# HG changeset patch # User fgiacomoni # Date 1516372697 18000 # Node ID 6091a80df9516fe12aa40055ce9b81fad56d6c99 # Parent 505956db90c55b424964333989461eb52810f4d7 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 diff -r 505956db90c5 -r 6091a80df951 lib/hmdb.pm --- a/lib/hmdb.pm Mon Feb 20 09:55:54 2017 -0500 +++ b/lib/hmdb.pm Fri Jan 19 09:38:17 2018 -0500 @@ -271,23 +271,46 @@ # print Dumper $csv ; foreach my $line (@{$csv}) { - - if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { - my @entry = split(/,/, $line) ; - - if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } + ## HMDB csv output - [DEPRECATED]... +# if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { +# my @entry = split(/,/, $line) ; +# +# if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } +# +# $features{ENTRY_ENTRY_ID} = $entry[1] ; +# $features{ENTRY_FORMULA} = $entry[2] ; +# $features{ENTRY_CPD_MZ} = $entry[3] ; +# $features{ENTRY_ADDUCT} = $entry[4] ; +# $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; +# $features{ENTRY_ADDUCT_MZ} = $entry[6] ; +# $features{ENTRY_DELTA} = $entry[7] ; +# +# my %temp = %features ; +# +# push (@{$result_by_entry{$entry[0]} }, \%temp) ; +# } + ## NEW HMDB format V4.0 - dec2017 + if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) { - $features{ENTRY_ENTRY_ID} = $entry[1] ; - $features{ENTRY_FORMULA} = $entry[2] ; - $features{ENTRY_CPD_MZ} = $entry[3] ; - $features{ENTRY_ADDUCT} = $entry[4] ; - $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; - $features{ENTRY_ADDUCT_MZ} = $entry[6] ; - $features{ENTRY_DELTA} = $entry[7] ; - - my %temp = %features ; - - push (@{$result_by_entry{$entry[0]} }, \%temp) ; + if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { + my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; + + if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } + + $features{ENTRY_ENTRY_ID} = $entry[1] ; + $features{ENTRY_FORMULA} = $entry[4] ; + $features{ENTRY_CPD_MZ} = $entry[5] ; + $features{ENTRY_ADDUCT} = $entry[6] ; + $features{ENTRY_ADDUCT_TYPE} = $entry[7] ; + $features{ENTRY_ADDUCT_MZ} = $entry[8] ; + $features{ENTRY_DELTA} = $entry[9] ; + + my %temp = %features ; + push (@{$result_by_entry{$entry[0]} }, \%temp) ; + } + else { + warn "The parsed line ($line) does not match your pattern\n " ; + } } else { next ; diff -r 505956db90c5 -r 6091a80df951 t/hmdb_managerTest.pl --- a/t/hmdb_managerTest.pl Mon Feb 20 09:55:54 2017 -0500 +++ b/t/hmdb_managerTest.pl Fri Jan 19 09:38:17 2018 -0500 @@ -48,14 +48,22 @@ is_deeply( get_matches_from_hmdb_uaTest( '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'), [ - 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', - '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', - '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', - '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', - '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', - '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', +# '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', +# '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', +# '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', +# '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', +# '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', +# '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', +# '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + ## Update format - 2018-01-19... HMDB V04 + '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', + '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', + '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', + '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', + '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5', + '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', + '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', ], 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb'); @@ -77,29 +85,38 @@ print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; is_deeply ( parse_hmdb_csv_resultsTest ( [ - 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', - '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', - '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', - '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', - '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', - '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', +# '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', +# '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', +# '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', +# '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', +# '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', +# '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', +# '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + ## Update format - 2018-01-19... HMDB V04 + '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', + '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', + '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', + '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', + '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5', + '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', + '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', ], - ['175.01', '238.19', '420.16'] + ['175.01', '238.19', '420.16'], + 10 ), [ [ - { 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_DELTA' => '0.000125', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ENTRY_ID' => 'HMDB60293', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_CPD_MZ' => '113.94453531' }, - { 'ENTRY_ADDUCT' => 'M+CH3OH+H', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000676', 