxy-6,4'-dimethoxyisoflavone C17H14O6 314.08 Polyketides [PK] Flavonoids [PK12] Isoflavonoids [PK1205]
29
+ LMPK12050385 Tectorigenin 5,7,4'-Trihydroxy-6-methoxyisoflavone C16H12O6 300.06 Polyketides [PK] Flavonoids [PK12] Isoflavonoids [PK1205]
30
+ LMPK12050386 6-Hydroxygenistein - C15H10O6 286.05 Polyketides [PK] Flavonoids [PK12] Isoflavonoids [PK1205]
31
+ LMPK12050387 Irisolone 4'-Hydroxy-5-methoxy-6,7-methylenedioxyisoflavone C17H12O6 312.06 Polyketides [PK] Flavonoids [PK12] Isoflavonoids [PK1205]
32
+ LMPK12050388 7-O-Methyltectorigenin 5,4'-Dihydroxy-6,7-dimethoxyisoflavone C17H14O6 314.08 Polyketides [PK] Flavonoids [PK12] Isoflavonoids [PK1205]
data/spec/testfiles/lipidmaps_sd_download.tsv ADDED
@@ -0,0 +1,11 @@
1
+ LM_ID SYSTEMATIC_NAME SYNONYMS CATEGORY MAIN_CLASS EXACT_MASS FORMULA PUBCHEM_SID INCHI_KEY LIPID_MAPS_CMPD_URL PUBCHEM_SUBSTANCE_URL COMMON_NAME KEGG_ID CHEBI_ID SUB_CLASS HMDBID LIPIDBANK_ID LIPIDAT_ID METABOLOMICS_ID CLASS_LEVEL4 StructureDataString
2
+ LMFA00000001 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride Acetylenic acids Fatty Acyls [FA] Other Fatty Acyls [FA00] 626.491002 C40H66O5 74380251 VOGBKCAANIAXCI-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000001 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380251 LMFA00000001| LIPDMAPS01251212252D|| 45 44 0 0 0 0 0 0 0 0999 V2000| 16.4440 9.0927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.6562 7.5630 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 16.4440 9.8589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 15.7757 8.7097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.1072 9.0927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.4385 8.7097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.7699 9.0927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.1013 9.4758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.4326 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.7642 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.0955 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.4269 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.7583 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0896 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.4210 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.7524 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.0839 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.4152 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7466 9.8589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0780 9.4759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0896 8.7097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.3707 6.0144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.3584 5.2483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 15.7088 6.4081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.0340 6.0359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3717 6.4297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.6970 6.0576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.0223 5.6854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.3475 5.3132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.6852 5.7070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.0105 5.3348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.3482 5.7285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.6735 5.3564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0111 5.7502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.3364 5.3780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.6741 5.7718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.9994 5.3997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.3370 5.7935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.6623 5.4213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 5.8150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0235 6.5162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.7757 7.9437 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 15.1086 7.5585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.7212 7.1740 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 16.3945 7.5485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 1 3 2 0 0 0 0| 1 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 3 0 0 0 0| 8 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 1 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 1 0 0 0 0| 15 16 1 0 0 0 0| 16 17 1 0 0 0 0| 17 18 1 0 0 0 0| 18 19 1 0 0 0 0| 19 20 2 0 0 0 0| 14 21 1 0 0 0 0| 22 23 2 0 0 0 0| 22 24 1 0 0 0 0| 24 25 1 0 0 0 0| 25 26 1 0 0 0 0| 26 27 1 0 0 0 0| 27 28 3 0 0 0 0| 28 29 1 0 0 0 0| 29 30 1 0 0 0 0| 30 31 1 0 0 0 0| 31 32 1 0 0 0 0| 32 33 1 0 0 0 0| 33 34 1 0 0 0 0| 34 35 1 0 0 0 0| 35 36 1 0 0 0 0| 36 37 1 0 0 0 0| 37 38 1 0 0 0 0| 38 39 1 0 0 0 0| 39 40 2 0 0 0 0| 34 41 1 0 0 0 0| 2 22 1 0 0 0 0| 4 42 1 0 0 0 0| 42 43 1 0 0 0 0| 24 44 1 0 0 0 0| 44 45 1 0 0 0 0|M STY 2 1 SUP 2 SUP|M SAL 1 2 42 43|M SBL 1 1 41|M SMT 1 OCH3|M SAL 2 2 44 45|M SBL 2 1 43|M SMT 2 OCH3|M END
3
