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

Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids

Volumn 1862, Issue 8, 2017, Pages 766-770

  Koelmel, Jeremy P ^a   Ulmer, Candice Z ^b   Jones, Christina M ^b   Yost, Richard A ^a,c   Bowden, John A ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID;

BIOLOGY; DEGRADATION; HUMAN; ISOMER; LIPIDOMICS; MASS; MEDICAL LITERATURE; MOLECULAR BIOLOGY; NOTE; PRACTICE GUIDELINE; PRIORITY JOURNAL; TANDEM MASS SPECTROMETRY; CHEMISTRY; FACTUAL DATABASE; INFORMATION PROCESSING; PROCEDURES;

DATA CURATION; DATABASES, FACTUAL; HUMANS; LIPIDS; TANDEM MASS SPECTROMETRY;

EID: 85014565310     PISSN: 13881981     EISSN: 18792618     Source Type: Journal    
DOI: 10.1016/j.bbalip.2017.02.016     Document Type: Note

References (51)

1. Yetukuri, L., Ekroos, K., Vidal-Puig, A., Oresic, M., Informatics and computational strategies for the study of lipids. Mol. BioSyst. 4 (2008), 121–127, 10.1039/B715468B.
2. van Meer, G., Cellular lipidomics. EMBO J. 24 (2005), 3159–3165, 10.1038/sj.emboj.7600798.
3. Wenk, M.R., The emerging field of lipidomics. Nat. Rev. Drug Discov. 4 (2005), 594–610, 10.1038/nrd1776.
4. Ekroos, K., Ejsing, C.S., Bahr, U., Karas, M., Simons, K., Shevchenko, A., Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation. J. Lipid Res. 44 (2003), 2181–2192, 10.1194/jlr.D300020-JLR200.
5. Kyle, J.E., Zhang, X., Weitz, K.K., Monroe, M.E., Ibrahim, Y.M., Moore, R.J., Cha, J., Sun, X., Lovelace, E.S., Wagoner, J., Polyak, S.J., Metz, T.O., Dey, S.K., Smith, R.D., Burnum-Johnson, K.E., Baker, E.S., Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst 141 (2016), 1649–1659, 10.1039/C5AN02062J.
6. Shinzawa-Itoh, K., Aoyama, H., Muramoto, K., Terada, H., Kurauchi, T., Tadehara, Y., Yamasaki, A., Sugimura, T., Kurono, S., Tsujimoto, K., Mizushima, T., Yamashita, E., Tsukihara, T., Yoshikawa, S., Structures and physiological roles of 13 integral lipids of bovine heart cytochrome. EMBO J. 26 (2007), 1713–1725, 10.1038/sj.emboj.7601618.
7. Churruca, I., Fernández-Quintela, A., Portillo, M.P., Conjugated linoleic acid isomers: Differences in metabolism and biological effects. Biofactors 35 (2009), 105–111, 10.1002/biof.13.
8. Tricon, S., Burdge, G.C., Kew, S., Banerjee, T., Russell, J.J., Jones, E.L., Grimble, R.F., Williams, C.M., Yaqoob, P., Calder, P.C., Opposing effects of cis-9,trans-11 and trans-10,cis-12 conjugated linoleic acid on blood lipids in healthy humans. Am. J. Clin. Nutr. 80 (2004), 614–620.
9. Kelley, N.S., Hubbard, N.E., Erickson, K.L., Conjugated linoleic acid isomers and cancer. J. Nutr. 137 (2007), 2599–2607.
10. Brügger, B., Erben, G., Sandhoff, R., Wieland, F.T., Lehmann, W.D., Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass spectrometry. Proc. Natl. Acad. Sci. 94 (1997), 2339–2344.
11. Ejsing, C.S., Duchoslav, E., Sampaio, J., Simons, K., Bonner, R., Thiele, C., Ekroos, K., Shevchenko, A., Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning. Anal. Chem. 78 (2006), 6202–6214, 10.1021/ac060545x.