'ENTRY_FORMULA' => 'C2H6O3S2', 'ENTRY_ENTRY_ID' => 'HMDB03745', 'ENTRY_ADDUCT_MZ' => '175.009324', 'ENTRY_CPD_MZ' => '141.975835438' }, - { 'ENTRY_CPD_MZ' => '95.987885149', 'ENTRY_FORMULA' => 'H4O4Si', 'ENTRY_ENTRY_ID' => 'HMDB31436', 'ENTRY_ADDUCT_MZ' => '175.009105', 'ENTRY_DELTA' => '0.000895', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+DMSO+H' }, - { 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000914', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_CPD_MZ' => '310.047738052', 'ENTRY_ENTRY_ID' => 'HMDB33657', 'ENTRY_ADDUCT_MZ' => '175.009086', 'ENTRY_FORMULA' => 'C17H10O6' }, - { 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_DELTA' => '0.000914', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_FORMULA' => 'C17H10O6', 'ENTRY_ADDUCT_MZ' => '175.009086', 'ENTRY_ENTRY_ID' => 'HMDB35230', 'ENTRY_CPD_MZ' => '310.047738052' } + { 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_ENTRY_ID' => 'HMDB0060293', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_DELTA' => '1', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+IsoProp+H' }, + {'ENTRY_DELTA' => '4','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+CH3OH+H','ENTRY_CPD_MZ' => '141.975835438','ENTRY_ENTRY_ID' => 'HMDB0003745','ENTRY_FORMULA' => 'C2H6O3S2','ENTRY_ADDUCT_MZ' => '175.009324'}, + {'ENTRY_ENTRY_ID' => 'HMDB0031436','ENTRY_CPD_MZ' => '95.987885149','ENTRY_ADDUCT_MZ' => '175.009105','ENTRY_FORMULA' => 'H4O4Si','ENTRY_DELTA' => '5','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+DMSO+H'}, + {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0033657','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT' => 'M+H+K','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '5'}, + {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0035230','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+H+K','ENTRY_DELTA' => '5'} ], [], [ - { 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000683', 'ENTRY_ENTRY_ID' => 'HMDB60838', 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_CPD_MZ' => '359.093976737' }, - { 'ENTRY_CPD_MZ' => '359.093976737', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_ID' => 'HMDB60836', 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_DELTA' => '0.000683', 'ENTRY_ADDUCT' => 'M+IsoProp+H' } + {'ENTRY_FORMULA' => 'C17H17N3O4S','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ENTRY_ID' => 'HMDB0060838','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '2'}, + {'ENTRY_DELTA' => '2','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ENTRY_ID' => 'HMDB0060836','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_FORMULA' => 'C17H17N3O4S'} ] ], 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; diff -r 505956db90c5 -r 6091a80df951 t/lib/hmdbTest.pm --- a/t/lib/hmdbTest.pm Mon Feb 20 09:55:54 2017 -0500 +++ b/t/lib/hmdbTest.pm Fri Jan 19 09:38:17 2018 -0500 @@ -71,10 +71,10 @@ ## sub sub parse_hmdb_csv_resultsTest { - my ($hmdb_pages, $mzs ) = @_ ; + my ($hmdb_pages, $mzs, $max ) = @_ ; my $oHmdb = lib::hmdb->new() ; - my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result + my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max) ; ## hash format result return($result) ; } diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.html --- a/test-data/out_test02.html Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test02.html Fri Jan 19 09:38:17 2018 -0500 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000275.05547146
N-NitrosodimethylamineHMDB31419C2H6N2O74.048012824M+H+75.0552890.00018246InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3-0.53
AcetylhydrazineHMDB60428C2H6N2O74.048012824M+H+75.0552890.00018246InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)-0.78
CreatineHMDB00064C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)-1.59
Beta-Guanidinopropionic acidHMDB13222C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)-1.70
Nitrogen oxidesHMDB32439H3NO33.021463723M+ACN+H+75.0552870.00018446InChI=1S/H3NO/c1-2/h1H3NA
mz_0000375.08059797
1-ButanolHMDB04327C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H30.84
UNKNOWNHMDB62103C4H10O74.073164942M+H+75.0804410.00015697NANA
2-ButanolHMDB11469C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H30.66
IsobutanolHMDB06006C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H30.60
2-Methylpropan-2-olHMDB31456C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H30.70
mz_0000476.03942694
L-Aspartic acidHMDB00191C4H7NO4133.037507717M+H+NH4+76.0393040.00012294InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1-3.52
Ethyl nitriteHMDB31239C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H30.42
GlycineHMDB00123C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)-3.34
Acetohydroxamic AcidHMDB14691C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)-1.46
Iminodiacetic acidHMDB11753C4H7NO4133.037507717M+H+NH4+76.0393040.00012294InChI=1S/C4H7NO4/c6-3(7)1-5-2-4(8)9/h5H,1-2H2,(H,6,7)(H,8,9)-2.50
mz_0000576.07584477
1-Amino-propan-2-olHMDB12136C3H9NO75.068413915M+H+76.075690.00015477InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
Trimethylamine N-oxideHMDB00925C3H9NO75.068413915M+H+76.075690.00015477InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB31652C3H6O58.041864814M+NH4+76.0756880.00015677InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
UNKNOWNHMDB62143C3H6O58.041864813M+NH4+76.0756880.00015677NANA
MethyloxiraneHMDB31558C3H6O58.041864814M+NH4+76.0756880.00015677InChI=1/C3H6O/c1-3-2-4-3/h3H,2H2,1H30.04
mz_0000676.07593168
1-Amino-propan-2-olHMDB12136C3H9NO75.068413915M+H+76.075690.00024168InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