+ LMFA00000002 N-(3S-hydroxydecanoyl)-L-serine Fatty Acyls [FA] Other Fatty Acyls [FA00] 275.173247 C13H25NO5 74380252 NDDJIMSGSZNACM-QWRGUYRKSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000002 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380252 Serratamic acid LMFA00000002| LIPDMAPS01251212252D|| 20 19 0 0 0 0 0 0 0 0999 V2000| 14.0520 6.8541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.4680 6.5015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.7930 6.4454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.5510 7.0073 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 11.7588 6.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.7588 5.8286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 13.1258 5.9088 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0| 11.0078 6.9835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.2568 6.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.5059 6.9835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.7549 6.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.0039 6.9835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.2530 6.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.5020 6.9835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7510 6.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 6.9835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.2568 5.7627 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 14.0737 5.8959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.7163 6.0680 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 13.9014 5.2531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 1 3 1 0 0 0 0| 2 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 2 0 0 0 0| 2 7 1 6 0 0 0| 5 8 1 0 0 0 0| 8 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 1 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 1 0 0 0 0| 15 16 1 0 0 0 0| 9 17 1 1 0 0 0| 2 18 1 1 0 0 0| 18 19 2 0 0 0 0| 18 20 1 0 0 0 0|M STY 1 1 SUP|M SAL 1 3 18 19 20|M SBL 1 1 17|M SMT 1 COOH|M END
4
+ LMFA00000003 N-(3-(hexadecanoyloxy)-heptadecanoyl)-L-ornithine Fatty Acyls [FA] Other Fatty Acyls [FA00] 638.559742 C38H74N2O5 74380253 GSCCUVDKVJUMTG-HTIIIDOHSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000003 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380253 LMFA00000003| LIPDMAPS01251212252D|| 46 45 0 0 0 0 0 0 0 0999 V2000| 20.8486 7.4144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.2749 7.0679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 21.5765 7.0127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 22.2883 7.4424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 23.0162 7.0409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 19.3741 7.5649 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 18.5957 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 18.5957 6.4068 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 17.8951 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.1945 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.4937 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.7931 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.0924 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3918 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.6911 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.9904 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.2898 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.5891 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.8884 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.1878 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.4871 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.7865 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.0858 7.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.3851 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.9387 6.4857 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0| 17.1945 6.4496 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 16.5223 6.0615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.5223 5.2499 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 15.8879 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.1102 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3325 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.5548 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.7771 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.9993 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.2217 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.4440 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.6662 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.8886 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.1108 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.3331 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.5555 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7777 5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 6.4277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.8698 6.4729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 21.5012 6.6421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.7007 5.8416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 1 3 1 0 0 0 0| 3 4 1 0 0 0 0| 4 5 1 0 0 0 0| 2 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 2 0 0 0 0| 7 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 1 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 1 0 0 0 0| 15 16 1 0 0 0 0| 16 17 1 0 0 0 0| 17 18 1 0 0 0 0| 18 19 1 0 0 0 0| 19 20 1 0 0 0 0| 20 21 1 0 0 0 0| 21 22 1 0 0 0 0| 22 23 1 0 0 0 0| 23 24 1 0 0 0 0| 2 25 1 6 0 0 0| 10 26 1 0 0 0 0| 26 27 1 0 0 0 0| 27 28 2 0 0 0 0| 27 29 1 0 0 0 0| 29 30 1 0 0 0 0| 30 31 1 0 0 0 0| 31 32 1 0 0 0 0| 32 33 1 0 0 0 0| 33 34 1 0 0 0 0| 34 35 1 0 0 0 0| 35 36 1 0 0 0 0| 36 37 1 0 0 0 0| 37 38 1 0 0 0 0| 38 39 1 0 0 0 0| 39 40 1 0 0 0 0| 40 41 1 0 0 0 0| 41 42 1 0 0 0 0| 42 43 1 0 0 0 0| 2 44 1 1 0 0 0| 44 45 2 0 0 0 0| 44 46 1 0 0 0 0|M STY 1 1 SUP|M SAL 1 3 44 45 46|M SBL 1 1 43|M SMT 1 COOH|M END
