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Metabolomics using SWATH™ Acquisition Brigitte Simons, Ph.D. AB SCIEX, Toronto, CAN
2 © 2012 AB SCIEX Non-alcoholic fatty liver disease (NAFLD) includes the manifestation of non-alcohol steatohepatitis (NASH) and hepatic steatosis (SS) PC/PE ratio can provide monitoring of the integrity of hepatocyte cell membranes and an important marker in NAFLD pathogenesis Fatty acid profile can provide insights into hepatic enzymatic activity and fat metabolism Puri, P., Wiest, M.M., Cheung, O., Mirshahi, F., Sargeant, C., Min, H.K., Contos, M.J., Sterling, R.K., Fuchs, M., Zhou, H., et al The plasma lipidomic signature of nonalcoholic steatohepatitis. Hepatology 50: Non-Alcoholic Fatty Liver Disease Lipid Profiling of Liver Tissue Research Study
3 © 2012 AB SCIEX NAFLD and Lipid Analysis Changes in FA composition has been shown in NAFLD vs. controls –Lower n-6 and n-3 PUFA, n6/n3 ratio higher –Due to oxidative stress, altered desaturase activity (Allard et al J Hepatol; Puri et al Hepatol; Araya et al. Clin Sci 2004) Liver: Lower amount of PC associated with steatosis, but lower PC/PE ratio with inflammation (Li et al. Cell Metab 2006) Fatty Liver in the ob/ob mouse model: –Decreased number of correlations among lipid species, showing decreased co-regulation –Short, medium chain TAG and ceramides (Yetukuri et al BMC Syst Biol) Adipose tissue in adipose women with/without fatty liver: –154 lipid species significantly altered –Especially TAG, particularly long chain, and ceramides, specifically Cer(d18:1/24:1) (Kolak et al Diabetes)
4 © 2012 AB SCIEX Study Design Cross-sectional study Including patients with NAFLD (n=28), chronic Hepatitis C (n=13) and healthy living liver donors as controls (n=9) Lipidomic analysis (including PC/PE ratio) in liver tissue Other measurements: Demographics, anthropometry, dietary intake
5 © 2012 AB SCIEX Molecular Lipidomics Platforms H.R. Jung et al. (2011) Biochimica et Biophysica Acta; 1811; μl liver homogenate (containing 0.15 – 2.49 mg of liver tissue) mixed with 4 ml of chloroform: methanol (2:1) (v/v) with 0.02% butylated hydroxytoluene as antioxidant 1 part aqueous (sample extract), 2 parts MeOH, 0.9 part CH 2 Cl 2 ; Add 1 part H 2 O, 1 part CH 2 Cl 2, 10 mM LiCl; Vortex & spin - take lower layer Lipids were diluted with chloroform to 0.08 mg/mL final concentration and diheptadecanoyl PC and PE were added as internal standards at 0.15 μmol/L final concentration. Samples were further diluted 1:1 with chloroform:methanol (1:2, v/v) with 5 mM ammonium acetate and analyzed by nanoelectrospray infusion tandem mass spectrometry
6 © 2012 AB SCIEX Shotgun Lipidomics of Human NAFLD Liver Tissue Lipid Profiling of Complex Extracts by Direct Infusion Total lipid extracts Total lipid extracts Multiple Precursor Ion Scanning Multiple Precursor Ion Scanning Automated sample infusion Automated sample infusion Lipid identification and quantification Lipid identification and quantification Result reporting QTRAP® 5500 System Advion NanoMate TriVersa LipidView™ Software Liver Biopsies Infusion-quantitation Ekroos, K et al., Methods in Pharmacology and Toxicology: Biomarker Methods in Drug Discovery and Development, Humana Press 2008 Ståhlman, M et al. High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry, J Chrom B 2009 Arendt et al., Non-alcoholic fatty liver disease is associated with lower hepatic and erythrocyte ratios of phosphatidylcholine to phosphatidylethanolamine, Applied Physiology, Nutrition and Metabolism, Oct Clinical lipid biopsies: healthy controls = 9 samples ; NAFLD = 28 samples; CHC = 13 < 1 min 3.1 min per sample 30 min analysis time >30 min
7 © 2012 AB SCIEX Multiplexed Precursor Ion Scanning [XPIS] Technical benefits of Multiplexed Precursor Ion Scanning [XPIS] for lipid quantitation –All desired lipid classes and their internal standards are detected in parallel looped acquisitions Spectra are directly interpretable and can be overlaid for comprehensive lipid characterization Transitioning from PIS to MRM can be easily achieved for highly multiplexed and robust relative lipid quantitation Scan Precursors Select lipid-specific fragment CAD Q1LINAC Q2 Q3 Full range Q1 scan m/z Exp 1 m/z Exp 2 m/z Exp 3 Ekroos, K et al. Analytical Chemistry 2002.