Trimethylamine N-oxideHMDB00925C3H9NO75.068413915M+H+76.075690.00024168InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB31652C3H6O58.041864814M+NH4+76.0756880.00024368InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
UNKNOWNHMDB62143C3H6O58.041864813M+NH4+76.0756880.00024368NANA
MethyloxiraneHMDB31558C3H6O58.041864814M+NH4+76.0756880.00024368InChI=1/C3H6O/c1-3-2-4-3/h3H,2H2,1H30.04
\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000275.05547146
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3-0.53
AcetylhydrazineHMDB0060428C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)-0.78
glycinamideHMDB0062472C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c3-1-2(4)5/h1,3H2,(H2,4,5)-2.49
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)-1.59
Beta-Guanidinopropionic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)-1.70
mz_0000375.08059797
UNKNOWNHMDB0155221H4O7P2177.943225506M+H+2Na+75.0805990NANA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H30.84
UNKNOWNHMDB0062103C4H10O74.073164942M+H+75.0804412NANA
1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl etherHMDB0062326C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-3-5-4-2/h3-4H2,1-2H31.12
2-ButanolHMDB0011469C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H30.66
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1-3.52
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H30.42
1-deoxy-1-(N6-lysino)-D-fructoseHMDB0062186C4H7NO4133.037507709M+H+NH4+76.0393042InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)-3.52
GlycineHMDB0000123C2H5NO275.032028409M+H+76.0393042InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)-3.34
Acetohydroxamic AcidHMDB0014691C2H5NO275.032028409M+H+76.0393042InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)-1.46
mz_0000576.07584477
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2-1.01
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
2-(methylamino)ethan-1-olHMDB0142449C3H9NO75.068413914M+H+76.075692InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3-1.05
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB0031652C3H6O58.041864814M+NH4+76.0756882InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
mz_0000676.07593168
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2-1.01
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
2-(methylamino)ethan-1-olHMDB0142449C3H9NO75.068413914M+H+76.075693InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3-1.05
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB0031652C3H6O58.041864814M+NH4+76.0756883InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
\ No newline at end of file diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.tabular --- a/test-data/out_test02.tabular Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test02.tabular Fri Jan 19 09:38:17 2018 -0500 @@ -1,7 +1,7 @@ id mz rt hmdb(delta::name::mz::formula::adduct::id) 1 7.02080998 49.38210915 NONE -2 75.05547146 0.658528069 0.00018246::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB31419 | 0.00018246::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB60428 | 0.00018346::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB00064 | 0.00018346::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB13222 | 0.00018446::[Nitrogen oxides]::33.021463723::H3NO::[M+ACN+H]::HMDB32439 -3 75.08059797 1743.94267 0.00015697::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB04327 | 0.00015697::[UNKNOWN]::74.073164942::C4H10O::[M+H]::HMDB62103 | 0.00015697::[2-Butanol]::74.073164942::C4H10O::[M+H]::HMDB11469 | 0.00015697::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB06006 | 0.00015697::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB31456 -4 76.03942694 51.23158899 0.00012294::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB00191 | 0.00012294::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB31239 | 0.00012294::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB00123 | 0.00012294::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB14691 | 0.00012294::[Iminodiacetic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB11753 -5 76.07584477 50.51249853 0.00015477::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB12136 | 0.00015477::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB00925 | 0.00015677::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB31652 | 0.00015677::[UNKNOWN]::58.041864813::C3H6O::[M+NH4]::HMDB62143 | 0.00015677::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB31558 -6 76.07593168 0.149308136 0.00024168::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB12136 | 0.00024168::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB00925 | 0.00024368::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB31652 | 0.00024368::[UNKNOWN]::58.041864813::C3H6O::[M+NH4]::HMDB62143 | 0.00024368::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB31558 +2 75.05547146 0.658528069 2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222 +3 75.08059797 1743.94267 0::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[UNKNOWN]::74.073164942::C4H10O::[M+H]::HMDB0062103 | 2::[1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether]::74.073164942::C4H10O::[M+H]::HMDB0062326 | 2::[2-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0011469 +4 76.03942694 51.23158899 2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB0000123 | 2::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB0014691 +5 76.07584477 50.51249853 2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652 +6 76.07593168 0.149308136 3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652 diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.txt --- a/test-data/out_test02.txt Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test02.txt Fri Jan 19 09:38:17 2018 -0500 @@ -1,27 +1,27 @@ ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID mz_00001 7.02080998 0 UNKNOWN N/A N/A N/A N/A N/A -mz_00002 75.05547146 0.00018246 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB31419 -mz_00002 75.05547146 0.00018246 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB60428 -mz_00002 75.05547146 0.00018346 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB00064 -mz_00002 75.05547146 0.00018346 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB13222 -mz_00002 75.05547146 0.00018446 [Nitrogen oxides] 33.021463723 H3NO [M+ACN+H] 75.055287 HMDB32439 -mz_00003 75.08059797 0.00015697 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB04327 -mz_00003 75.08059797 0.00015697 [UNKNOWN] 74.073164942 C4H10O [M+H] 75.080441 HMDB62103 -mz_00003 75.08059797 0.00015697 [2-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB11469 -mz_00003 75.08059797 0.00015697 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB06006 -mz_00003 75.08059797 0.00015697 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB31456 -mz_00004 76.03942694 0.00012294 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB00191 -mz_00004 76.03942694 0.00012294 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB31239 -mz_00004 76.03942694 0.00012294 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB00123 -mz_00004 76.03942694 0.00012294 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB14691 -mz_00004 76.03942694 0.00012294 [Iminodiacetic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB11753 -mz_00005 76.07584477 0.00015477 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB12136 -mz_00005 76.07584477 0.00015477 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB00925 -mz_00005 76.07584477 0.00015677 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31652 -mz_00005 76.07584477 0.00015677 [UNKNOWN] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB62143 -mz_00005 76.07584477 0.00015677 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31558 -mz_00006 76.07593168 0.00024168 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB12136 -mz_00006 76.07593168 0.00024168 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB00925 -mz_00006 76.07593168 0.00024368 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31652 -mz_00006 76.07593168 0.00024368 [UNKNOWN] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB62143 -mz_00006 76.07593168 0.00024368 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31558 +mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419 +mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 +mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 +mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064 +mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 +mz_00003 75.08059797 0 [UNKNOWN] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221 +mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327 +mz_00003 75.08059797 2 [UNKNOWN] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062103 +mz_00003 75.08059797 2 [1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062326 +mz_00003 75.08059797 2 [2-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0011469 +mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191 +mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239 +mz_00004 76.03942694 2 [1-deoxy-1-(N6-lysino)-D-fructose] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186 +mz_00004 76.03942694 2 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0000123 +mz_00004 76.03942694 2 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0014691 +mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00005 76.07584477 2 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 +mz_00005 76.07584477 2 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031652 +mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00006 76.07593168 3 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 +mz_00006 76.07593168 3 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031652 diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.html --- a/test-data/out_test03.html Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test03.html Fri Jan 19 09:38:17 2018 -0500 @@ -1,1 +1,1 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
HydroxidodioxidosulfidosulfateHMDB60293H2O3S2113.94453531M+IsoProp+H+175.0098750.000125InChI=1S/H2O3S2/c1-5(2,3)4/h(H2,1,2,3,4)NA
MesnaHMDB03745C2H6O3S2141.975835438M+CH3OH+H+175.0093240.000676InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)-1.53
Silicic acidHMDB31436H4O4Si95.987885149M+DMSO+H+175.0091050.000895InChI=1S/H4O4Si/c1-5(2,3)4/h1-4HNA
De-O-methylsterigmatocystinHMDB33657C17H10O6310.047738052M+H+K+175.0090860.000914InChI=1/C17H10O6/c18-8-2-1-3-10-13(8)15(20)14-9(19)6-11-12(16(14)22-10)7-4-5-21-17(7)23-11/h1-7,17-19H2.72
Aurantricholide BHMDB35230C17H10O6310.047738052M+H+K+175.0090860.000914InChI=1S/C17H10O6/c18-10-3-1-8(2-4-10)15-16-14(23-17(15)21)6-9-5-11(19)12(20)7-13(9)22-16/h1-7,18-20H3.05
mz_00002238.19
Alpha-TerpineolHMDB04043C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m0/s13.17
(S)-alpha-TerpineolHMDB36086C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m1/s13.17
EucalyptolHMDB04472C10H18O154.1357652M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-9(2)8-4-6-10(3,11-9)7-5-8/h8H,4-7H2,1-3H33.36
GeraniolHMDB05812C10H18O154.1357652M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,7,11H,4,6,8H2,1-3H3/b10-7-2.89
trans-(-)-p-Menth-1-en-3-olHMDB35861C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-7(2)9-5-4-8(3)6-10(9)11/h6-7,9-11H,4-5H2,1-3H3/t9-,10+/m0/s12.64
