Merge commit 'b6dbdfdd848e4081df6cd476d52f64845462d757'

lifs-tools · Mar 26, 2023 · 22120dc · 22120dc
2 parents a49976d + b6dbdfd
commit 22120dc
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diff --git a/src/cppgoslin/cppgoslin/domain/Adduct.h b/src/cppgoslin/cppgoslin/domain/Adduct.h
@@ -47,15 +47,17 @@ class Adduct {
     string adduct_string;
     int charge;
     int charge_sign;
+    ElementTable heavy_elements;
 
     static const map<string, int> adduct_charges;
 
-    Adduct(string _sum_formula, string _adduct_string, int _charge = 1, int _sign = 1);
+    Adduct(string _sum_formula, string _adduct_string, int _charge = 0, int _sign = 1);
     Adduct(Adduct *a);
     void set_charge_sign(int sign);
     string get_lipid_string();
     ElementTable* get_elements();
     int get_charge();
+    string get_heavy_isotope_string();
 };
 
 

diff --git a/src/cppgoslin/cppgoslin/domain/Element.h b/src/cppgoslin/cppgoslin/domain/Element.h
@@ -8,7 +8,7 @@ of this software and associated documentation files (the "Software"), to deal
 in the Software without restriction, including without limitation the rights
 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+furnished to do so, subject to the following conditions,
 
 The above copyright notice and this permission notice shall be included in all
 copies or substantial portions of the Software.
@@ -51,9 +51,14 @@ const map<string, Element> element_positions = {{"C", ELEMENT_C}, {"H", ELEMENT_
 const map<Element, double> element_masses = {{ELEMENT_C, 12.0},  {ELEMENT_H, 1.007825035},  {ELEMENT_N, 14.0030740}, {ELEMENT_O, 15.99491463}, {ELEMENT_P, 30.973762},  {ELEMENT_S, 31.9720707}, {ELEMENT_H2, 2.014101779},  {ELEMENT_C13, 13.0033548378},  {ELEMENT_N15, 15.0001088984}, {ELEMENT_O17, 16.9991315}, {ELEMENT_O18, 17.9991604}, {ELEMENT_P32, 31.973907274}, {ELEMENT_S33, 32.97145876}, {ELEMENT_S34, 33.96786690}, {ELEMENT_F, 18.9984031}, {ELEMENT_Cl, 34.968853}, {ELEMENT_Br, 78.918327}, {ELEMENT_I, 126.904473}, {ELEMENT_As, 74.921595}};
 
 
-
 const map<Element, string> element_shortcut = {{ELEMENT_C, "C"}, {ELEMENT_H, "H"}, {ELEMENT_N, "N"}, {ELEMENT_O, "O"}, {ELEMENT_P, "P"}, {ELEMENT_S, "S"}, {ELEMENT_F, "F"}, {ELEMENT_Cl, "Cl"}, {ELEMENT_Br, "Br"}, {ELEMENT_I, "I"}, {ELEMENT_As, "As"}, {ELEMENT_H2, "H'"}, {ELEMENT_C13, "C'"}, {ELEMENT_N15, "N'"}, {ELEMENT_O17, "O'"}, {ELEMENT_O18, "O''"}, {ELEMENT_P32, "P'"}, {ELEMENT_S33, "S'"}, {ELEMENT_S34, "S''"}};
 