12. O'Connor, P.B., Pittman, J.L., Thomson, B.A., Budnik, B.A., Cournoyer, J.C., Jebanathirajah, J., Lin, C., Moyer, S., Zhao, C., A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics. Rapid Commun. Mass Spectrom. 20 (2006), 259–266, 10.1002/rcm.2307.
13. Makarov, A., Denisov, E., Kholomeev, A., Balschun, W., Lange, O., Strupat, K., Horning, S., Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal. Chem. 78 (2006), 2113–2120, 10.1021/ac0518811.
14. Schwudke, D., Hannich, J.T., Surendranath, V., Grimard, V., Moehring, T., Burton, L., Kurzchalia, T., Shevchenko, A., Top-down lipidomic screens by multivariate analysis of high-resolution survey mass spectra. Anal. Chem. 79 (2007), 4083–4093, 10.1021/ac062455y.
15. Olsen, J.V., de Godoy, L.M.F., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., Mann, M., Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4 (2005), 2010–2021, 10.1074/mcp.T500030-MCP200.
16. Schwudke, D., Schuhmann, K., Herzog, R., Bornstein, S.R., Shevchenko, A., Shotgun lipidomics on high resolution mass spectrometers, Cold Spring Harb. Perspect. Biol., 3, 2011, 10.1101/cshperspect.a004614.
17. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of glycolipids. Eur. J. Biochem. 257 (1998), 293–298, 10.1046/j.1432–1327.1998.2570293.x.
18. The nomenclature of lipids (recommendations, IUPAC-IUB Commission on Biochemical Nomenclature. J. Lipid Res. 19:1978 (1976), 114–128.
19. IUPAC-IUB Commission on Biochemical Nomenclature (CBN): the nomenclature of lipids. Eur. J. Biochem. 2 (1967), 127–131, 10.1111/j.1432–1033.1967.tb00116.x.
20. Fahy, E., Subramaniam, S., Murphy, R.C., Nishijima, M., Raetz, C.R.H., Shimizu, T., Spener, F., van Meer, G., Wakelam, M.J.O., Dennis, E.A., Update of the LIPID MAPS comprehensive classification system for lipids. J. Lipid Res. 50 (2009), S9–S14, 10.1194/jlr.R800095-JLR200.
21. Fahy, E., Subramaniam, S., Brown, H.A., Glass, C.K., Merrill, A.H., Murphy, R.C., Raetz, C.R.H., Russell, D.W., Seyama, Y., Shaw, W., Shimizu, T., Spener, F., van Meer, G., VanNieuwenhze, M.S., White, S.H., Witztum, J.L., Dennis, E.A., A comprehensive classification system for lipids. J. Lipid Res. 46 (2005), 839–862, 10.1194/jlr.E400004-JLR200.
22. Sud, M., Fahy, E., Cotter, D., Brown, A., Dennis, E.A., Glass, C.K., Merrill, A.H., Murphy, R.C., Raetz, C.R.H., Russell, D.W., Subramaniam, S., LMSD: LIPID MAPS structure database. Nucleic Acids Res. 35 (2007), D527–D532, 10.1093/nar/gkl838.
23. Liebisch, G., Vizcaíno, J.A., Köfeler, H., Trötzmüller, M., Griffiths, W.J., Schmitz, G., Spener, F., Wakelam, M.J.O., Shorthand notation for lipid structures derived from mass spectrometry. J. Lipid Res. 54 (2013), 1523–1530, 10.1194/jlr.M033506.
24. Gerspach, C., Imhasly, S., Gubler, M., Naegeli, H., Ruetten, M., Laczko, E., Altered plasma lipidome profile of dairy cows with fatty liver disease. Res. Vet. Sci. 110 (2017), 47–59, 10.1016/j.rvsc.2016.10.001.
25. Smith, R., Mathis, A.D., Ventura, D., Prince, J.T., Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. BMC Bioinf., 15, 2014, S9, 10.1186/1471-2105-15-S7-S9.
26. Ding, J., Sorensen, C.M., Jaitly, N., Jiang, H., Orton, D.J., Monroe, M.E., Moore, R.J., Smith, R.D., Metz, T.O., Application of the accurate mass and time tag approach in studies of the human blood lipidome. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 871 (2008), 243–252, 10.1016/j.jchromb.2008.04.040.