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB60836C17H17N3O4S359.093976737M+IsoProp+H+420.1593170.000683InChI=1/C17H17N3O4S/c21-13-2-1-7-18-15(13)19-8-9-24-12-5-3-11(4-6-12)10-14-16(22)20-17(23)25-14/h1-7,14,21H,8-10H2,(H,18,19)(H,20,22,23)2.33
N-Desmethyl-p-hydroxyrosiglitazoneHMDB60838C17H17N3O4S359.093976737M+IsoProp+H+420.1593170.000683InChI=1/C17H17N3O4S/c21-12-3-6-15(19-10-12)18-7-8-24-13-4-1-11(2-5-13)9-14-16(22)20-17(23)25-14/h1-6,10,14,21H,7-9H2,(H,18,19)(H,20,22,23)2.31
Benzyl glycinate 4-methylbenzenesulfonate saltHMDB33374C16H19NO5S337.098393413M+2ACN+H+420.1587630.001237InChI=1S/C9H11NO2.C7H8O3S/c10-6-9(11)12-7-8-4-2-1-3-5-8;1-6-2-4-7(5-3-6)11(8,9)10/h1-5H,6-7,10H2;2-5H,1H3,(H,8,9,10)NA
GlutarylglycineHMDB00590C7H11NO5189.0637224672M+ACN+H+420.1612680.001268InChI=1S/C7H11NO5/c9-5(8-4-7(12)13)2-1-3-6(10)11/h1-4H2,(H,8,9)(H,10,11)(H,12,13)-0.82
N-Acetylglutamic acidHMDB01138C7H11NO5189.0637224672M+ACN+H+420.1612680.001268InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)-0.67
mz_00004780.32
Niazicinin AHMDB31947C17H23NO8369.1423667172M+ACN+H+780.3185560.001444InChI=1S/C17H23NO8/c1-9-15(25-10(2)19)13(20)14(21)16(24-9)26-12-6-4-11(5-7-12)8-18-17(22)23-3/h4-7,9,13-16,20-21H,8H2,1-3H3,(H,18,22)0.57
Mulberrofuran THMDB35940C44H44O9716.298533006M+ACN+Na+780.3142980.005702InChI=1/C44H44O9/c1-22(2)6-10-29-34(46)15-13-31(42(29)51)43(52)40-32(28-12-9-27(45)21-36(28)48)16-24(5)17-33(40)41-37(49)18-26(19-38(41)50)39-20-25-8-14-35(47)30(44(25)53-39)11-7-23(3)4/h6-9,12-15,17-21,32-33,40,45-51H,10-11,16H2,1-5H35.95
2'-Hydroxy-3',4',5',7,8-pentamethoxyflavanHMDB33906C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-22-14-9-7-11-6-8-13(27-17(11)18(14)24-3)12-10-15(23-2)19(25-4)20(26-5)16(12)21/h7,9-10,13,21H,6,8H2,1-5H32.58
trans-Grandmarin isovalerateHMDB39032C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-10(2)8-15(22)26-19-17(23)16-13(27-20(19,3)4)9-12(24-5)11-6-7-14(21)25-18(11)16/h6-7,9-10,17,19,23H,8H2,1-5H32.89
(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olideHMDB32731C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-5-11(2)18(23)27-16-9-20(4,25)7-6-14(22)13(10-21)8-15-17(16)12(3)19(24)26-15/h5-8,15-17,21,25H,3,9-10H2,1-2,4H3/b7-6-,11-5+,13-8-0.83
mz_00005956.25
Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranosideHMDB35451C43H49O23933.266462874M+Na+956.2556810.005681InChI=1/C43H48O23/c1-58-25-10-17(2-8-22(25)48)3-9-30(49)59-16-29-33(52)36(55)40(66-42-38(57)35(54)32(51)28(15-45)64-42)43(65-29)62-26-13-21-23(60-39(26)18-4-6-19(46)7-5-18)11-20(47)12-24(21)61-41-37(56)34(53)31(50)27(14-44)63-41/h2-13,27-29,31-38,40-45,50-57H,14-16H2,1H3,(H2-,46,47,48,49)/p+11.22
PetaninHMDB38095C43H49O23933.266462874M+Na+956.2556810.005681InChI=1/C43H48O23/c1-16-39(66-29(48)8-5-17-3-6-19(45)7-4-17)35(54)38(57)41(60-16)59-15-28-32(51)34(53)37(56)43(65-28)63-26-13-21-23(61-40(26)18-9-22(47)30(49)25(10-18)58-2)11-20(46)12-24(21)62-42-36(55)33(52)31(50)27(14-44)64-42/h3-13,16,27-28,31-39,41-44,50-57H,14-15H2,1-2H3,(H3-,45,46,47,48,49)/p+11.58
Kaempferide 3-rhamnosideHMDB40803C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1/C22H22O10/c1-9-16(25)18(27)19(28)22(30-9)32-21-17(26)15-13(24)7-11(23)8-14(15)31-20(21)10-3-5-12(29-2)6-4-10/h3-9,16,18-19,22-25,27-28H,1-2H31.45
GlycitinHMDB02219C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1S/C22H22O10/c1-29-15-6-12-14(30-9-13(18(12)25)10-2-4-11(24)5-3-10)7-16(15)31-22-21(28)20(27)19(26)17(8-23)32-22/h2-7,9,17,19-24,26-28H,8H2,1H30.83
Calycosin 7-galactosideHMDB38821C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1/C22H22O10/c1-29-15-5-2-10(6-14(15)24)13-9-30-16-7-11(3-4-12(16)18(13)25)31-22-21(28)20(27)19(26)17(8-23)32-22/h2-7,9,17,19-24,26-28H,8H2,1H30.80
mz_000061100.45
NPCHMDB60499C28H30N4O6518.2165347122M+ACN+Na+1100.4488340.001166InChI=1/C28H30N4O6/c1-3-17-18-11-16(38-27(35)31-9-7-15(29)8-10-31)5-6-22(18)30-24-19(17)13-32-23(24)12-21-20(25(32)33)14-37-26(34)28(21,36)4-2/h5-6,11-12,15,36H,3-4,7-10,13-14,29H2,1-2H3/t28-/s22.40
Cellulose triacetateHMDB32198C30H34Cl2N4O536.2109671442M+3H2O+2H+1100.4450540.004946InChI=1S/C30H34Cl2N4O/c31-21-17-24(32)29-27(18-21)36-26-12-7-5-10-23(26)30(29)34-15-8-2-1-3-13-28(37)33-16-14-20-19-35-25-11-6-4-9-22(20)25/h4,6,9,11,17-19,35H,1-3,5,7-8,10,12-16H2,(H,33,37)(H,34,36)7.37
Lewis X trisaccharideHMDB06568C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)35-17(8(3-22)21-7(2)25)18(9(26)4-23)36-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1-2.26
O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-GalactoseHMDB02060C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=1S/C20H35NO15/c1-6-11(27)14(30)16(32)19(33-6)36-18-15(31)13(29)10(5-24)34-20(18)35-17(12(28)9(26)4-23)8(3-22)21-7(2)25/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13-,14+,15-,16-,17+,18+,19-,20-/m0/s1-2.25
Lewis a trisaccharideHMDB06582C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)36-18(9(26)4-23)17(8(3-22)21-7(2)25)35-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1-2.27
\ No newline at end of file +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
HydroxidodioxidosulfidosulfateHMDB0060293H2O3S2113.94453531M+IsoProp+H+175.0098751InChI=1S/H2O3S2/c1-5(2,3)4/h(H2,1,2,3,4)NA
MesnaHMDB0003745C2H6O3S2141.975835438M+CH3OH+H+175.0093244InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)-1.53
Silicic acidHMDB0031436H4O4Si95.987885149M+DMSO+H+175.0091055InChI=1S/H4O4Si/c1-5(2,3)4/h1-4HNA
De-O-methylsterigmatocystinHMDB0033657C17H10O6310.047738052M+H+K+175.0090865InChI=1S/C17H10O6/c18-8-2-1-3-10-13(8)15(20)14-9(19)6-11-12(16(14)22-10)7-4-5-21-17(7)23-11/h1-7,17-19H2.72