+const map<Element, string> heavy_shortcut = {{ELEMENT_C, "C"}, {ELEMENT_H, "H"}, {ELEMENT_N, "N"}, {ELEMENT_O, "O"}, {ELEMENT_P, "P"}, {ELEMENT_S, "S"}, {ELEMENT_F, "F"}, {ELEMENT_I, "I"}, {ELEMENT_As, "As"}, {ELEMENT_Br, "Br"}, {ELEMENT_Cl, "Cl"}, {ELEMENT_H2, "H2"}, {ELEMENT_C13, "C13"}, {ELEMENT_N15, "N15"}, {ELEMENT_O17, "O17"}, {ELEMENT_O18, "O18"}, {ELEMENT_P32, "P32"}, {ELEMENT_S33, "S33"}, {ELEMENT_S34, "S34"}};
+
+
+const map<Element, Element> heavy_to_regular = {{ELEMENT_H2, ELEMENT_H}, {ELEMENT_C13, ELEMENT_C}, {ELEMENT_N15, ELEMENT_N}, {ELEMENT_O17, ELEMENT_O}, {ELEMENT_O18, ELEMENT_O}, {ELEMENT_P32, ELEMENT_P}, {ELEMENT_S33, ELEMENT_S}, {ELEMENT_S34, ELEMENT_S}};
+
+
 const vector<Element> element_order = {ELEMENT_C, ELEMENT_H, ELEMENT_As, ELEMENT_Br, ELEMENT_Cl, ELEMENT_F, ELEMENT_I, ELEMENT_N, ELEMENT_O, ELEMENT_P, ELEMENT_S, ELEMENT_H2, ELEMENT_C13, ELEMENT_N15, ELEMENT_O17, ELEMENT_O18, ELEMENT_P32, ELEMENT_S33, ELEMENT_S34};
 }
 

diff --git a/src/cppgoslin/cppgoslin/domain/LipidEnums.h b/src/cppgoslin/cppgoslin/domain/LipidEnums.h
@@ -95,7 +95,8 @@ struct LipidClassMeta {
 
 
 typedef map<LipidClass, LipidClassMeta> ClassMap;
-enum LipidFaBondType { LCB_REGULAR, LCB_EXCEPTION, ETHER_PLASMANYL, ETHER_PLASMENYL, ETHER, ETHER_UNSPECIFIED, ESTER, AMIDE, NO_FA, UNDEFINED_FA, };
+enum LipidFaBondType {LCB_REGULAR = 0, LCB_EXCEPTION = 1, ETHER_PLASMANYL = 2, ETHER_PLASMENYL = 3, ETHER = 4, ETHER_UNSPECIFIED = 5, ESTER = 6, AMIDE = 7, UNDEFINED_FA = 8, NO_FA = 9};
+
 
 static const set<LipidFaBondType> LCB_STATES {LCB_REGULAR, LCB_EXCEPTION};
 

diff --git a/src/cppgoslin/cppgoslin/parser/LipidMapsParserEventHandler.h b/src/cppgoslin/cppgoslin/parser/LipidMapsParserEventHandler.h
@@ -96,9 +96,13 @@ class LipidMapsParserEventHandler : public LipidBaseParserEventHandler {
     void add_adduct(TreeNode *node);
     void add_charge(TreeNode *node);
     void add_charge_sign(TreeNode *node);
+    void add_additional_modifier(TreeNode *node);
+    void set_heavy_element(TreeNode *node);
+    void set_heavy_number(TreeNode *node);
 
     static const map<string, int> acer_heads;
-
+    int heavy_number;
+    Element heavy_element;
 };
 
 

diff --git a/src/cppgoslin/data/goslin/LipidMaps.g4 b/src/cppgoslin/data/goslin/LipidMaps.g4
@@ -34,21 +34,23 @@ lipid_mono: lipid_pure | lipid_pure isoform;
 lipid_pure: pure_fa | gl | pl | sl | pk | sterol | mediator;
 isoform: square_open_bracket isoform_inner square_close_bracket;
 isoform_inner : 'rac' | 'iso' | 'iso' number | 'R';
-isotope: SPACE round_open_bracket isotope_element number round_close_bracket | DASH round_open_bracket isotope_element number round_close_bracket | DASH isotope_element number;
-isotope_element: 'd';
+isotope: SPACE round_open_bracket isotope_pair round_close_bracket | round_open_bracket isotope_pair round_close_bracket | DASH round_open_bracket isotope_pair round_close_bracket | DASH isotope_pair | SPACE isotope_pair | isotope_pair;
+isotope_pair: isotope_element isotope_number;
+isotope_number: number;
+isotope_element: 'd' | 'D';
 
 
 /* adduct information */
 adduct_info : adduct_sep | adduct_separator adduct_sep;
-adduct_sep : '[M' adduct ']' charge_sign | '[M' adduct ']' charge charge_sign;
+adduct_sep : '[M' adduct ']' | '[M' adduct ']' charge_sign | '[M' adduct ']' charge charge_sign;
 adduct : adduct_set;
 adduct_set : adduct_element | adduct_element adduct_set;
 adduct_element : element | element number | number element | plus_minus element | plus_minus element number | plus_minus number element;
 