5
+ LMFA00000004 N-(9Z,12Z,15Z-octadecatrienoyl)-glutamine Fatty Acyls [FA] Other Fatty Acyls [FA00] 406.283131 C23H38N2O4 74380254 FEFAAEYMDHYUFL-IWFQAGGASA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000004 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380254 N-linolenoyl-glutamine LMFA00000004| LIPDMAPS01251212252D|| 30 29 0 0 0 0 0 0 0 0999 V2000| 18.2876 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.0633 8.2231 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 18.2876 6.8797 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 17.5063 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.7247 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.9430 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.1615 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3798 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.5981 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.8166 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.0349 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.2532 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.4716 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.6899 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.9082 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.1266 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.3450 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.5634 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7817 8.2231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 7.7753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.6931 8.9755 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.0534 8.3514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.6931 7.7273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.0534 7.1032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.6931 6.4791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.0534 5.8549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.7066 8.3514 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 19.7027 5.2475 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.7485 5.6688 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 20.3917 7.7273 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 1 3 2 0 0 0 0| 1 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 1 0 0 0 0| 8 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 2 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 2 0 0 0 0| 15 16 1 0 0 0 0| 16 17 1 0 0 0 0| 17 18 2 0 0 0 0| 18 19 1 0 0 0 0| 19 20 1 0 0 0 0| 21 22 2 0 0 0 0| 22 23 1 0 0 0 0| 23 24 1 0 0 0 0| 24 25 1 0 0 0 0| 25 26 1 0 0 0 0| 23 2 1 6 0 0 0| 22 27 1 0 0 0 0| 26 28 2 0 0 0 0| 26 29 1 0 0 0 0| 23 30 1 1 0 0 0|M END
6
+ LMFA00000005 N-(3-(15-methyl-hexadecanoyloxy)-13-methyl-tetradecanoyl)-L-serine Fatty Acyls [FA] Other Fatty Acyls [FA00] 625.528108 C37H71NO6 74380255 WTGXHHUORCSXNB-DNKZHYAASA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000005 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380255 LMFA00000005| LIPDMAPS01251212252D|| 45 44 0 0 0 0 0 0 0 0999 V2000| 7.5246 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.2657 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0067 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.7478 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.4888 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.2298 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.9709 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.7119 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.4530 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.1940 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.9351 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.6761 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.4171 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.1582 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.8993 7.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 18.6403 7.0339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.3813 7.4618 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 18.6403 6.3055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 17.1582 6.2424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 16.4295 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.6634 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.8973 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.1313 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.3653 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.5992 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.8332 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.0672 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.3011 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.5351 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.7691 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.0030 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.2370 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.4709 6.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7050 5.8216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.2657 6.