Aurantricholide BHMDB0035230C17H10O6310.047738052M+H+K+175.0090865InChI=1S/C17H10O6/c18-10-3-1-8(2-4-10)15-16-14(23-17(15)21)6-9-5-11(19)12(20)7-13(9)22-16/h1-7,18-20H3.05
mz_00002238.19
Alpha-TerpineolHMDB0004043C10H18O154.135765198M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m0/s13.17
(S)-alpha-TerpineolHMDB0036086C10H18O154.135765198M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m0/s13.17
EucalyptolHMDB0004472C10H18O154.1357652M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-9(2)8-4-6-10(3,11-9)7-5-8/h8H,4-7H2,1-3H33.36
GeraniolHMDB0005812C10H18O154.1357652M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,7,11H,4,6,8H2,1-3H3/b10-7-2.89
trans-(-)-p-Menth-1-en-3-olHMDB0035861C10H18O154.135765198M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-7(2)9-5-4-8(3)6-10(9)11/h6-7,9-11H,4-5H2,1-3H3/t9-,10+/m0/s12.64
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB0060836C17H17N3O4S359.093976737M+IsoProp+H+420.1593172InChI=1S/C17H17N3O4S/c21-13-2-1-7-18-15(13)19-8-9-24-12-5-3-11(4-6-12)10-14-16(22)20-17(23)25-14/h1-7,14,21H,8-10H2,(H,18,19)(H,20,22,23)2.33
N-Desmethyl-p-hydroxyrosiglitazoneHMDB0060838C17H17N3O4S359.093976737M+IsoProp+H+420.1593172InChI=1S/C17H17N3O4S/c21-12-3-6-15(19-10-12)18-7-8-24-13-4-1-11(2-5-13)9-14-16(22)20-17(23)25-14/h1-6,10,14,21H,7-9H2,(H,18,19)(H,20,22,23)2.31
Benzyl glycinate 4-methylbenzenesulfonate saltHMDB0033374C16H19NO5S337.098393413M+2ACN+H+420.1587633InChI=1S/C9H11NO2.C7H8O3S/c10-6-9(11)12-7-8-4-2-1-3-5-8;1-6-2-4-7(5-3-6)11(8,9)10/h1-5H,6-7,10H2;2-5H,1H3,(H,8,9,10)NA
GlutarylglycineHMDB0000590C7H11NO5189.0637224672M+ACN+H+420.1612683InChI=1S/C7H11NO5/c9-5(8-4-7(12)13)2-1-3-6(10)11/h1-4H2,(H,8,9)(H,10,11)(H,12,13)-0.82
N-Acetylglutamic acidHMDB0001138C7H11NO5189.0637224672M+ACN+H+420.1612683InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)-0.67
mz_00004780.32
Niazicinin AHMDB0031947C17H23NO8369.1423667172M+ACN+H+780.3185562InChI=1S/C17H23NO8/c1-9-15(25-10(2)19)13(20)14(21)16(24-9)26-12-6-4-11(5-7-12)8-18-17(22)23-3/h4-7,9,13-16,20-21H,8H2,1-3H3,(H,18,22)0.57
Mulberrofuran THMDB0035940C44H44O9716.298533006M+ACN+Na+780.3142987InChI=1S/C44H44O9/c1-22(2)6-10-29-34(46)15-13-31(42(29)51)43(52)40-32(28-12-9-27(45)21-36(28)48)16-24(5)17-33(40)41-37(49)18-26(19-38(41)50)39-20-25-8-14-35(47)30(44(25)53-39)11-7-23(3)4/h6-9,12-15,17-21,32-33,40,45-51H,10-11,16H2,1-5H35.95
2'-Hydroxy-3',4',5',7,8-pentamethoxyflavanHMDB0033906C20H24O7376.1522031222M+3H2O+2H+780.32752610InChI=1S/C20H24O7/c1-22-14-9-7-11-6-8-13(27-17(11)18(14)24-3)12-10-15(23-2)19(25-4)20(26-5)16(12)21/h7,9-10,13,21H,6,8H2,1-5H32.58
trans-Grandmarin isovalerateHMDB0039032C20H24O7376.1522031222M+3H2O+2H+780.32752610InChI=1S/C20H24O7/c1-10(2)8-15(22)26-19-17(23)16-13(27-20(19,3)4)9-12(24-5)11-6-7-14(21)25-18(11)16/h6-7,9-10,17,19,23H,8H2,1-5H32.89
(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olideHMDB0032731C20H24O7376.1522031222M+3H2O+2H+780.32752610InChI=1S/C20H24O7/c1-5-11(2)18(23)27-16-9-20(4,25)7-6-14(22)13(10-21)8-15-17(16)12(3)19(24)26-15/h5-8,15-17,21,25H,3,9-10H2,1-2,4H3/b7-6-,11-5+,13-8-0.83
mz_00005956.25
Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranosideHMDB0035451C43H49O23933.266462874M+Na+956.2556816InChI=1S/C43H48O23/c1-58-25-10-17(2-8-22(25)48)3-9-30(49)59-16-29-33(52)36(55)40(66-42-38(57)35(54)32(51)28(15-45)64-42)43(65-29)62-26-13-21-23(60-39(26)18-4-6-19(46)7-5-18)11-20(47)12-24(21)61-41-37(56)34(53)31(50)27(14-44)63-41/h2-13,27-29,31-38,40-45,50-57H,14-16H2,1H3,(H2-,46,47,48,49)/p+11.22
PetaninHMDB0038095C43H49O23933.266462874M+Na+956.2556816InChI=1S/C43H48O23/c1-16-39(66-29(48)8-5-17-3-6-19(45)7-4-17)35(54)38(57)41(60-16)59-15-28-32(51)34(53)37(56)43(65-28)63-26-13-21-23(61-40(26)18-9-22(47)30(49)25(10-18)58-2)11-20(46)12-24(21)62-42-36(55)33(52)31(50)27(14-44)64-42/h3-13,16,27-28,31-39,41-44,50-57H,14-15H2,1-2H3,(H3-,45,46,47,48,49)/p+11.58
UNKNOWNHMDB0153300C22H22O10446.1212969082M+ACN+Na+956.2583599NANA
Kaempferide 3-rhamnosideHMDB0040803C22H22O10446.1212969242M+ACN+Na+956.2583599InChI=1S/C22H22O10/c1-9-16(25)18(27)19(28)22(30-9)32-21-17(26)15-13(24)7-11(23)8-14(15)31-20(21)10-3-5-12(29-2)6-4-10/h3-9,16,18-19,22-25,27-28H,1-2H31.45
2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-oneHMDB0141944C22H22O10446.1212969082M+ACN+Na+956.2583599InChI=1S/C22H22O10/c1-29-17-6-10(2-5-13(17)24)15-8-14(25)12-4-3-11(7-16(12)31-15)30-22-21(28)20(27)19(26)18(9-23)32-22/h2-8,18-24,26-28H,9H2,1H30.81
mz_000061100.45
NPCHMDB0060499C28H30N4O6518.2165347122M+ACN+Na+1100.4488341InChI=1S/C28H30N4O6/c1-3-17-18-11-16(38-27(35)31-9-7-15(29)8-10-31)5-6-22(18)30-24-19(17)13-32-23(24)12-21-20(25(32)33)14-37-26(34)28(21,36)4-2/h5-6,11-12,15,36H,3-4,7-10,13-14,29H2,1-2H3/t28-/m0/s12.40
Cellulose triacetateHMDB0032198C30H34Cl2N4O536.2109671442M+3H2O+2H+1100.4450544InChI=1S/C30H34Cl2N4O/c31-21-17-24(32)29-27(18-21)36-26-12-7-5-10-23(26)30(29)34-15-8-2-1-3-13-28(37)33-16-14-20-19-35-25-11-6-4-9-22(20)25/h4,6,9,11,17-19,35H,1-3,5,7-8,10,12-16H2,(H,33,37)(H,34,36)7.37
Lewis X trisaccharideHMDB0006568C20H35NO15529.2006694552M+ACN+H+1100.43516213InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)35-17(8(3-22)21-7(2)25)18(9(26)4-23)36-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1-2.26
O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-GalactoseHMDB0002060C20H35NO15529.2006694552M+ACN+H+1100.43516213InChI=1S/C20H35NO15/c1-6-11(27)14(30)16(32)19(33-6)36-18-15(31)13(29)10(5-24)34-20(18)35-17(12(28)9(26)4-23)8(3-22)21-7(2)25/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13-,14+,15-,16-,17+,18+,19-,20-/m0/s1-2.25
Lewis a trisaccharideHMDB0006582C20H35NO15529.2006694552M+ACN+H+1100.43516213InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)36-18(9(26)4-23)17(8(3-22)21-7(2)25)35-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1-2.27