 
 
 /* pure fatty acid */
-pure_fa: hg_fa pure_fa_species | fa_no_hg;
+pure_fa: hg_fa pure_fa_species | hg_fa headgroup_separator pure_fa_species | fa_no_hg;
 fa_no_hg: fa;
 pure_fa_species: round_open_bracket fa round_close_bracket | fa | round_open_bracket fa2 round_close_bracket;
 hg_fa: 'FA' | 'WE' | 'CoA' | 'CAR' | 'FAHFA' | 'CoA';
@@ -128,7 +130,7 @@ dsl_subspecies: round_open_bracket lcb_fa_sorted round_close_bracket | lcb_fa_so
 
 hg_dslc: hg_dsl_global | hg_dsl_global headgroup_separator;
 hg_dsl_global : hg_dsl | special_cer | special_glyco;
-hg_dsl: 'Cer' | 'CerP' | 'EPC' | glyco_sphingo_lipid | 'Hex3Cer' | 'Hex2Cer' | 'HexCer' | 'IPC' | 'M(IP)2C' | 'MIPC' | 'SHexCer' | 'SulfoHexCer' | 'SM' | 'PE-Cer' | 'PI-Cer' | 'GlcCer' | 'FMC-5' | 'FMC-6' | 'LacCer' | 'GalCer' | 'C1P' | '(3\'-sulfo)Galbeta-Cer' | omega_linoleoyloxy_Cer;
+hg_dsl: 'Cer' | 'CerP' | 'EPC' | glyco_sphingo_lipid | 'CMH' | 'CMH-OH' | 'MHCer' | 'MHCER' | 'CDH' | 'DHCer' | 'DHCER' | 'Hex3Cer' | 'Hex2Cer' | 'HexCer' | 'IPC' | 'M(IP)2C' | 'MIPC' | 'SHexCer' | 'SulfoHexCer' | 'SM' | 'PE-Cer' | 'PI-Cer' | 'GlcCer' | 'FMC-5' | 'FMC-6' | 'LacCer' | 'GalCer' | 'C1P' | '(3\'-sulfo)Galbeta-Cer' | omega_linoleoyloxy_Cer;
 glyco_sphingo_lipid : 'GA1' | 'Ga1' | 'GA2' | 'Ga2' |
  'GB3' | 'Gb3' | 'GB4' | 'Gb4' |
  'GD1' | 'Gd1' | 'GD2' | 'Gd2' | 'GD3' | 'Gd3' |
@@ -165,7 +167,7 @@ pk_fa : round_open_bracket fa round_close_bracket;
 /* sterol lipids */
 sterol: chc | chec;
 chc: ch | ch headgroup_separator;
-ch: 'Cholesterol';
+ch: 'Cholesterol' | 'cholesterol';
 chec: che | che headgroup_separator | che_fa;
 che: fa headgroup_separator hg_che;
 che_fa: hg_che round_open_bracket fa round_close_bracket;
@@ -187,7 +189,7 @@ mediator_oxo: 'Oxo' | 'oxo';
 
 
 /* generic rules */
-fa: fa_unmod | fa_unmod fa_mod | fa_unmod fa_mod_separator fa_mod;
+fa: fa_unmod | fa_unmod fa_mod | fa_unmod fa_mod_separator fa_mod | fa_no_db;
 fa_unmod: round_open_bracket fa_pure ether_suffix round_close_bracket | round_open_bracket ether_prefix fa_pure round_close_bracket | round_open_bracket fa_pure round_close_bracket | ether_prefix fa_pure | fa_pure ether_suffix | fa_pure;
 fa_mod: round_open_bracket modification round_close_bracket;
 modification: modification ',' modification | single_mod;
@@ -200,8 +202,10 @@ mod_text: 'OH' | 'Ke' | 'OOH' | 'My' | 'Me' | 'Br' | 'CHO' | 'COOH' | 'Cp' | 'Ep
 ether_prefix : 'P-' | 'O-';
 ether_suffix : 'p' | 'e';
 stereo : 'R' | 'S';
-fa_pure: carbon carbon_db_separator db | carbon carbon_db_separator db db_hydroxyl_separator hydroxyl;
+fa_no_db: carbon DASH single_mod;
+fa_pure: carbon carbon_db_separator db | carbon carbon_db_separator db db_hydroxyl_separator hydroxyl | additional_modifier carbon carbon_db_separator db | additional_modifier carbon carbon_db_separator db db_hydroxyl_separator hydroxyl;
 lcb_pure_fa : lcb_fa;
+additional_modifier : 'C' | 'h';
 lcb_fa: lcb_fa_unmod | lcb_fa_unmod lcb_fa_mod;
 lcb_fa_unmod: carbon carbon_db_separator db;
 lcb_fa_mod: round_open_bracket modification round_close_bracket;