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.9901 8.1311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.3324 7.5382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.9901 6.9454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.3324 6.3526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.9901 5.7597 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.9529 7.5382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 20.6538 6.9454 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0| 16.4295 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 6.2385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7050 5.0848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 1 2 1 0 0 0 0| 2 3 1 0 0 0 0| 3 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 1 0 0 0 0| 8 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 1 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 1 0 0 0 0| 15 16 1 0 0 0 0| 16 17 1 0 0 0 0| 16 18 2 0 0 0 0| 14 19 1 0 0 0 0| 19 20 1 0 0 0 0| 20 21 1 0 0 0 0| 21 22 1 0 0 0 0| 22 23 1 0 0 0 0| 23 24 1 0 0 0 0| 24 25 1 0 0 0 0| 25 26 1 0 0 0 0| 26 27 1 0 0 0 0| 27 28 1 0 0 0 0| 28 29 1 0 0 0 0| 29 30 1 0 0 0 0| 30 31 1 0 0 0 0| 31 32 1 0 0 0 0| 32 33 1 0 0 0 0| 33 34 1 0 0 0 0| 2 35 1 0 0 0 0| 36 37 2 0 0 0 0| 37 38 1 0 0 0 0| 38 39 1 0 0 0 0| 39 40 1 0 0 0 0| 37 41 1 0 0 0 0| 38 42 1 1 0 0 0| 38 17 1 6 0 0 0| 20 43 2 0 0 0 0| 34 44 1 0 0 0 0| 34 45 1 0 0 0 0|M END
7
+ LMFA00000006 2-((2S)-6-amino-2-(3-hydroxy-14-methylpentadecanamido)hexanoyloxy)ethyl 2-hydroxy-13-methyltetradecanoate Fatty Acyls [FA] Other Fatty Acyls [FA00] 684.565213 C39H76N2O7 74380256 RAKAWZJMWJKWRH-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000006 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=74380256 Lysine-containing siolipin LMFA00000006| LIPDMAPS01251212252D|| 49 48 0 0 0 0 0 0 0 0999 V2000| 13.7885 7.8760 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 13.1424 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.1424 6.9146 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.5609 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.9794 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.3976 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.8161 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.2344 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.6529 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.0713 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.4896 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.9080 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.3264 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.7447 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.1631 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.5815 7.8387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 7.5029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.9794 6.9501 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 5.5815 8.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3491 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.9097 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.4702 7.5523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 16.0308 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.5914 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.1520 7.8760 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 17.7126 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 18.2731 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 18.8337 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 19.3943 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.9097 8.4768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 17.7126 6.9702 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 18.2731 8.4353 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 19.9548 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 20.5154 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 21.0760 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 21.6365 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 22.1971 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 22.7577 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 23.3183 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 23.8789 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 24.4394 7.5523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 25.0000 7.8760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 24.4394 6.9499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.0544 7.0418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3491 6.5314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.0544 6.0209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.3491 5.5105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.0544 5.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 14.8089 7.0925 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0| 1 2 1 0 0 0 0| 2 3 2 0 0 0 0| 2 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 1 0 0 0 0| 8 9 1 0 0 0 0| 9 10 1 0 0 0 0| 10 11 1 0 0 0 0| 11 12 1 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 1 0 0 0 0| 15 16 1 0 0 0 0| 16 17 1 0 0 0 0| 5 18 1 0 0 0 0| 16 19 1 0 0 0 0| 20 1 1 6 0 0 0| 20 21 1 0 0 0 0| 21 22 1 0 0 0 0| 22 23 1 0 0 0 0| 23 24 1 0 0 0 0| 24 25 1 0 0 0 0| 25 26 1 0 0 0 0| 26 27 1 0 0 0 0| 27 28 1 0 0 0 0| 28 29 1 0 0 0 0| 21 30 2 0 0 0 0| 26 31 2 0 0 0 0| 27 32 1 0 0 0 0| 29 33 1 0 0 0 0| 33 34 1 0 0 0 0| 34 35 1 0 0 0 0| 35 36 1 0 0 0 0| 36 37 1 0 0 0 0| 37 38 1 0 0 0 0| 38 39 1 0 0 0 0| 39 40 1 0 0 0 0| 40 41 1 0 0 0 0| 41 42 1 0 0 0 0| 41 43 1 0 0 0 0| 20 44 1 0 0 0 0| 44 45 1 0 0 0 0| 45 46 1 0 0 0 0| 46 47 1 0 0 0 0| 47 48 1 0 0 0 0| 20 49 1 1 0 0 0|M END