27. Schwudke, D., Oegema, J., Burton, L., Entchev, E., Hannich, J.T., Ejsing, C.S., Kurzchalia, T., Shevchenko, A., Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Anal. Chem. 78 (2006), 585–595, 10.1021/ac051605m.
28. Liu, Y., Chen, Y., Momin, A., Shaner, R., Wang, E., Bowen, N.J., Matyunina, L.V., Walker, L.D., McDonald, J.F., Sullards, M.C., Merrill, A.H., Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry. Mol. Cancer, 9, 2010, 186, 10.1186/1476-4598-9-186.
29. Jin, R., Li, L., Feng, J., Dai, Z., Huang, Y.-W., Shen, Q., Zwitterionic hydrophilic interaction solid-phase extraction and multi-dimensional mass spectrometry for shotgun lipidomic study of Hypophthalmichthys nobilis. Food Chem. 216 (2017), 347–354, 10.1016/j.foodchem.2016.08.074.
30. Axelsen, P.H., Murphy, R.C., Quantitative analysis of phospholipids containing arachidonate and docosahexaenoate chains in microdissected regions of mouse brain. J. Lipid Res. 51 (2010), 660–671, 10.1194/jlr.D001750.
31. Liebisch, G., Ejsing, C.S., Ekroos, K., Identification and annotation of lipid species in metabolomics studies need improvement. Clin. Chem. 61 (2015), 1542–1544, 10.1373/clinchem.2015.244830.
32. Narváez-Rivas, M., Vu, N., Chen, G.-Y., Zhang, Q., Off-line mixed-mode liquid chromatography coupled with reversed phase high performance liquid chromatography-high resolution mass spectrometry to improve coverage in lipidomics analysis. Anal. Chim. Acta 954 (2017), 140–150, 10.1016/j.aca.2016.12.003.
33. Li, Q., Zhao, Y., Zhu, D., Pang, X., Liu, Y., Frew, R., Chen, G., Lipidomics profiling of goat milk, soymilk and bovine milk by UPLC-Q-exactive orbitrap mass spectrometry. Food Chem. 224 (2017), 302–309, 10.1016/j.foodchem.2016.12.083.
34. Skotland, T., Ekroos, K., Kauhanen, D., Simolin, H., Seierstad, T., Berge, V., Sandvig, K., Llorente, A., Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers. Eur. J. Cancer 70 (2017), 122–132, 10.1016/j.ejca.2016.10.011.
35. Gallego, S.F., Sprenger, R.R., Neess, D., Pauling, J.K., Færgeman, N.J., Ejsing, C.S., Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP deficient mice. Biochim. Biophys. Acta BBA - Mol. Cell Biol. Lipids. 1862 (2017), 145–155, 10.1016/j.bbalip.2016.10.012.
36. Zhong, H., Xiao, M., Zarkovic, K., Zhu, M., Sa, R., Lu, J., Tao, Y., Chen, Q., Xia, L., Cheng, S., Waeg, G., Zarkovic, N., Yin, H., Mitochondrial control of apoptosis through modulation of cardiolipin oxidation in hepatocellular carcinoma: a novel link between oxidative stress and cancer. Free Radic. Biol. Med. 102 (2017), 67–76, 10.1016/j.freeradbiomed.2016.10.494.
37. Lerner, R., Post, J., Loch, S., Lutz, B., Bindila, L., Targeting brain and peripheral plasticity of the lipidome in acute kainic acid-induced epileptic seizures in mice via quantitative mass spectrometry. Biochim. Biophys. Acta BBA - Mol. Cell Biol. Lipids. 1862 (2017), 255–267, 10.1016/j.bbalip.2016.11.008.