diff --git a/src/cppgoslin/data/goslin/README.md b/src/cppgoslin/data/goslin/README.md
@@ -8,17 +8,21 @@ Goslin defines multiple grammers compatible with ANTLRv4 for different sources o
 [Overview of Goslin and Tutorials](docs/README.adoc)
 
 
-> Goslin 2.0 is currently under development and will support the [updated lipid shorthand nomenclature with new structural levels](https://pubmed.ncbi.nlm.nih.gov/33037133/).
+> Goslin 2.0 supports the [updated lipid shorthand nomenclature with new structural levels](https://pubmed.ncbi.nlm.nih.gov/33037133/).
 
 ## Citing Goslin
-If you use Goslin or any of the specific implementations in your work, we kindly ask you to cite:
+If you use Goslin or any of the specific implementations in your work, we kindly ask you to cite the original publication:
 
-[D. Kopczynski _et al._, **Goslin - A Grammar of Succinct Lipid Nomenclature**, Analytical Chemistry, June 26th, 2020.](https://pubs.acs.org/doi/10.1021/acs.analchem.0c01690) [doi:10.1021/acs.analchem.0c01690](https://doi.org/10.1021/acs.analchem.0c01690)
+* [D. Kopczynski _et al._, **Goslin - A Grammar of Succinct Lipid Nomenclature**, Analytical Chemistry, June 26th, 2020.](https://pubs.acs.org/doi/10.1021/acs.analchem.0c01690) [doi:10.1021/acs.analchem.0c01690](https://doi.org/10.1021/acs.analchem.0c01690)
+
+If you are using any of the new features of Goslin 2.0, please cite the following, updated Goslin 2.0 publication:
+
+* [D. Kopczynski _et al._, **Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures**, Analytical Chemistry, April 11th, 2022.](https://pubs.acs.org/doi/full/10.1021/acs.analchem.1c05430) [doi:10.1021/acs.analchem.1c05430](https://doi.org/10.1021/acs.analchem.1c05430)
 
 ## References
-* [D. Kopczynski et al., Biorxiv, Nov xth, 2021 (Preprint)](#)
-* [D. Kopczynski et al., Analytical Chemistry, June 26th, 2020](https://pubs.acs.org/doi/10.1021/acs.analchem.0c01690)
-* [D. Kopczynski et al., Biorxiv, April 20th, 2020 (Preprint)](https://doi.org/10.1101/2020.04.17.046656)
+* [D. Kopczynski, N. Hoffmann *et al.*, Analytical Chemistry, April 11th, 2022](https://doi.org/10.1021/acs.analchem.1c05430)
+* [D. Kopczynski, N. Hoffmann *et al.*, Analytical Chemistry, June 26th, 2020](https://pubs.acs.org/doi/10.1021/acs.analchem.0c01690)
+* [D. Kopczynski, N. Hoffmann *et al.*, Biorxiv, April 20th, 2020 (Preprint)](https://doi.org/10.1101/2020.04.17.046656)
 
