Supporting Information

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1 Supporting Information Anion-exchange chromatography coupled to high resolution mass spectrometry: a powerful tool for merging targeted and non-targeted metabolomics Michaela Schwaiger, Evelyn Rampler, Gerrit Hermann,, Walter Miklos, Walter Berger, Gunda Koellensperger,, * Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria ISOtopic solutions, Waehringerstr. 38, 1090 Vienna, Austria Institute of Cancer Research, Department of Internal Medicine I, Medical University of Vienna, Borschkegasse 8a, 1090 Vienna, Austria Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria Corresponding Author * gunda.koellensperger@univie.ac.at 1

2 Table S-1. Previously published ion chromatography methods analyzing the same groups of metabolites. Compound classes Compounds IC method MS Run time LOD on column Application Reference Sugar phosphates PYR, G1P, F6P, FBP, 2PG, 3PG, PEP IonPac AS11, 1000 µl µin-1 MS/MS 42 min pmol Saccharomyces cerevisiae [10] Sugar phosphates, nucleotides 5-keto-d-gluconate (5kDG), M1P, G1P, Gly3P, hydroxyglutarate (OH-glu), F1P, G3P, E4P, camp, G6P, F6P, M6P, pentose 5-P, damp, AMP, DHAP, 6PGA, 3PG/2PG, CDP, cgmp, dump, TMP, UDP-GlcNAc, PEP, UMP, dadp, dimp, ADP, IMP, GMP, FBP, dctp, CTP, TDP, UDP, datp, phosphoribosyl pyrophosphate (PRPP), ATP, Ac-CoA, dgdp, dutp, GDP, TTP, UTP, dgtp, ITP, GTP, CoA Monolithic alkanol quaternary ammonium ion IonSwift MAX- 100 capillary column, 12 µl min -1 rate, make-up flow: 30 µl min -1 (90% ACN in water, 0.01% NH 4 OH) IV: 5 µl MS/MS 75 min fmol Hek293 cells [11] Sugar phosphates G6P, F6P, R5P, S7P, 6PGA, 3PG, PEP IonPac AS11 HC, 350 µl µin -1 MS/MS 70 min n.a. (flux analysis) Escherichia coli [12] Hexose- Phosphates, nucleotidesugars Gal1P, M1P, G1P, G6P, F6P, M6P, UDP- GalNAc, UDP-GlcNAc, GDP-Man, GDP-Glc, ADP-Glc, GDP-Fuc, UDP-GalA, UDP-GlcA, UDP-Gal, UDP-Glc, UDP-Ara, UDP-Xyl IonPac AS11 HC, 350 µl µin -1 MS/MS 85 min pmol Plant tissue (Arabidopsis thaliana, Trigonella foenumgraecum) [13] Organic acids, sugar phosphates, nucleotides Glc, mevalonate, Lac, Uridine, G1P, G6P, F6P, camp, Tartrate, 2-oxoglutarate, AMP, 2PG, Cit, I-Cit, cis-aco, trans-aco, PEP, F1,6BP, F2,6BP, DHAP, IMP CapIC, IonPac AS11, 25 µl min -1 Q Exactive 45 min fmol Stem like cancer cells, UM1 cells [14] 2

3 Compound classes Compounds IC method MS Run time LOD on column Application Reference Organic acids, sugar phosphates Quantitative: Pyr, Suc, AKG, Mali, Fum, Cit 11 sugar monophosphates 9 sugar diphosphates identified via MS/MS Metlin IonPac AS11 HC, 380 µl min -1 IV: 2 µl partial loop Orbitrap Q Exactive HF 20 min fmol/μl to nmol/μl Head and neck cancer cells [15] Organic acids, sugar phosphates, nucleotides Fum, Malonate, Pyr, Glc, Aco, camp, GlcON, UMP, IMP, CMP, Cysteate, R5P, G6P, 6PGA, Suc, Lac, 2-Oxoglutarate, Mali, Sucrose, Orotidine, Cit, 3PG, ADP, GDP, GTP, CTP, ATP, Maleic acid, F6P, Pyrophosphate IonPac AS-19 (standards) and IonPac AS-20 (trypanosome extracts), capic: 10 µl min -1, make-up flow: 10 µl min -1 MeOH LTQ Orbitrap Velos 60 min pmol Trypanosoma brucei (cellular extracts) [16] Organic acids 28 organic acids IonPac AS11 HC, 350 µl µin -1 Thermo Quantiva TSQ triple quadrupole 19.1 min LOQ: µm Quadriceps muscle of mice [17] 3

4 Table S-2. Retention times, detailed values for intermediate repeatability, recovery of metabolite concentrations in a QC sample prepared independently from calibration (giving the trueness bias), LODs and LOQs, and calibration results for an injection volume of 5 µl. Compound RT [min] RT RSD [%] Area RSD [%] Conc. RSD [%] QC 1µM, N=5 Recovery LOD b [nm] LOQ b [nm] Lowest cal level [nm] Upper cal level [µm] Corr. coeff. c R² Mannitol % Hexoses % Lactic acid % Pyruvic acid % Mannitol-1-phosphate % Glucose-1-phosphate % dcmp % CMP % Succinic acid % Malic acid % Fructose-1-phosphate % Glucose-6-phosphate a % Fructose-6-phosphate a % alpha-ketoglutaric acid % Mannose-6-phosphate a % Pentose-5-phosphates % Fumaric acid % Sedoheptulose-7- phosphate % AMP % camp % Oxaloacetic acid % Phosphogluconic acid % PG + 3PG % CDP % Citric acid % TMP % Isocitric acid % Phosphoenolpyruvic acid % cis-aconitic acid % UMP % ADP % S-4

