mspire-lipid 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
@@ -0,0 +1,70 @@
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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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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
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
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
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
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
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
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
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
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
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
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]
data/spec/testfiles/lipidmaps_programmatic_short.tsv ADDED
@@ -0,0 +1,32 @@
1
+ LM_ID COMMON_NAME SYSTEMATIC_NAME FORMULA MASS CATEGORY MAIN_CLASS SUB_CLASS
2
+ LMFA00000007 n-decanohydroxamic acid N-hydroxydecanamide C10H21NO2 187.16 Fatty Acyls [FA] Other Fatty Acyls [FA00]
3
+ 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]
5
+ 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]
8
+ 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]
9
+ LMGL02010065 DG(18:0/19:0/0:0)[iso2] 1-octadecanoyl-2-nonadecanoyl-sn-glycerol C40H78O5 638.58 Glycerolipids [GL] Diradylglycerols [GL02] Diacylglycerols [GL0201]
10
+ MGP01011596 PC(18:1(9Z)/13:0) 1-(9Z-octadecenoyl)-2-tridecanoyl-glycero-3-phosphocholine C39H76NO8P 717.53 Glycerophospholipids [GP] Glycerophosphocholines [GP01] Diacylglycerophosphocholines [GP0101]
11
+ 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]
15
+ 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]
16
+ 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]
17
+ LMSP0502AO00 - Galbeta1-3Galalpha1-4Galbeta1-4Glcbeta-Cer - - Sphingolipids [SP] Neutral glycosphingolipids [SP05] GalNAcbeta1-3Galalpha1-4Galbeta1-4Glc- (Globo series) [SP0502]
18
+ 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]
20
+ 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
20
+ 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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+ 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: 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