 ## Related Projects
 

diff --git a/src/cppgoslin/data/goslin/lipid-list.csv b/src/cppgoslin/data/goslin/lipid-list.csv
@@ -166,10 +166,10 @@ GT2,SP,Glycosphingolipids,2,2,,C53H82N4O39,Gt2,,,,,,,
 GT3,SP,Glycosphingolipids,2,2,,C45H69N3O34,Gt3,,,,,,,
 HC,FA,Hydrocarbons [FA11],1,1,HC,H,,,,,,,,
 LacCer,SP,Neutral glycosphingolipids [SP05],2,2,,C12H21O10,,,,,,,,
-Hex2Cer,SP,Neutral glycosphingolipids [SP05],2,2,,C12H21O10,,,,,,,,
+Hex2Cer,SP,Neutral glycosphingolipids [SP05],2,2,,C12H21O10,CDH,DHCer,DHCER,,,,,
 Hex3Cer,SP,Neutral glycosphingolipids [SP05],2,2,,C18H31O15,,,,,,,,
 GB3,SP,Neutral glycosphingolipids [SP05],2,2,,C18H31O15,Gb3,GB3Cer,Gb3Cer,,,,,
-HexCer,SP,Neutral glycosphingolipids [SP05],2,2,,C6H11O5,Glucosylceramide,,,,,,,
+HexCer,SP,Neutral glycosphingolipids [SP05],2,2,,C6H11O5,Glucosylceramide,CMH,CMH-OH,MHCER,MHCer,,,
 GalCer,SP,Neutral glycosphingolipids [SP05],2,2,,C6H11O5,,,,,,,,
 GlcCer,SP,Neutral glycosphingolipids [SP05],2,2,,C6H11O5,,,,,,,,
 i-Forssman,SP,Glycosphingolipids,2,2,,C34H57N2O25,,,,,,,,
@@ -302,7 +302,7 @@ SPB,SP,Sphingoid base homologs and variants [SP0104],1,1,Lyso;SP_Exception,H2,Sp
 SPBP,SP,Sphingoid base 1-phosphates [SP0105],1,1,Lyso,H3O3P,Sphingosine-1-phosphate,S1P,SPH-P,SIP,Sphinganine-1-phosphate,Sa1P,LCBP,SPA1P
 SQDG,GL,Glycosyldiacylglycerols [GL0501],2,2,Sugar,C9H16O10S,,,,,,,,
 SQMG,GL,Glycosylmonoacylglycerols [GL0401],2,1,Sugar,C9H16O10S,,,,,,,,
-ST 27:1;O,ST,Cholesterol and derivatives [ST0101],0,0,,C27H46O,CH,FC,Cholesterol,Ch,ST,ST 27:1;1,Chol,
+ST 27:1;O,ST,Cholesterol and derivatives [ST0101],0,0,,C27H46O,CH,FC,Cholesterol,Ch,ST,ST 27:1;1,Chol,cholesterol
 ST 27:2;O,ST,Cholesterol and derivatives [ST0101],0,0,,C27H44O,Desmosterol,ST 27:2;1,,,,,,
 ST 28:2;O,ST,Ergosterols and C24-methyl derivatives [ST0103],0,0,,C28H46O,Ergostadienol,ST 28:2;1,,,,,,
 ST 28:3;O,ST,Ergosterols and C24-methyl derivatives [ST0103],0,0,,C28H44O,Ergosterol,ST 28:3;1,,,,,,