8
+ LMFA00000007 N-hydroxydecanamide Decanohydroxamic acid; caprinohydroxamic acid; n-Decanohydroxamic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 187.157216 C10H21NO2 85291220 QZXOLBPUAUOQFB-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000007 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291220 n-decanohydroxamic acid C12889 32350 LMFA00000007| LIPDMAPS01251212252D|| 13 12 0 0 0 0 0 0 0 0999 V2000| 10.7157 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.0012 5.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.2869 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.5724 5.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.8579 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.1435 5.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.4290 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7145 5.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.4302 5.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.4302 6.2375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.1447 5.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 12.8592 5.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 1 10 1 0 0 0 0| 12 10 1 0 0 0 0| 2 1 1 0 0 0 0| 3 2 1 0 0 0 0| 4 3 1 0 0 0 0| 5 4 1 0 0 0 0| 6 5 1 0 0 0 0| 7 6 1 0 0 0 0| 8 7 1 0 0 0 0| 9 8 1 0 0 0 0| 10 11 2 0 0 0 0| 12 13 1 0 0 0 0|M END
9
+ LMFA00000008 (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid (9S,10S)-10-hydroxy-9-(phosphonooxy)stearic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 396.227658 C18H37O7P 85291221 UELBXEKQONEDKM-IRXDYDNUSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000008 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291221 (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoic acid C15989 49253 LMFA00000008| LIPDMAPS01251212252D|| 26 25 0 0 0 0 0 0 0 0999 V2000| 17.1460 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 16.4315 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.1460 7.3100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 15.7170 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.0026 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.2881 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.5736 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.8592 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.1447 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 17.8605 6.0725 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 10.0013 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.2868 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.5723 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.8579 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.1434 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.4289 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.7144 6.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 6.0725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.4302 6.4850 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0| 10.7157 6.0725 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0| 10.7157 5.2475 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 11.4302 7.3100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.1447 8.5475 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.8591 7.3100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.1447 7.7225 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0| 12.3582 6.9256 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 1 2 1 0 0 0 0| 1 3 2 0 0 0 0| 2 4 1 0 0 0 0| 4 5 1 0 0 0 0| 5 6 1 0 0 0 0| 6 7 1 0 0 0 0| 7 8 1 0 0 0 0| 8 9 1 0 0 0 0| 9 19 1 0 0 0 0| 19 20 1 0 0 0 0| 1 10 1 0 0 0 0| 11 20 1 0 0 0 0| 12 11 1 0 0 0 0| 13 12 1 0 0 0 0| 14 13 1 0 0 0 0| 15 14 1 0 0 0 0| 16 15 1 0 0 0 0| 17 16 1 0 0 0 0| 18 17 1 0 0 0 0| 19 22 1 1 0 0 0| 20 21 1 1 0 0 0| 22 25 1 0 0 0 0| 25 23 2 0 0 0 0| 25 24 1 0 0 0 0| 25 26 1 0 0 0 0|M END
10
+ LMFA00000009 6-(6-aminohexanamido)hexanoic acid Fatty Acyls [FA] Other Fatty Acyls [FA00] 244.178671 C12H24N2O3 85291222 IWENLYKHSZCPRD-UHFFFAOYSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000009 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=85291222 N-(6-aminohexanoyl)-6-aminohexanoic acid C01255 49255 LMFA00000009| LIPDMAPS01251212252D|| 17 16 0 0 0 0 0 0 0 0999 V2000| 5.0000 5.7720 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 5.7337 6.1835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.4570 5.7537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.1908 6.1652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.9140 5.7354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.6478 6.1468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.3710 5.7171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.1048 6.1286 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 10.8281 5.6988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.5619 6.1102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.2851 5.6805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.0189 6.0919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.7421 5.6622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.4759 6.0736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 15.1991 5.6439 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 14.4682 6.7787 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 9.3805 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 3 2 1 0 0 0 0| 4 3 1 0 0 0 0| 5 4 1 0 0 0 0| 6 5 1 0 0 0 0| 7 6 1 0 0 0 0| 8 7 1 0 0 0 0| 9 8 1 0 0 0 0| 10 9 1 0 0 0 0| 11 10 1 0 0 0 0| 12 11 1 0 0 0 0| 13 12 1 0 0 0 0| 14 13 1 0 0 0 0| 15 14 1 0 0 0 0| 16 14 2 0 0 0 0| 17 7 2 0 0 0 0|M END
