Ion Mobility Derived Collision Cross Sections to Support Metabolomics Applications

Metabolomics is a rapidly evolving analytical approach in life and health sciences. The structural elucidation of the metabolites of interest remains a major analytical challenge in the metabolomics workflow. Here, we investigate the use of ion mobility as a tool to aid metabolite identification. Ion mobility allows for the measurement of the rotationally averaged collision cross-section (CCS), which gives information about the ionic shape of a molecule in the gas phase. We measured the CCSs of 125 common metabolites using traveling-wave ion mobility-mass spectrometry (TW-IM-MS). CCS measurements were highly reproducible on instruments located in three independent laboratories (RSD < 5% for 99%). We also determined the reproducibility of CCS measurements in various biological matrixes including urine, plasma, platelets, and red blood cells using ultra performance liquid chromatography (UPLC) coupled with TW-IM-MS. The mean RSD was < 2% for 97% of the CCS values, compared to 80% of retention times. Finally, as proof of concept, we used UPLC–TW-IM-MS to compare the cellular metabolome of epithelial and mesenchymal cells, an in vitro model used to study cancer development. Experimentally determined and computationally derived CCS values were used as orthogonal analytical parameters in combination with retention time and accurate mass information to confirm the identity of key metabolites potentially involved in cancer. Thus, our results indicate that adding CCS data to searchable databases and to routine metabolomics workflows will increase the identification confidence compared to traditional analytical approaches.

[1]  E. Want,et al.  HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. , 2011, Analytical chemistry.

[2]  B. Hammock,et al.  Mass spectrometry-based metabolomics. , 2007, Mass spectrometry reviews.

[3]  C. Creaser,et al.  Metabolic profiling of human saliva before and after induced physiological stress by ultra-high performance liquid chromatography–ion mobility–mass spectrometry , 2013, Metabolomics.

[4]  Royston Goodacre,et al.  Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. , 2011, Chemical Society reviews.

[5]  Joshua D. Knowles,et al.  Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry , 2011, Nature Protocols.

[6]  M. Eberlin,et al.  Separation of isomeric disaccharides by traveling wave ion mobility mass spectrometry using CO2 as drift gas. , 2012, Journal of mass spectrometry : JMS.

[7]  C. Robinson,et al.  Ion mobility mass spectrometry of peptide ions: effects of drift gas and calibration strategies. , 2012, Analytical chemistry.

[8]  P. Tso,et al.  Monitoring dynamic changes in lymph metabolome of fasting and fed rats by electrospray ionization-ion mobility mass spectrometry (ESI-IMMS). , 2009, Analytical chemistry.

[9]  E. Want,et al.  Global metabolic profiling procedures for urine using UPLC–MS , 2010, Nature Protocols.

[10]  Stefan Tenzer,et al.  Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics , 2013, Nature Methods.

[11]  Nigel W. Hardy,et al.  Proposed minimum reporting standards for chemical analysis , 2007, Metabolomics.

[12]  Stephen F Previs,et al.  Enhanced data-independent analysis of lipids using ion mobility-TOFMSE to unravel quantitative and qualitative information in human plasma. , 2013, Rapid communications in mass spectrometry : RCM.

[13]  A. Shvartsburg,et al.  An exact hard-spheres scattering model for the mobilities of polyatomic ions , 1996 .

[14]  Jody C. May,et al.  Lipid analysis and lipidomics by structurally selective ion mobility-mass spectrometry. , 2011, Biochimica et biophysica acta.

[15]  Ralf Tautenhahn,et al.  Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. , 2013, Analytical chemistry.

[16]  Ian D Wilson,et al.  An approach to enhancing coverage of the urinary metabonome using liquid chromatography-ion mobility-mass spectrometry. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[17]  Ronan M. T. Fleming,et al.  Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS) , 2011, Analytical and Bioanalytical Chemistry.

[18]  Larissa S Fenn,et al.  Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples , 2009, Analytical and bioanalytical chemistry.

[19]  Ines Thiele,et al.  Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies. , 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[20]  Keith Richardson,et al.  Structural characterization of drug-like compounds by ion mobility mass spectrometry: comparison of theoretical and experimentally derived nitrogen collision cross sections. , 2012, Analytical chemistry.