diff --git a/src/cppgoslin/data/goslin/testfiles/lipid-maps-test.csv b/src/cppgoslin/data/goslin/testfiles/lipid-maps-test.csv
@@ -249,7 +249,7 @@
 "4R-methyl-7Z,11Z-heptadecadienoic acid",
 "Arachidonic acid","Arachidonic acid"
 "Oleic acid",
-"Arachidonic Acid (d8)","Arachidonic Acid"
+"Arachidonic Acid (d8)","Arachidonic Acid[M8H2]"
 "Vinyl acetic acid",
 "beta-ethyl acrylic acid",
 "beta-penteic acid",
@@ -407,8 +407,8 @@
 "Drosophilin C",
 "Norlinolenic acid",
 "EPA","EPA"
-"EPA (d5)","EPA"
-"DHA (d5)","DHA"
+"EPA (d5)","EPA[M5H2]"
+"DHA (d5)","DHA[M5H2]"
 "Oleic acid (d5)",
 "cis-parinaric acid",
 "(5Z,9E,14Z)-icosa-5,9,14-trienoic acid",
@@ -1405,10 +1405,10 @@
 "13S-HODE","13S-HODE"
 "9,10-DiHOME",
 "12,13-DiHOME",
-"9S-HODE-d4","9S-HODE"
+"9S-HODE-d4","9S-HODE[M4H2]"
 "12,13 diHOME-(d4)",
 "9,10-diHOME-(d4)",
-"13S-HODE-(d4)","13S-HODE"
+"13S-HODE-(d4)","13S-HODE[M4H2]"
 "(R)-10-hydroxystearic acid",
 "(9S,10S)-9,10-dihydroxyoctadecanoic acid",
 "17-hydroxy-linolenic acid",
@@ -1738,9 +1738,9 @@
 "PGE2","PGE2"
 "PGD2","PGD2"
 "PGA1",
-"PGF2alpha-d4","PGF2alpha"
-"PGD2-d4","PGD2"
-"PGE2-d4","PGE2"
+"PGF2alpha-d4","PGF2alpha[M4H2]"
+"PGD2-d4","PGD2[M4H2]"
+"PGE2-d4","PGE2[M4H2]"
 "PGG2",
 "PGH2",
 "2,3-dinor-11b-PGF2alpha",
@@ -1945,7 +1945,7 @@
 "LTA4",
 "12-oxo-LTB4",
 "20-hydroxy-LTE4",
-"LTB4-d4","LTB4"
+"LTB4-d4","LTB4[M4H2]"
 "14,15-LTC4",
 "14,15-LTD4",
 "14,15-LTE4",
@@ -1999,7 +1999,7 @@
 "TXB3","TXB3"
 "TXB1","TXB1"
 "11-dehydro-TXB3",
-"TXB2-d4","TXB2"
+"TXB2-d4","TXB2[M4H2]"
 "11-dehydro-TXB2-d4",
 "2,3-Dinor-TXB1",
 "11-dehydro-2,3-dinor-TXB2",
@@ -2039,7 +2039,7 @@
 "15S-HETE","15S-HETE"
 "5S-HETE","5S-HETE"
 "11S-HETE","11S-HETE"
-"5S-HETE-d8","5S-HETE"
+"5S-HETE-d8","5S-HETE[M8H2]"
 "8S-HETE","8S-HETE"
 "12S-HETE","12S-HETE"
 "12R-HETE","12R-HETE"
@@ -2079,10 +2079,10 @@
 "14,15-DiHETE","14,15-DiHETE"
 "17,18-DiHETE","17,18-DiHETE"
 "11,12-DiHETE","11,12-DiHETE"
-"15S-HETE-d8","15S-HETE"
-"12S-HETE-d8","12S-HETE"
-"20-HETE-d6","20-HETE"
-"5-Oxo-ETE-d7","5-Oxo-ETE"
+"15S-HETE-d8","15S-HETE[M8H2]"
+"12S-HETE-d8","12S-HETE[M8H2]"
+"20-HETE-d6","20-HETE[M6H2]"
+"5-Oxo-ETE-d7","5-Oxo-ETE[M7H2]"
 "5-HETE","5-HETE"
 "11-HETE","11-HETE"
 "8-HETE","8-HETE"
@@ -5749,19 +5749,19 @@
 "DG(22:5(7Z,10Z,13Z,16Z,19Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/0:0)[iso2]","DG 22:5(7Z,10Z,13Z,16Z,19Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/0:0"