11
+ LMFA00000014 2-aminoethyl-5Z,8Z,11Z,14Z-eicosatetraenoate Fatty Acyls [FA] Other Fatty Acyls [FA00] 347.282416 C22H37NO2 123060035 DLHLOYYQQGSXCC-DOFZRALJSA-N http://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA00000014 http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=123060035 Virodhamine [pretend subclass] LMFA00000014| LIPDMAPS01251212252D|| 25 24 0 0 0 0 0 0 0 0999 V2000| 11.4410 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.7351 6.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.0294 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 9.3236 6.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.6177 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.8028 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.0971 6.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.3913 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.5764 6.4959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.0000 5.9195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 5.5764 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 6.3913 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.0971 5.6549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 7.8028 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 8.6177 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.4410 7.1913 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 12.1494 6.0867 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0| 9.3141 5.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.0103 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 10.7067 5.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 11.4029 5.2475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.0992 5.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 12.9734 6.5626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 13.7820 6.0958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0| 14.5629 6.5467 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0| 2 1 1 0 0 0 0| 3 2 1 0 0 0 0| 4 3 1 0 0 0 0| 5 4 1 0 0 0 0| 5 6 2 0 0 0 0| 6 7 1 0 0 0 0| 7 8 1 0 0 0 0| 8 9 2 0 0 0 0| 9 10 1 0 0 0 0| 11 12 2 0 0 0 0| 12 13 1 0 0 0 0| 13 14 1 0 0 0 0| 14 15 2 0 0 0 0| 10 11 1 0 0 0 0| 1 16 2 0 0 0 0| 1 17 1 0 0 0 0| 18 15 1 0 0 0 0| 19 18 1 0 0 0 0| 20 19 1 0 0 0 0| 21 20 1 0 0 0 0| 22 21 1 0 0 0 0| 17 23 1 0 0 0 0| 23 24 1 0 0 0 0| 24 25 1 0 0 0 0|M END
metadata ADDED
@@ -0,0 +1,202 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: mspire-lipid
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.2.0
5
+ platform: ruby
6
+ authors:
7
+ - John T. Prince
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2014-08-14 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: mspire-molecular_formula
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - "~>"
18
+ - !ruby/object:Gem::Version
19
+ version: 0.1.0
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
25
+ - !ruby/object:Gem::Version
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+ version: 0.1.0
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+ - !ruby/object:Gem::Dependency
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+ name: rubabel
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.1.6
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.1.6
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - "~>"
46
+ - !ruby/object:Gem::Version
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+ version: 1.6.2
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 1.6.2
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+ - !ruby/object:Gem::Dependency
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+ name: rake
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
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+ - - ">="
60
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 2.14.1
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 2.14.1
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 4.1.1
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ - !ruby/object:Gem::Dependency
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+ name: simplecov
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 0.8.2
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+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - "~>"
109
+ - !ruby/object:Gem::Version
110
+ version: 0.8.2
111
+ - !ruby/object:Gem::Dependency
112
+ name: fftw3
113
+ requirement: !ruby/object:Gem::Requirement
114
+ requirements:
115
+ - - ">="
116
+ - !ruby/object:Gem::Version
117
+ version: '0'
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ requirements:
122
+ - - ">="
123
+ - !ruby/object:Gem::Version
124
+ version: '0'
125
+ description: mass spectrometry based lipidomics - especially shotgun lipidomics.