38. Tsugawa, H., Cajka, T., Kind, T., Ma, Y., Higgins, B., Ikeda, K., Kanazawa, M., VanderGheynst, J., Fiehn, O., Arita, M., MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat. Methods 12 (2015), 523–526, 10.1038/nmeth.3393.
39. Kind, T., Liu, K.-H., Lee, D.Y., DeFelice, B., Meissen, J.K., Fiehn, O., LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat. Methods 10 (2013), 755–758, 10.1038/nmeth.2551.
40. Kochen, M.A., Chambers, M.C., Holman, J.D., Nesvizhskii, A.I., Weintraub, S.T., Belisle, J.T., Islam, M.N., Griss, J., Tabb, D.L., Greazy: open-source software for automated phospholipid tandem mass spectrometry identification. Anal. Chem. 88 (2016), 5733–5741, 10.1021/acs.analchem.6b00021.
41. Zemski Berry, K.A., Murphy, R.C., Electrospray ionization tandem mass spectrometry of glycerophosphoethanolamine plasmalogen phospholipids. J. Am. Soc. Mass Spectrom. 15 (2004), 1499–1508, 10.1016/j.jasms.2004.07.009.
42. Koelmel, J.P., Kroeger, N.M., Gill, E.L., Ulmer, C.Z., Bowden, J.A., Patterson, R.E., Yost, R.A., Garrett, T.J., Expanding lipidome coverage using LC-MS/MS data-dependent acquisition with automated exclusion list generation. J. Am. Soc. Mass Spectrom., 2017 (Accepted).
43. Gil, A., Siegel, D., Permentier, H., Reijngoud, D.-J., Dekker, F., Bischoff, R., Stability of energy metabolites? An often overlooked issue in metabolomics studies: a review. Electrophoresis 36 (2015), 2156–2169, 10.1002/elps.201500031.
44. Lorenz, M.A., Burant, C.F., Kennedy, R.T., Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. Anal. Chem. 83 (2011), 3406–3414, 10.1021/ac103313x.
45. Plueckthun, A., Dennis, E.A., Acyl and phosphoryl migration in lysophospholipids: importance in phospholipid synthesis and phospholipase specificity. Biochemistry (Mosc) 21 (1982), 1743–1750.
46. Heller, S.R., McNaught, A., Pletnev, I., Stein, S., Tchekhovskoi, D., InChI, the IUPAC International Chemical Identifier. J. Cheminformatics, 7, 2015, 23, 10.1186/s13321-015-0068-4.
47. Homer, R.W., Swanson, J., Jilek, R.J., Hurst, T., Clark, R.D., SYBYL Line Notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries. J. Chem. Inf. Model. 48 (2008), 2294–2307, 10.1021/ci7004687.
48. Brown, S.H.J., Mitchell, T.W., Blanksby, S.J., Analysis of unsaturated lipids by ozone-induced dissociation. Biochim. Biophys. Acta BBA - Mol. Cell Biol. Lipids. 1811 (2011), 807–817, 10.1016/j.bbalip.2011.04.015.
49. Kyle, J.E., Zhang, X., Weitz, K.K., Monroe, M.E., Ibrahim, Y.M., Moore, R.J., Cha, J., Sun, X., Lovelace, E.S., Wagoner, J., Polyak, S.J., Metz, T.O., Dey, S.K., Smith, R.D., Burnum-Johnson, K.E., Baker, E.S., Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst 141 (2016), 1649–1659, 10.1039/C5AN02062J.
50. Zhang, X., Garimella, S.V.B., Prost, S.A., Webb, I.K., Chen, T.-C., Tang, K., Tolmachev, A.V., Norheim, R.V., Baker, E.S., Anderson, G.A., Ibrahim, Y.M., Smith, R.D., Ion trapping, storage, and ejection in structures for lossless ion manipulations. Anal. Chem. 87 (2015), 6010–6016, 10.1021/acs.analchem.5b00214.
51. Ulmer, C.Z., Koelmel, J.P., Ragland, J.M., Garrett, T.J., Bowden, J.A., LipidPioneer: a comprehensive user-generated exact mass template for lipidomics. J. Am. Soc. Mass Spectrom., 1–4, 2017, 10.1007/s13361-016-1579-6.