 "DG(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/0:0)","DG 22:6(4Z,7Z,10Z,13Z,16Z,19Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/0:0"
 "DG(16:0/18:1(11Z)/0:0)","DG 16:0/18:1(11Z)/0:0"
-"DG(20:5(5Z,8Z,11Z,14Z,17Z)/0:0/20:5(5Z,8Z,11Z,14Z,17Z)) (d5)","DG 20:5(5Z,8Z,11Z,14Z,17Z)/0:0/20:5(5Z,8Z,11Z,14Z,17Z)"
-"DG(14:0/0:0/14:0) (d5)","DG 14:0/0:0/14:0"
-"DG(15:0/0:0/15:0) (d5)","DG 15:0/0:0/15:0"
-"DG(16:0/0:0/16:0) (d5)","DG 16:0/0:0/16:0"
-"DG(17:0/0:0/17:0) (d5)","DG 17:0/0:0/17:0"
-"DG(19:0/0:0/19:0) (d5)","DG 19:0/0:0/19:0"
-"DG(20:0/0:0/20:0) (d5)","DG 20:0/0:0/20:0"
-"DG(20:2(11Z,14Z)/0:0/20:2(11Z,14Z)) (d5)","DG 20:2(11Z,14Z)/0:0/20:2(11Z,14Z)"
-"DG(20:4(5Z,8Z,11Z,14Z)/0:0/20:4(5Z,8Z,11Z,14Z)) (d5)","DG 20:4(5Z,8Z,11Z,14Z)/0:0/20:4(5Z,8Z,11Z,14Z)"
-"DG(16:1(9Z)/0:0/16:1(9Z)) (d5)","DG 16:1(9Z)/0:0/16:1(9Z)"
-"DG(18:0/0:0/18:0) (d5)","DG 18:0/0:0/18:0"
-"DG(18:1(9Z)/0:0/18:1(9Z)) (d5)","DG 18:1(9Z)/0:0/18:1(9Z)"
-"DG(18:2(9Z,12Z)/0:0/18:2(9Z,12Z)) (d5)","DG 18:2(9Z,12Z)/0:0/18:2(9Z,12Z)"
+"DG(20:5(5Z,8Z,11Z,14Z,17Z)/0:0/20:5(5Z,8Z,11Z,14Z,17Z)) (d5)","DG 20:5(5Z,8Z,11Z,14Z,17Z)/0:0/20:5(5Z,8Z,11Z,14Z,17Z)[M5H2]"
+"DG(14:0/0:0/14:0) (d5)","DG 14:0/0:0/14:0[M5H2]"
+"DG(15:0/0:0/15:0) (d5)","DG 15:0/0:0/15:0[M5H2]"
+"DG(16:0/0:0/16:0) (d5)","DG 16:0/0:0/16:0[M5H2]"
+"DG(17:0/0:0/17:0) (d5)","DG 17:0/0:0/17:0[M5H2]"
+"DG(19:0/0:0/19:0) (d5)","DG 19:0/0:0/19:0[M5H2]"
+"DG(20:0/0:0/20:0) (d5)","DG 20:0/0:0/20:0[M5H2]"
+"DG(20:2(11Z,14Z)/0:0/20:2(11Z,14Z)) (d5)","DG 20:2(11Z,14Z)/0:0/20:2(11Z,14Z)[M5H2]"
+"DG(20:4(5Z,8Z,11Z,14Z)/0:0/20:4(5Z,8Z,11Z,14Z)) (d5)","DG 20:4(5Z,8Z,11Z,14Z)/0:0/20:4(5Z,8Z,11Z,14Z)[M5H2]"
+"DG(16:1(9Z)/0:0/16:1(9Z)) (d5)","DG 16:1(9Z)/0:0/16:1(9Z)[M5H2]"
+"DG(18:0/0:0/18:0) (d5)","DG 18:0/0:0/18:0[M5H2]"
+"DG(18:1(9Z)/0:0/18:1(9Z)) (d5)","DG 18:1(9Z)/0:0/18:1(9Z)[M5H2]"
+"DG(18:2(9Z,12Z)/0:0/18:2(9Z,12Z)) (d5)","DG 18:2(9Z,12Z)/0:0/18:2(9Z,12Z)[M5H2]"
 "1,2-dimyristoyl-sn-glycerol",
 "DG(12:0/16:1(9Z)/0:0)[iso2]","DG 12:0/16:1(9Z)/0:0"
 "DG(12:0/12:0/0:0)[iso2]","DG 12:0/12:0/0:0"
@@ -6001,15 +6001,15 @@
 "TG(16:0/16:0/18:1(11E))","TG 16:0/16:0/18:1(11E)"
 "TG(16:0/16:0/18:1(9Z))","TG 16:0/16:0/18:1(9Z)"
 "TG(12:0/16:0/18:0)","TG 12:0/16:0/18:0"
-"TG(20:5(5Z,8Z,11Z,14Z,17Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z)) (d5)","TG 20:5(5Z,8Z,11Z,14Z,17Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z)"
-"TG(14:0/16:1(9Z)/14:0) (d5)","TG 14:0/16:1(9Z)/14:0"
