Common cases of improper lipid annotation using high-resolution tandem mass spectrometry data and corresponding limitations in biological interpretation.

a University of Florida, Department of Chemistry, 214 Leigh Hall, Gainesville, FL 32611, United States b National Institute of Standards and Technology, Chemical Science Division, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States c University of Florida, Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, 1600 SW Archer Rd, Gainesville, FL 32603, United States

[1]  M. Mann,et al.  Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap*S , 2005, Molecular & Cellular Proteomics.

[2]  Masanori Arita,et al.  MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis , 2015, Nature Methods.

[3]  Guan-Yuan Chen,et al.  Off-line mixed-mode liquid chromatography coupled with reversed phase high performance liquid chromatography-high resolution mass spectrometry to improve coverage in lipidomics analysis. , 2017, Analytica chimica acta.

[4]  Yehia M. Ibrahim,et al.  Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations. , 2015, Analytical chemistry.

[5]  R. Murphy,et al.  Electrospray ionization tandem mass spectrometry of glycerophosphoethanolamine plasmalogen phospholipids , 2004, Journal of the American Society for Mass Spectrometry.

[6]  A. Plückthun,et al.  Acyl and phosphoryl migration in lysophospholipids: importance in phospholipid synthesis and phospholipase specificity. , 1982, Biochemistry.

[7]  Eoin Fahy,et al.  A comprehensive classification system for lipids11 The evaluation of this manuscript was handled by the former Editor-in-Chief Trudy Forte. Published, JLR Papers in Press, February 16, 2005. DOI 10.1194/jlr.E400004-JLR200 , 2005, Journal of Lipid Research.

[8]  W. Lehmann,et al.  Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass spectrometry. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Junli Feng,et al.  Zwitterionic hydrophilic interaction solid-phase extraction and multi-dimensional mass spectrometry for shotgun lipidomic study of Hypophthalmichthys nobilis. , 2017, Food chemistry.

[10]  Markus R. Wenk,et al.  The emerging field of lipidomics , 2005 .

[11]  G. Dakubo Mitochondrial Control of Apoptosis and Cancer , 2010 .

[12]  Matej Oresic,et al.  Informatics and computational strategies for the study of lipids. , 2008, Molecular bioSystems.

[13]  John A. Bowden,et al.  Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation , 2017, Journal of The American Society for Mass Spectrometry.

[14]  Christer S. Ejsing,et al.  Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. , 2006, Analytical chemistry.

[15]  Christer S. Ejsing,et al.  Identification and Annotation of Lipid Species in Metabolomics Studies Need Improvement. , 2015, Clinical chemistry.

[16]  Dan Ventura,et al.  Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view , 2014, BMC Bioinformatics.

[17]  David W. Russell,et al.  LMSD: LIPID MAPS structure database , 2006, Nucleic Acids Res..

[18]  Ronald J Moore,et al.  Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. , 2016, The Analyst.

[19]  P. Axelsen,et al.  Quantitative analysis of phospholipids containing arachidonate and docosahexaenoate chains in microdissected regions of mouse brain[S] , 2010, Journal of Lipid Research.

[20]  H. Naegeli,et al.  Altered plasma lipidome profile of dairy cows with fatty liver disease. , 2017, Research in veterinary science.

[21]  M. Portillo,et al.  Conjugated linoleic acid isomers: Differences in metabolism and biological effects , 2009, BioFactors.

[22]  A. Shevchenko,et al.  Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. , 2007, Analytical chemistry.

[23]  Juan Antonio Vizcaíno,et al.  Shorthand notation for lipid structures derived from mass spectrometry , 2013, Journal of Lipid Research.

[24]  M.Alan Chester,et al.  IUPAC-IUB joint commission on biochemical nomenclature (JCBN) nomenclature of glycolipids: Recommendations 1997 , 1999 .

[25]  A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics. , 2006, Rapid communications in mass spectrometry : RCM.

[26]  G. van Meer,et al.  Cellular lipidomics , 2005, The EMBO journal.

[27]  A. Llorente,et al.  Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers. , 2017, European journal of cancer.

[28]  Kai Simons,et al.  Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. , 2006, Analytical chemistry.

[29]  Ronald J Moore,et al.  Application of the accurate mass and time tag approach in studies of the human blood lipidome. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[30]  Jeremy P. Koelmel,et al.  LipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics , 2017, Journal of The American Society for Mass Spectrometry.

[31]  Christer S. Ejsing,et al.  Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation Published, JLR Papers in Press, August 16, 2003. DOI 10.1194/jlr.D300020-JLR200 , 2003, Journal of Lipid Research.

[32]  S. Blanksby,et al.  Analysis of unsaturated lipids by ozone-induced dissociation. , 2011, Biochimica et biophysica acta.

[33]  Stefan R Bornstein,et al.  Shotgun lipidomics on high resolution mass spectrometers. , 2011, Cold Spring Harbor perspectives in biology.

[34]  Johannes Griss,et al.  Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification. , 2016, Analytical chemistry.

[35]  Gang Chen,et al.  Lipidomics profiling of goat milk, soymilk and bovine milk by UPLC-Q-Exactive Orbitrap Mass Spectrometry. , 2017, Food chemistry.

[36]  Oliver Fiehn,et al.  LipidBlast - in-silico tandem mass spectrometry database for lipid identification , 2013, Nature Methods.

[37]  Christer S. Ejsing,et al.  Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP deficient mice. , 2017, Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids.

[38]  K. Erickson,et al.  Conjugated linoleic acid isomers and cancer. , 2007, The Journal of nutrition.

[39]  Robert D. Clark,et al.  SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries , 2008, J. Chem. Inf. Model..

[40]  P. Calder,et al.  Opposing effects of cis-9,trans-11 and trans-10,cis-12 conjugated linoleic acid on blood lipids in healthy humans. , 2004, The American journal of clinical nutrition.

[41]  A. Makarov,et al.  Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. , 2006, Analytical chemistry.

[42]  C. Burant,et al.  Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. , 2011, Analytical chemistry.

[43]  B. Lutz,et al.  Targeting brain and peripheral plasticity of the lipidome in acute kainic acid-induced epileptic seizures in mice via quantitative mass spectrometry. , 2017, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[44]  Rainer Bischoff,et al.  Stability of energy metabolites—An often overlooked issue in metabolomics studies: A review , 2015, Electrophoresis.

[45]  Takashi Sugimura,et al.  Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase , 2007, The EMBO journal.

[46]  Stephen R. Heller,et al.  InChI, the IUPAC International Chemical Identifier , 2015, Journal of Cheminformatics.

[47]  Ying Liu,et al.  Elevation of sulfatides in ovarian cancer: An integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry , 2010, Molecular Cancer.