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GC–MS-Based Urinary Organic Acid Profiling Reveals Multiple

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GC–MS-Based Urinary Organic Acid Profiling Reveals Multiple GC–MS-based urinary organic acid profiling reveals multiple dysregulated metabolic pathways following experimental acute alcohol consumption — Supplementary Information Cindy Irwin, Lodewyk J. Mienie, Ron A. Wevers, Shayne Mason, Johan A. Westerhuis, Mari van Reenen, Carolus J. Reinecke CONTENTS: 1. Sample preparation, organic acid extraction and GC–MS analysis 2. Data used for the alcohol intervention study: Supplementary Table S1 — An excerpt of the data used for the alcohol intervention. The full data set is given as a separate file in Excel format. 3. Details of the 172 identified features: Supplementary Table S2 — Separation and classification details of the 172 identified features 4. Statistical Methods & Additional Results 4.1 Power 4.2 Data pre-processing 4.3 Statistical methods for variable selection 4.4 Correlation analysis 4.5 Statistical methods for repeated measures data 4.6 The vehicle/hippuric acid effect 4.7 Statistical software 5. Example of informed consent form 6. References 1 1. Sample preparation, organic acid extraction and GC–MS analysis 1.1 Extraction and derivatization of organic acids The 5 mL aliquots used for the analyses were thawed at room temperature and vortexed before use. The volume of urine used for the organic acid analysis was based on the creatinine value of each of the samples: • For creatinine values higher than 100 mg% use 0.5 ml urine • For creatinine values less than 100 mg% but higher than 5 mg% use 0.5 ml urine • For creatinine values less than 5 mg% but higher than 2 mg% use 2 ml urine • For creatinine values less than 2 mg% use 3 ml urine. The correct volume of urine was transferred to a 6 ml Kimax tube and 6 drops of 5M HCl was added to adjust the pH of the urine to below 2. The volume of internal standard (IS) added was determined by multiplying the creatinine value (in mg%) with five times the volume of urine used. A mix of malonic acid (RT ~14 minutes) and 4-phenylbutyric acid (RT ~20 minutes) was used as internal standard. The IS was prepared by dissolving 52.5 mg of each in 50 ml milli-Q water. The solution was sonicated for 30 minutes to ensure that all compounds were properly dissolved. 4-Phenylbutyric acid was used owing to its absence in normal urine and in known pathological conditions. In addition, it elutes almost in the middle of the organic acid profile and theoretically co-elutes with very few, if any, other organic acids. Malonic acid was added as a second IS reference peak in the GC chromatogram. The first extraction was done by adding 6 ml of ethylacetate to each of the samples. The tubes were capped and checked for leakage by inverting the tubes before being mixed on a rotary wheel for 30 minutes. The samples were then centrifuged at 3000 rpm for 3 minutes and the organic phase (top phase) was aspirated into a clean 6 ml Kimax tube. The second extraction was done by adding 3 ml of diethylether to the aqueous phase (lower phase) and the tubes were once again capped and checked for leakage. The samples were then mixed on the rotary wheel for 10 minutes and centrifuged at 3000 rpm for 3 minutes. The organic phase was aspirated and added to the ethylacetate phase and the aqueous phase was discarded. Approximately 2 ml of anhydrous sodium sulphate (Na2SO4) was added to each sample and the tubes were capped and vortexed to mix. Proper dispersion of the Na2SO4 ensures that all the water is removed from the organic phase. The samples were then centrifuged at 3000 rpm for 1 minute and the organic phase was decanted into a clean 3 ml Kimax tube. The samples were finally evaporated 2 to dryness in a heating block at 37ºC under nitrogen gas for approximately 45 minutes. Using a Hamilton syringe, the derivatization reagents O- bis(trimethylsilyl)trifluoroacetamide (BSTFA), trimethylchlorosilane (TMCS) and pyridine were added to the dried samples. The volume of BSTFA added was determined by multiplying the creatinine value (in mg%) with three times the volume of urine used. The volume of TMCS and pyridine added was determined by multiplying the creatinine value (in mg%) with 0.6 times the volume of urine used. The tubes were capped and incubated at 70ºC for 45 minutes. The derivatized samples were then transferred to 1.5 ml GC–MS vials with inserts, capped, and placed in the GC–MS autosampler for GC–MS analysis. Blank (hexane), QC and repeat samples were included in the injection sequence, as described in the main text. The internal standards 4-phenylbutyric acid and malonic acid as well as the anhydrous Na2SO4 were purchased from BDH. Ethylacetate and dietylether were obtained from Merck Chemicals. The derivatization reagents O- bis(trimethylsilyl)trifluoroacetamide (BSTFA), trimethylchlorosilane (TMCS) and pyridine were purchased from Sigma Chemical Company. 