-"TG(15:0/18:1(9Z)/15:0) (d5)","TG 15:0/18:1(9Z)/15:0"
-"TG(16:0/18:0/16:0) (d5)","TG 16:0/18:0/16:0"
-"TG(17:0/17:1(10Z)/17:0) (d5)","TG 17:0/17:1(10Z)/17:0"
-"TG(19:0/12:0/19:0) (d5)","TG 19:0/12:0/19:0"
-"TG(20:0/20:1(11Z)/20:0) (d5)","TG 20:0/20:1(11Z)/20:0"
-"TG(20:2(11Z,14Z)/18:3(6Z,9Z,12Z)/20:2(11Z,14Z)) (d5)","TG 20:2(11Z,14Z)/18:3(6Z,9Z,12Z)/20:2(11Z,14Z)"
-"TG(20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)) (d5)","TG 20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)"
+"TG(20:5(5Z,8Z,11Z,14Z,17Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z)) (d5)","TG 20:5(5Z,8Z,11Z,14Z,17Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/20:5(5Z,8Z,11Z,14Z,17Z)[M5H2]"
+"TG(14:0/16:1(9Z)/14:0) (d5)","TG 14:0/16:1(9Z)/14:0[M5H2]"
+"TG(15:0/18:1(9Z)/15:0) (d5)","TG 15:0/18:1(9Z)/15:0[M5H2]"
+"TG(16:0/18:0/16:0) (d5)","TG 16:0/18:0/16:0[M5H2]"
+"TG(17:0/17:1(10Z)/17:0) (d5)","TG 17:0/17:1(10Z)/17:0[M5H2]"
+"TG(19:0/12:0/19:0) (d5)","TG 19:0/12:0/19:0[M5H2]"
+"TG(20:0/20:1(11Z)/20:0) (d5)","TG 20:0/20:1(11Z)/20:0[M5H2]"
+"TG(20:2(11Z,14Z)/18:3(6Z,9Z,12Z)/20:2(11Z,14Z)) (d5)","TG 20:2(11Z,14Z)/18:3(6Z,9Z,12Z)/20:2(11Z,14Z)[M5H2]"
+"TG(20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)) (d5)","TG 20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)[M5H2]"
 "TG(16:0/16:0/16:1(9Z))[iso3]","TG 16:0/16:0/16:1(9Z)"
 "TG(16:0/16:1(9Z)/16:1(9Z))[iso3]","TG 16:0/16:1(9Z)/16:1(9Z)"
 "TG(16:0/16:0/17:0)[iso3]","TG 16:0/16:0/17:0"
@@ -31355,7 +31355,7 @@
 "Lathosterol",
 "Desmosterol(d6)",
 "24-hydroxy-cholesterol(d6)",
-"Cholesterol(d7)",
+"Cholesterol(d7)","ST 27:1;O[M7H2]"
 "22-dehydrocholesterol",
 "Zymostenol",
 "Epi-cholestanol",
@@ -31574,7 +31574,7 @@
 "15:0 Cholesteryl ester","SE 27:1/15:0"
 "Cholesteryl nitrolinoleate",
 "Cholesteryl 11-hydroperoxy-eicosatetraenoate",
-"18:1 Cholesteryl ester (d5)","SE 27:1/18:1"
+"18:1 Cholesteryl ester (d5)","SE 27:1/18:1[M5H2]"
 "22:5 Cholesteryl ester","SE 27:1/22:5"
 "lanosteryl oleate",
 "lanosteryl palmitoleate",

diff --git a/src/cppgoslin/makefile b/src/cppgoslin/makefile
@@ -9,7 +9,7 @@ else
 endif
 install_dir = /usr
 ifeq ($(origin CC),default)
-CC  = g++
+CC = g++
 endif
 #CC = g++ -std=c++11
 #CC = clang++-10
@@ -34,7 +34,8 @@ ifeq ($(OS),Windows_NT)
   flags = -fopenmp
 endif
 
-opt = -std=c++11 -O3 ${MARCH} -Wvla -Wall ${flags} -D_FORTIFY_SOURCE=2
+opt = -std=c++11 -O3 ${flags} -D_FORTIFY_SOURCE=2
+# -Wvla -Wall ${MARCH}
 
 main: ${bin}