Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids - Building a Spectral Library of Recurrent Spectra for Urine Analysis.

A large fraction of ions observed in electrospray liquid chromatography-mass spectrometry (LC-ESI-MS) experiments of biological samples remain unidentified. One of the main reasons for this is that spectral libraries of pure compounds fail to account for the complexity of the metabolite profiling of complex materials. Recently, the NIST Mass Spectrometry Data Center has been developing a novel type of searchable mass spectral library that includes all recurrent unidentified spectra found in the sample profile. These libraries, in conjunction with the NIST tandem mass spectral library, allow analysts to explore most of the chemical space accessible to LC-MS analysis. In this work, we demonstrate how these libraries can provide a reliable fingerprint of the material by applying them to a variety of urine samples, including an extremely altered urine from cancer patients undergoing total body irradiation. The same workflow is applicable to any other biological fluid. The selected class of acylcarnitines is examined in detail and derived libraries and related software are freely available. They are intended to serve as online resources for continuing community review and improvement.

[1]  S. Stein,et al.  Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures. , 2016, Rapid communications in mass spectrometry : RCM.

[2]  S. Stein,et al.  Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra , 2017, Journal of The American Society for Mass Spectrometry.

[3]  Caroline H. Johnson,et al.  Metabolomics: beyond biomarkers and towards mechanisms , 2016, Nature Reviews Molecular Cell Biology.

[4]  Liang Li,et al.  Ultra-high performance liquid chromatography tandem mass spectrometry for comprehensive analysis of urinary acylcarnitines. , 2011, Analytica chimica acta.

[5]  Adam P. Arkin,et al.  Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses , 2014, Analytical chemistry.

[6]  Dmitrii V. Tchekhovskoi,et al.  Combining Fragment-Ion and Neutral-Loss Matching during Mass Spectral Library Searching: A New General Purpose Algorithm Applicable to Illicit Drug Identification. , 2017, Analytical chemistry.

[7]  Emma L. Schymanski,et al.  Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods. , 2015, Journal of chromatography. A.

[8]  Adrian D Hegeman,et al.  A study on retention "projection" as a supplementary means for compound identification by liquid chromatography-mass spectrometry capable of predicting retention with different gradients, flow rates, and instruments. , 2011, Journal of chromatography. A.

[9]  Ruedi Aebersold,et al.  Building consensus spectral libraries for peptide identification in proteomics , 2008, Nature Methods.

[10]  Meghan C. Burke,et al.  The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics. , 2017, Journal of proteome research.

[11]  P. Boswell,et al.  Calculation of retention time tolerance windows with absolute confidence from shared liquid chromatographic retention data. , 2015, Journal of chromatography. A.

[12]  Oliver Fiehn,et al.  Mass Spectral Feature List Optimizer (MS-FLO): A Tool To Minimize False Positive Peak Reports in Untargeted Liquid Chromatography-Mass Spectroscopy (LC-MS) Data Processing. , 2017, Analytical chemistry.

[13]  S. Stein,et al.  Estimating probabilities of correct identification from results of mass spectral library searches , 1994, Journal of the American Society for Mass Spectrometry.

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

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

[16]  Liang Li,et al.  A method for comprehensive analysis of urinary acylglycines by using ultra-performance liquid chromatography quadrupole linear ion trap mass spectrometry , 2010, Journal of the American Society for Mass Spectrometry.

[17]  Ying Zhang,et al.  HMDB: the Human Metabolome Database , 2007, Nucleic Acids Res..

[18]  Stephen E. Stein,et al.  Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources. , 2013, Analytical chemistry.

[19]  Xinjian Yan,et al.  In-Depth Characterization and Spectral Library Building of Glycopeptides in the Tryptic Digest of a Monoclonal Antibody Using 1D and 2D LC-MS/MS. , 2016, Journal of proteome research.

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

[21]  Stephen E Stein,et al.  Quality control for building libraries from electrospray ionization tandem mass spectra. , 2014, Analytical chemistry.

[22]  Yuri A. Mirokhin,et al.  Creation of libraries of recurring mass spectra from large data sets assisted by a dual-column workflow. , 2014, Analytical chemistry.

[23]  Stephen Stein,et al.  Mass spectral reference libraries: an ever-expanding resource for chemical identification. , 2012, Analytical chemistry.

[24]  Xin Lu,et al.  Strategy for Comprehensive Identification of Acylcarnitines Based on Liquid Chromatography-High-Resolution Mass Spectrometry. , 2018, Analytical chemistry.

[25]  Jian Ji,et al.  Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics , 2018, Metabolites.

[26]  M. Barrett,et al.  Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. , 2012, Analytical chemistry.

[27]  J. Lindon,et al.  Systems biology: Metabonomics , 2008, Nature.

[28]  D. Wishart.  Advances in metabolite identification. , 2011, Bioanalysis.

[29]  Christophe Junot,et al.  Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. , 2012, Analytical chemistry.

[30]  G. Siuzdak,et al.  XCMS Online: a web-based platform to process untargeted metabolomic data. , 2012, Analytical chemistry.

[31]  Gary J Patti,et al.  Systems-Level Annotation of a Metabolomics Data Set Reduces 25 000 Features to Fewer than 1000 Unique Metabolites. , 2017, Analytical chemistry.