[21]  T. Hankemeier,et al.  Localization of Fatty Acyl and Double Bond Positions in Phosphatidylcholines Using a Dual Stage CID Fragmentation Coupled with Ion Mobility Mass Spectrometry , 2011, Journal of the American Society for Mass Spectrometry.

[22]  R. Abagyan,et al.  METLIN: A Metabolite Mass Spectral Database , 2005, Therapeutic drug monitoring.

[23]  Caroline H. Johnson,et al.  Monitoring metabolic responses to chemotherapy in single cells and tumors using nanostructure-initiator mass spectrometry (NIMS) imaging , 2013, Cancer & metabolism.

[24]  Julian L Griffin,et al.  A practical guide to metabolomic profiling as a discovery tool for human heart disease. , 2013, Journal of molecular and cellular cardiology.

[25]  M. Clench,et al.  MALDI-MS imaging of lipids in ex vivo human skin , 2011, Analytical and bioanalytical chemistry.

[26]  B. McManus,et al.  The Human Serum Metabolome , 2011, PloS one.

[27]  H. Hill,et al.  Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source. , 2010, Journal of mass spectrometry : JMS.

[28]  Martin F. Jarrold,et al.  Structural Information from Ion Mobility Measurements: Effects of the Long-Range Potential , 1996 .

[29]  Gary Siuzdak,et al.  Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database , 2013, Nature Protocols.

[30]  H. Hill,et al.  Metabolic Profiling of Human Blood by High Resolution Ion Mobility Mass Spectrometry (IM-MS). , 2010, International journal of mass spectrometry.

[31]  Steven Lai,et al.  MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures. , 2012, Analytical chemistry.

[32]  R. Foisner,et al.  The transcription factor ZEB1 (δEF1) promotes tumour cell dedifferentiation by repressing master regulators of epithelial polarity , 2007, Oncogene.

[33]  R. Caprioli,et al.  Structural characterization of phospholipids and peptides directly from tissue sections by MALDI traveling-wave ion mobility-mass spectrometry. , 2010, Analytical chemistry.

[34]  B. Chowdhry,et al.  Ion mobility spectrometry-mass spectrometry (IMS-MS) of small molecules: separating and assigning structures to ions. , 2013, Mass spectrometry reviews.

[35]  Markus Ringnér,et al.  Endothelial Induced EMT in Breast Epithelial Cells with Stem Cell Properties , 2011, PloS one.

[36]  B. Palsson,et al.  UPLC-UV-MSE analysis for quantification and identification of major carotenoid and chlorophyll species in algae , 2012, Analytical and Bioanalytical Chemistry.

[37]  G. Corso,et al.  Desorption electrospray ionization mass spectrometry analysis of lipids after two-dimensional high-performance thin-layer chromatography partial separation. , 2010, Analytical chemistry.

[38]  Prabha Dwivedi,et al.  Ion mobility-mass spectrometry. , 2008, Journal of mass spectrometry : JMS.

[39]  Laurent Gatto,et al.  Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. , 2013, Journal of proteome research.

[40]  G. Siuzdak,et al.  Innovation: Metabolomics: the apogee of the omics trilogy , 2012, Nature Reviews Molecular Cell Biology.

[41]  Yanli Wang,et al.  PubChem: Integrated Platform of Small Molecules and Biological Activities , 2008 .

[42]  Johannes P C Vissers,et al.  Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples , 2012, Analytical and Bioanalytical Chemistry.

[43]  P. Sadler,et al.  Use of ion mobility mass spectrometry and a collision cross-section algorithm to study an organometallic ruthenium anticancer complex and its adducts with a DNA oligonucleotide. , 2009, Rapid communications in mass spectrometry : RCM.

[44]  T. Hankemeier,et al.  Comprehensive LC-MS E lipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients. , 2010, Journal of proteome research.

[45]  David S. Wishart,et al.  HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..

[46]  Héctor Peinado,et al.  Snail, Zeb and bHLH factors in tumour progression: an alliance against the epithelial phenotype? , 2007, Nature Reviews Cancer.

[47]  Niki S. C. Wong,et al.  Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture. , 2009, Rapid communications in mass spectrometry : RCM.