8 © 2012 AB SCIEX Technical Benefits of Multiplexing PIS Precursor Fragmentation Profiles Are Overlaid for Lipid Species Characterization and Quantitation PE 38:4
9 © 2012 AB SCIEX Hepatic PC/PE Ratios Calculated Individually Per Patient by IS Corrected Peak Area Ratios Mean = 3.27 ± 0.60 Mean = 1.25 ± 0.79 Arendt et al., Non-alcoholic fatty liver disease is associated with lower hepatic and erythrocyte ratios of phosphatidylcholine to phosphatidylethanolamine, Applied Physiology, Nutrition and Metabolism, Oct 2012.
10 © 2012 AB SCIEX Hepatic PC Measured by IS Corrected Peak Area Ratios
11 © 2012 AB SCIEX Hepatic PE Measured by IS Corrected Peak Area Ratios Arendt et al., Non-alcoholic fatty liver disease is associated with lower hepatic and erythrocyte ratios of phosphatidylcholine to phosphatidylethanolamine, Applied Physiology, Nutrition and Metabolism, Oct 2012.
12 © 2012 AB SCIEX RBC lipid extract Liver Tissue Lipid Extract Multiplexed Precursor Ion Scanning on the QTRAP ® 5500 System Enabling Up to 60 Precursor Ion Experiments Scanned in Parallel in Both Polarities
13 © 2011 AB SCIEX AB Sciex Confidential ASMS 2012 – AB Sciex User Meeting © 2012 AB SCIEX ASMS 2012 – AB Sciex User Meeting The advent of High Resolution MS in metabolomics… –Improved the quality and confidence in the answers obtained –By providing elemental formula confirmation, isotope pattern match –Accurate mass fragment information for improved structure interpretation –Enable simultaneous Qualitative and Quantitative data collection –Stream lined a generic data collection practice of MS and NOW MS/MS simultaneously ….MS/MS data simultaneously collected is advantageous yet reproducibility and remains challenging –Targeted MS/MS data collection is still the best in terms of selectivity –But not realistic in discovery mode –Automated data collection using IDA imposes prioritization –Mass defect filters, isotope filters, background subtraction… –Very effective, but each compound requires its own MS/MS trigger point –MS all (or MS e ) can make acquisition more generic –But this approach heavily relies on LC separation capability –Related compounds (drugs, inhibitors, activators) can easily be handled by UPLC –But endogenous matrix species can increase complexity beyond UPLC’s capability –Multiple co-eluting species can complicate the MSMS information if no precursor selection occurs
14 © 2012 AB SCIEX SWATH™ Acquisition What is it? MS/MS ALL –A unique data-independent workflow enabled by TripleTOF ® system technology that acquires high resolution quantifiable MS/MS data for all detectable analytes in a complex sample, in single run How does it work? SWATH™ Acquisition –Use of a wide isolation window stepping across a mass range, collecting high resolution MS/MS spectra in a chromatographic time scale –Data processing via post-acquisition fragment ion XICs at high resolution for quantitation of thousands of peptides and confirmation of identity
15 © 2012 AB SCIEX Comprehensive Quantitation Wide Q1 isolation (25 Da) TripleTOF speed allows full coverage of mass range High resolution XIC data for all fragment ions cycle time ~ 2.5 s retention time SWATH = 25 Da m/z
16 © 2012 AB SCIEX Metabolite Fishing…. Acylcarnitine Profiling in CSF Extracts Accurate mass XICs of all 48 targeted acylcarnitine species XIC quant Summary Table
17 © 2012 AB SCIEX Acylcarnitine Quant Summary with Confirmation SWATH for Targeted Screening Acylcarnitine C18 C 25 H 49 NO 4 MS/MS for confirmation
18 © 2012 AB SCIEX Acylcarnitine Profiling in MeOH CSF & Plasma Extracts MarkerView Software for PCA and Multivariate Statistical Analyses Plasma CSF
19 © 2012 AB SCIEX Comprehensive Quant/Qual Metabolomics SWATH™ Acquisition Quantitative MRM Quantitation of Every Metabolite IDA for Metabolite Screening Qualitative Feature statistical alignment XIC Manager Fast targeted or untargeted XIC generation XIC Manager Fast targeted or untargeted XIC generation unknown compound identification
20 © 2012 AB SCIEX Metabolite Identification and Confirmation Against Accurate Mass Libraries Mass Accuracy Isotope Pattern Library high and Purity Score Retention Time
21 © 2012 AB SCIEX Data Independent SWATH MS for Lipidomics Full MS/MS Archive of Every Compound in the Sample Collection of High resolution MS/MS