5 Compound RT [min] RT RSD [%] Area RSD [%] Conc. RSD [%] QC 1µM, N=5 Recovery LOD b [nm] LOQ b [nm] Lowest cal level [nm] Upper cal level [µm] Corr. coeff. c R² dctp % Fructose-1-6-bisphosphate % CTP % IMP % GMP % UDP % cgmp % datp % ATP % TTP % UTP % GDP % dgtp % GTP % a Not baseline separated, for internal standardization the sum of the 13 C peaks was used. b LODs and LOQs were calculated according to EURACHEM, The Fitness for Purpose of Analytical Methods, 2 nd edition (2014). c Correlation coefficients were calculated over three repetitive injections of the calibration standards in the range given by the lowest and upper calibration level. S-5

6 Table S-3. Comparison of LODs, calibration ranges and correlation coefficients between the anion exchange chromatography coupled to a high resolution instrument (Q Exactive HF) and a published parallel column analysis coupled to a tandem mass spectrometer 31. For both methods internal standardization with uniformly 13 C labeled yeast cell extract was performed 26. Compound LOD [µm] IC QE HF LC-MS/MS [31] Calibration range [µm] Corr. coeff. R² LOD [µm] Calibration range [µm] Corr. coeff. R² AMP Citric acid CMP Fumaric acid GMP Isocitric acid Malic acid Succinic acid S-6

7 Table S-4. Concentrations, standard deviations and relative standard deviations of methanolic extracts of SW480 cancer cells (N=5 biological replicates, 1 x 10 6 cells seeded and extracted after 24 h incubation) based on isotope dilution using a fully 13 C labeled extract from Pichia pastoris. Compound RT [min] Resistant Extracted amount [nmol mg -1 protein] Sensitive AV SD AV SD 2PG + 3PG AMP Phosphogluconic acid ADP alpha-ketoglutaric acid ATP camp < LOQ CDP cgmp < LOD < LOD cis-aconitic acid Citric acid CMP 9.02 < LOQ CTP datp dcmp 7.91 < LOD < LOD dctp dgtp < LOD < LOD Fructose-1-6-bisphosphate Fructose-1-phosphate Fructose-6-phosphate Fumaric acid GDP Glucose-1-phosphate Glucose-6-phosphate GMP GTP Hexoses IMP Isocitric acid Lactic acid Malic acid Mannitol Mannitol-1-phosphate Mannose-6-phosphate Oxaloacetic acid < LOQ < LOQ Pentose-5-phosphates Phosphoenolpyruvic acid S-7

8 Compound RT [min] Resistant Extracted amount [nmol mg -1 protein] Sensitive AV SD AV SD Pyruvic acid Sedoheptulose-7-phosphate Succinic acid TMP TTP UDP UMP UTP S-8

9 ADP ISF of ATP ISF of dgtp AMP ISF of ADP ATP dgtp CDP ISF of CTP S-9

10 Citric acid Isocitric acid CMP ISF of CDP ATP dgtp ISF of Malic acid Fumaric acid GDP ISF of GTP GMP ISF of GDP S-10

11 G1P F6P M6P G6P F1P ISF of FBP S-11

12 Pyruvic acid ISF of Oxaloacetic acid UDP ISF of UTP UMP ISF of UDP S-12

13 ADP ISF of ATP AMP ISF of ADP S-13

14 ISF of Malic acid Fumaric acid GDP ISF of GTP GMP ISF of GDP S-14

15 UDP ISF of UTP S-15

16 Figure S-1: Extracted ion chromatograms (exact mass ± 5 ppm) of all 45 standard compounds in a 1 µm standard mix (QC_1000nM) and standard compounds > LOQ in a pooled sample (Pool_ISTD) both spiked with yeast based 13 C internal standard. QC_1000nM: For several compounds more than one peak was detected. These are either in-source fragments (ISF) or isomers as indicated in the chromatograms. In-source fragmentation is very pronounced for nucleotides hence two peaks for the mono- and di-phosphates can be observed. For ADP (m/z ) the three peaks correspond to ADP, the in-source fragment of ATP and the in-source fragment of dgtp, which is an isomer of ATP. Pentose-5-phosphates co-elute, the hexosemonophosphates (Hex-P) are not baseline separated. For fructose-1,6-bisphophosphate (FBP), an insource fragment at the mass of the hexose-monophosphates can be observed, which would lead to a trueness bias in quantification without chromatographic separation. Pool_ISTD: For some compounds in the pooled sample more peaks than in the standard mix can be observed. Those are isomeric compounds which were not included in the standard mix demonstrating that chromatographic separation is essential for accurate quantification. Furthermore, standards are inevitable for retention time comparison in order to allow for correct identification of metabolites. S-16

17 Figure S-2. Typical scheme of measurements and MS methods included in a non-targeted workflow. S-17

18 Samples without ISTD Samples with ISTD Figure S-3. Heat maps of sensitive and resistant SW480 cancer cell samples prepared without and with 13 C yeast based internal standard. 153 and 129 compounds, respectively, with an adjusted p-value < 0.05 are shown in the heat maps. The concentration of each compound was scaled between 0 and 1. For both sample groups (without and with internal standard) similar results were achieved. S-18