126
+ email:
127
+ - jtprince@gmail.com
128
+ executables:
129
+ - lipidomic-search.rb
130
+ extensions: []
131
+ extra_rdoc_files: []
132
+ files:
133
+ - ".document"
134
+ - ".gitignore"
135
+ - ".rspec"
136
+ - Gemfile
137
+ - LICENSE
138
+ - README.md
139
+ - Rakefile
140
+ - bin/lipidomic-search.rb
141
+ - lib/mspire/lipid.rb
142
+ - lib/mspire/lipid/ion.rb
143
+ - lib/mspire/lipid/ion/fragment.rb
144
+ - lib/mspire/lipid/modification.rb
145
+ - lib/mspire/lipid/search.rb
146
+ - lib/mspire/lipid/search/bin.rb
147
+ - lib/mspire/lipid/search/db_isobar_group.rb
148
+ - lib/mspire/lipid/search/hit.rb
149
+ - lib/mspire/lipid/search/probability_distribution.rb
150
+ - lib/mspire/lipid/search/query.rb
151
+ - lib/mspire/lipid/version.rb
152
+ - lib/mspire/lipid_maps.rb
153
+ - mspire-lipid.gemspec
154
+ - scratch/OBConversion_methods.txt
155
+ - scratch/atom_methods.txt
156
+ - scratch/bond_methods.txt
157
+ - scratch/mol_methods.txt
158
+ - scratch/split_molecules.rb
159
+ - script/find_nearest_lipid.rb
160
+ - spec/mspire/lipid/ion_spec.rb
161
+ - spec/mspire/lipid/modification_spec.rb
162
+ - spec/mspire/lipid/search_spec.rb
163
+ - spec/mspire/lipid_maps_spec.rb
164
+ - spec/mspire/lipid_spec.rb
165
+ - spec/spec_helper.rb
166
+ - spec/testfiles/lipidmaps_download.tsv
167
+ - spec/testfiles/lipidmaps_programmatic_short.tsv
168
+ - spec/testfiles/lipidmaps_sd_download.tsv
169
+ homepage: ''
170
+ licenses:
171
+ - MIT
172
+ metadata: {}
173
+ post_install_message:
174
+ rdoc_options: []
175
+ require_paths:
176
+ - lib
177
+ required_ruby_version: !ruby/object:Gem::Requirement
178
+ requirements:
179
+ - - ">="
180
+ - !ruby/object:Gem::Version
181
+ version: '0'
182
+ required_rubygems_version: !ruby/object:Gem::Requirement
183
+ requirements:
184
+ - - ">="
185
+ - !ruby/object:Gem::Version
186
+ version: '0'
187
+ requirements: []
188
+ rubyforge_project:
189
+ rubygems_version: 2.2.2
190
+ signing_key:
191
+ specification_version: 4
192
+ summary: mass spectrometry based lipidomics - especially shotgun lipidomics
193
+ test_files:
194
+ - spec/mspire/lipid/ion_spec.rb
195
+ - spec/mspire/lipid/modification_spec.rb
196
+ - spec/mspire/lipid/search_spec.rb
197
+ - spec/mspire/lipid_maps_spec.rb
198
+ - spec/mspire/lipid_spec.rb
199
+ - spec/spec_helper.rb
200
+ - spec/testfiles/lipidmaps_download.tsv
201
+ - spec/testfiles/lipidmaps_programmatic_short.tsv
202
+ - spec/testfiles/lipidmaps_sd_download.tsv