22 © 2012 AB SCIEX cycle time ~ 3.3 min acquisition time Q1 mass filter width = 0.7 Da MS/MS ALL Acquisition Method Set-up (m/z)
23 © 2012 AB SCIEX Diacyl phospholipids Ether-linked/plasmalogen phospholipids Storage lipids *Data processed by LipidView™ Software 450 Human Plasma Lipids Profiled in 6 min using SWATH™ Acquisition
24 © 2012 AB SCIEX PE 18:0/20:4 PI 18:0/20:4 Infusion SWATH of Human Plasma Total Ion Map
25 © 2012 AB SCIEX Sample infusion Make-up Flow Calibrant delivery (APCI) ESI Infusion SWATH Configuration Method Set-up 1. Bligh-Dyer extraction with surrogate standard cocktail 2. Infuse sample (µM) in 4:2:1 IPA/CHCl 3 /MeOH (10mM NH 4 OaC) 3. Positive and Negative TOF MS and MS/MS ALL acquired sequentially in 3.3 minutes 4. Data analysis, quantitation, results interpretation Shotgun Lipidomics by Sequential Precursor Ion Fragmentation on a Hybrid Quadrupole Time-of-Flight Mass Spectrometer Simons B, Kauhanen D, Sylvänne T, Tarasov K, Duchoslav E, Ekroos K. Metabolites 2012, 2,
26 © 2012 AB SCIEX + MS/MS ALL MS/MS for Lipid Identification Intensity, cps - MS/MS ALL measured mass: [C 45 H 80 NO 8 P+H] + theoretical mass: mass error: 0.5 ppm measured mass: [C 46 H 84 NO 7 P+H] + theoretical mass: mass error: 0.6 ppm
27 © 2012 AB SCIEX Definitive Lipid Molecular Species Identification Only MS/MS pos and neg spectra combined provide the distinguishing fragments to identify PC 37:5, PC O-38:5, & PE 40:5
28 © 2012 AB SCIEX Precursor Ion scanning on QTRAP ® 5500 System LC-MRM on 4000 QTRAP ® System MS/MS ALL on TripleTOF ® System Peak intensity ratio of m/z / m/z Concentration, µM R 2 > Lipid Relative Quantification of CER d17:0/17:0 Corrected by CER d17:1/18:0 IS Quantitative Performance of a QqQ Instrument Shotgun Lipidomics by Sequential Precursor Ion Fragmentation on a Hybrid Quadrupole Time-of-Flight Mass Spectrometer Simons B, Kauhanen D, Sylvänne T, Tarasov K, Duchoslav E, Ekroos K. Metabolites 2012, 2,
29 © 2012 AB SCIEX concentration, µM TAG Lipid Profiling in Plasma +MS TAG 52:3 Group A Group B +MS/MS of TAG 52:3 NL 18:0 Group B Group A
30 © 2012 AB SCIEX LC MRM SWATH [MS/MS ALL ]
31 © 2012 AB SCIEX Acknowledgments University of Toronto & Toronto General Hospital –Johanne Allard –Bianca Arendt –Elaheh Aghdassi –David Ma VTT Technical Research Institute of Finland –Kari Raino Zora Biosciences, Fi –Kaisa Koistinen –Kim Ekroos AB SCIEX –Ron Brejak –Paul Baker –Dan Puscasu –Eva Duchoslav –Gary Impey
32 © 2012 AB SCIEX Questions and Answers
33 © 2012 AB SCIEX Trademarks/Licensing For Research Use Only. Not for use in diagnostic procedures. The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners. AB SCIEX™ is being used under license. © 2012 AB SCIEX.
34 © 2012 AB SCIEX TripleTOF ® System Publically Available Application Data and Publications Lipidomics and Metabolite Identification
35 © 2012 AB SCIEX Conclusion MS/MS ALL with SWATH™ Acquisition is a novel data-independent acquisition strategy that provides: –Comprehensive high resolution MS/MS data for all detectable ions –High quality quantitation similar to MRM with no method development –Easy and retrospective data interrogation SWATH Acquisition is ideal for quantifying extremely large numbers of peptides in complex samples –Biomarker verification –Network biology SWATH data can be processed by PeakView and MarkerView or extracted for use with 3 rd party informatics tools
Data independent acquisition methods for metabolomics Stephen Tate, Ron Bonner AB SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8 Canada A high resolution.
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Finding the unexpected in SWATH™ Data Sets – Implications for Protein Quantification Ron Bonner; Stephen Tate; Adam Lau AB SCIEX, 71 Four Valley Drive,
Infusion MS/MS ALL Workflow; TripleTOF™ 5600 System for Lipid Analysis Brigitte Simons, Sr. Applications and Sales Specialist at AB SCIEX.
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Workflows to set up acquisition methods for scheduled sMRM-HR on the TripleTOF 5600 Start from a data dependent acquisition (DDA) Perform data base search.
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UAB Metabolomics Symposium December 12, 2012 Christopher B. Newgard, Ph.D. Sarah W. Stedman Nutrition and Metabolism Center Department of Pharmacology.
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