\ No newline at end of file diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.tabular --- a/test-data/out_test03.tabular Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test03.tabular Fri Jan 19 09:38:17 2018 -0500 @@ -1,31 +1,31 @@ ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0.000125 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB60293 -mz_00001 175.01 0.000676 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB03745 -mz_00001 175.01 0.000895 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB31436 -mz_00001 175.01 0.000914 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB33657 -mz_00001 175.01 0.000914 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB35230 -mz_00002 238.19 0.000875 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04043 -mz_00002 238.19 0.000875 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB36086 -mz_00002 238.19 0.000875 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04472 -mz_00002 238.19 0.000875 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB05812 -mz_00002 238.19 0.000875 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB35861 -mz_00003 420.16 0.000683 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60836 -mz_00003 420.16 0.000683 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60838 -mz_00003 420.16 0.001237 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB33374 -mz_00003 420.16 0.001268 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB00590 -mz_00003 420.16 0.001268 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB01138 -mz_00004 780.32 0.001444 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB31947 -mz_00004 780.32 0.005702 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB35940 -mz_00004 780.32 0.007526 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB33906 -mz_00004 780.32 0.007526 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB39032 -mz_00004 780.32 0.007526 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB32731 -mz_00005 956.25 0.005681 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB35451 -mz_00005 956.25 0.005681 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB38095 -mz_00005 956.25 0.008359 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB40803 -mz_00005 956.25 0.008359 [Glycitin] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB02219 -mz_00005 956.25 0.008359 [Calycosin 7-galactoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB38821 -mz_00006 1100.45 0.001166 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB60499 -mz_00006 1100.45 0.004946 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB32198 -mz_00006 1100.45 0.014838 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06568 -mz_00006 1100.45 0.014838 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB02060 -mz_00006 1100.45 0.014838 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06582 +mz_00001 175.01 1 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB0060293 +mz_00001 175.01 4 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB0003745 +mz_00001 175.01 5 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB0031436 +mz_00001 175.01 5 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0033657 +mz_00001 175.01 5 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0035230 +mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 +mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 +mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 +mz_00002 238.19 4 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0005812 +mz_00002 238.19 4 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0035861 +mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 +mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 +mz_00003 420.16 3 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB0033374 +mz_00003 420.16 3 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0000590 +mz_00003 420.16 3 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0001138 +mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 +mz_00004 780.32 7 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB0035940 +mz_00004 780.32 10 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0033906 +mz_00004 780.32 10 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0039032 +mz_00004 780.32 10 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0032731 +mz_00005 956.25 6 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0035451 +mz_00005 956.25 6 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0038095 +mz_00005 956.25 9 [UNKNOWN] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0153300 +mz_00005 956.25 9 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0040803 +mz_00005 956.25 9 [2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0141944 +mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 +mz_00006 1100.45 4 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB0032198 +mz_00006 1100.45 13 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006568 +mz_00006 1100.45 13 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0002060 +mz_00006 1100.45 13 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006582 diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.txt --- a/test-data/out_test03.txt Mon Feb 20 09:55:54 2017 -0500 +++ b/test-data/out_test03.txt Fri Jan 19 09:38:17 2018 -0500 @@ -1,31 +1,31 @@ ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0.000125 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB60293 -mz_00001 175.01 0.000676 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB03745 -mz_00001 175.01 0.000895 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB31436 -mz_00001 175.01 0.000914 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB33657 -mz_00001 175.01 0.000914 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB35230 -mz_00002 238.19 0.000875 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04043 -mz_00002 238.19 0.000875 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB36086 -mz_00002 238.19 0.000875 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04472 -mz_00002 238.19 0.000875 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB05812 -mz_00002 238.19 0.000875 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB35861 -mz_00003 420.16 0.000683 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60836 -mz_00003 420.16 0.000683 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60838 -mz_00003 420.16 0.001237 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB33374 -mz_00003 420.16 0.001268 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB00590 -mz_00003 420.16 0.001268 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB01138 -mz_00004 780.32 0.001444 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB31947 -mz_00004 780.32 0.005702 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB35940 -mz_00004 780.32 0.007526 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB33906 -mz_00004 780.32 0.007526 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB39032 -mz_00004 780.32 0.007526 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB32731 -mz_00005 956.25 0.005681 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB35451 -mz_00005 956.25 0.005681 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB38095 -mz_00005 956.25 0.008359 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB40803 -mz_00005 956.25 0.008359 [Glycitin] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB02219 -mz_00005 956.25 0.008359 [Calycosin 7-galactoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB38821 -mz_00006 1100.45 0.001166 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB60499 -mz_00006 1100.45 0.004946 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB32198 -mz_00006 1100.45 0.014838 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06568 -mz_00006 1100.45 0.014838 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB02060 -mz_00006 1100.45 0.014838 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06582 +mz_00001 175.01 1 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB0060293 +mz_00001 175.01 4 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB0003745 +mz_00001 175.01 5 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB0031436 +mz_00001 175.01 5 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0033657 +mz_00001 175.01 5 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0035230 +mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 +mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 +mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 +mz_00002 238.19 4 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0005812 +mz_00002 238.19 4 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0035861 +mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 +mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 +mz_00003 420.16 3 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB0033374 +mz_00003 420.16 3 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0000590 +mz_00003 420.16 3 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0001138 +mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 +mz_00004 780.32 7 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB0035940 +mz_00004 780.32 10 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0033906 +mz_00004 780.32 10 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0039032 +mz_00004 780.32 10 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0032731 +mz_00005 956.25 6 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0035451 +mz_00005 956.25 6 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0038095 +mz_00005 956.25 9 [UNKNOWN] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0153300 +mz_00005 956.25 9 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0040803 +mz_00005 956.25 9 [2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0141944 +mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 +mz_00006 1100.45 4 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB0032198 +mz_00006 1100.45 13 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006568 +mz_00006 1100.45 13 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0002060 +mz_00006 1100.45 13 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006582 diff -r 505956db90c5 -r 6091a80df951 wsdl_hmdb.pl --- a/wsdl_hmdb.pl Mon Feb 20 09:55:54 2017 -0500 +++ b/wsdl_hmdb.pl Fri Jan 19 09:38:17 2018 -0500 @@ -214,12 +214,12 @@ help of wsdl_hmdb # wsdl_hmdb is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. -# Input : formula or list of formula +# Input : accurate mz or list of accurate masses # Author : Franck Giacomoni and Marion Landi -# Email : fgiacomoni\@clermont.inra.fr -# Version : 1.4 +# Email : fgiacomoni\@inra.fr +# Version : 1.5 # Created : 08/07/2012 -# Updated : 21/01/2016 +# Updated : 19/01/2018 USAGE : wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] @@ -268,7 +268,7 @@ =head1 AUTHOR -Franck Giacomoni Efranck.giacomoni@clermont.inra.frE +Franck Giacomoni Efranck.giacomoni@inra.frE =head1 LICENSE @@ -284,4 +284,6 @@ version 1.4 : 21 / 01 / 2016 - a clean version for community +version 1.5 : 19 / 01 / 2018 - modifiy parser to match HMDB V4.0 formats + =cut \ No newline at end of file