1.2 GC–MS analysis An Agilent GC–MS system was used in this study and consisted of a model 7890A gas chromatograph, a model 5975C mass selective detector, a Hewlett Packard 5970C quadrupole mass spectrometer and Agilent Chemstation. GC separation was achieved on a WCOT fused silica capillary column [30 m x 0.32 mm (i.d.)] coated with SE30 CB, film thickness 0.30 µm (Machery Nagel). Samples were introduced into the column via a splitless injector at 280°C. The initial oven temperature was kept at 60°C for 2 minutes and then programmed to rise 6°C/min to a final temperature of 280°C. This temperature was maintained for 5 minutes. Helium was used as carrier gas at a pressure of 60 kPa and at a constant flow rate of 1 ml/min. The column was inserted directly into the ion source with an interface temperature of 280°C. The mass spectra of all GC peaks were generated by a mass spectrometer operated in the electron impact (EI) mode, with electron energy of 70 eV. The MS source and quadrupole temperatures were 250°C and 150°C respectively. 1.3 Qualitative analysis of metabolites in QC samples (metabolite identification) After GC separation, each peak at an indicated RT was analysed in EI mode in order to investigate the fragmentation pattern of each compound. The m/z values selected for feature identification were either the base peak ion or one of the more abundant characteristic fragment ions. 3 Deconvolution and data analyses were conducted using AMDIS software (Version 2.71) linked to NIST Mass Spectral Search Program for the NIST/EPA/NIH Mass Spectral Library (Version 2.0F, built Oct. 8, 2008). Where authentic standards were available, their respective response factors were used, and for those compounds where no authentic standards were available, a response factor of 1 was assumed. The analytical setting of the AMDIS software was as follows: minimum factor – 60%, threshold – “off”, Scan Direction – “high to low”, and type of analysis – ‘‘Use of an internal standard for RI’’. The deconvolution settings were: component width – 12, adjacent peak subtraction – 1, resolution – medium, sensitivity – low, and shape requirements – low. The first hit of identified compounds and integrated area of the peaks were exported to Microsoft Excel. 4 2. Data used for the alcohol intervention study Supplementary Table S1 shows an excerpt of the data used for the alcohol intervention study (the full data set is given as a separate file in Excel format). Supplementary Table S1 An excerpt of the data used for the alcohol intervention study 1 2 3 4 5 6 7 8 9 ... 119 120 Batch Time Glyoxylic- 1,2-Dihydr1,2-DihydrLactic-acidHexanoic- 2-HydroxyGlycolic-a Oxalic-acid2-Hydroxy OctadecanEicosanoic 1 0 0.181 0.825 6.424 8.188 0.198 8.959 7.566 2.127 3.362 1.918 0.030 1 1 0.004 0.863 0.586 6.011 0.194 7.354 3.867 1.043 1.983 1.086 0.035 1 2 0.000 3.348 23.576 73.513 1.017 37.804 11.328 1.472 5.640 0.125 0.014 1 3 0.004 1.715 2.798 14.757 0.219 11.194 1.895 1.719 2.231 5.534 0.057 1 4 0.004 1.544 3.411 16.042 0.525 12.337 3.209 0.507 1.175 3.472 0.012 2 0 0.380 6.090 3.299 10.635 0.213 13.432 5.542 1.656 2.546 1.380 0.006 2 1 0.577 6.087 5.495 31.238 0.207 51.693 12.475 3.070 8.968 7.982 0.015 2 2 2.431 10.583 6.763 19.799 0.040 24.936 3.507 4.564 4.293 16.834 0.064 2 3 0.165 6.804 2.695 8.701 0.031 13.519 1.426 2.046 2.385 3.687 0.016 2 4 0.392 5.628 0.717 11.225 0.016 22.899 4.268 1.535 3.195 2.861 0.018 3 0 0.057 6.082 1.117 5.128 0.017 7.560 2.057 0.249 1.832 0.587 0.002 3 1 0.263 6.834 1.312 6.123 0.005 11.984 2.682 0.708 2.046 0.579 0.008 3 2 0.074 7.555 3.482 11.516 0.041 10.888 1.091 0.437 0.051 4.187 0.009 3 3 0.009 7.164 0.762 2.578 0.011 4.549 0.295 0.566 0.173 1.701 0.000 3 4 0.142 7.788 2.470 7.058 0.023 10.243 1.352 2.480 0.027 5.931 0.012 4 0 1.260 5.450 14.115 13.301 0.008 19.194 3.939 1.727 3.589 1.668 0.004 4 1 0.786 6.998 4.797 7.539 0.005 11.048 1.319 0.234 0.600 2.648 0.019 4 2 5.384 8.793 7.255 22.786 0.074 34.901 1.477 1.401 2.113 20.830 1.148 4 3 0.452 6.635 2.458 3.065 0.002 6.041 0.249 0.109 0.308 1.754 0.022 4 4 10.047 5.740 14.662 20.996 0.176 32.883 3.912 0.401 2.180 5.673 0.038 5 0 0.190 5.314 1.160 13.823 0.059 18.080 6.760 1.977 3.394 1.605 0.040 5 1 0.348 5.662 2.762 16.770 0.036 20.638 8.213 2.311 4.511 3.696 0.830 5 2 0.004 13.903 16.727 58.947 0.143 44.790 9.347 11.309 9.393 20.223 0.187 5 3 0.041 9.541 9.511 52.548 0.150 29.792 5.183 1.630 3.260 21.992 0.056 5 4 3.452 6.023 1.227 12.596 0.041 19.668 4.064 1.310 1.860 5.391 0.045 5 3.
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