Analytical and Bioanalytical Chemistry

, Volume 407, Issue 25, pp 7603–7613 | Cite as

Correcting mass shifts: A lock mass-free recalibration procedure for mass spectrometry imaging data

  • Purva Kulkarni
  • Filip Kaftan
  • Philipp Kynast
  • Aleš Svatoš
  • Sebastian Böcker
Research Paper
Part of the following topical collections:
  1. Mass Spectrometry Imaging

Abstract

Mass spectrometry imaging (MSI) has become widely popular because of its potential to map the spatial distribution of thousands of compounds in a single measurement directly from tissue surfaces. With every MSI experiment, it is important to maintain high mass accuracy for correct identification of the observed ions. Many times this can be compromised due to different experimental factors, leading to erroneous assignment of peaks. This makes recalibration a crucial preprocessing step. We describe a lock mass-free mass spectra recalibration method, which enables to significantly reduce these mass shift effects. The recalibration method is applied in three steps: First, we decide on an order to process all the spectra. Herein, we describe three different methods for ordering the spectra—minimum spanning tree (MST), topological greedy (TG), and crystal growth (CG). Second, we construct a reference (consensus) spectrum, from the ordered spectra, and third, all spectra are individually corrected against this consensus spectrum. The performance of the recalibration method is demonstrated on three imaging datasets acquired from matrix-assisted laser desorptionionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging of whole-body Drosophila melanogaster fly. The applied recalibration method is shown to strongly reduce the observed mass shifts in the imaging datasets. Among the three ordering methods, CG and MST perform comparatively better than TG and highly decrease the overall standard deviation of the mass error distribution. Lock mass correction of MSI data is practically difficult, as not all spectra contain the selected lock mass peak. Our method eliminates this need.

Keywords

Mass spectrometry imaging Recalibration Mass shift correction Data processing 

Supplementary material

216_2015_8935_MOESM1_ESM.pdf (2.1 mb)
(PDF 2.10 MB)

References

  1. 1.
    Rubakhin SS, Jurchen JC, Monroe EB, Sweedler JV (2005). Drug Discov Today 10(12):823. doi:10.1016/S1359-6446(05)03458-6 CrossRefGoogle Scholar
  2. 2.
    Kaftan F, Vrkoslav V, Kynast P, Kulkarni P, Böcker S, Cvačka J, Knaden M, Svatoš A (2014) J Mass Spectrom 49(3):223. doi:10.1002/jms.3331 CrossRefGoogle Scholar
  3. 3.
    Niehoff AC, Kettling H, Pirkl A, Chiang YN, Dreisewerd K, Yew JY (2014) Anal Chem 86 (22):11086. doi:10.1021/ac503171f CrossRefGoogle Scholar
  4. 4.
    Khatib-Shahidi S, Andersson M, Herman JL, Gillespie TA, Caprioli RM (2006) Anal Chem 78 (18):6448. doi:10.1021/ac060788p CrossRefGoogle Scholar
  5. 5.
    Stoeckli M, Staab D, Schweitzer A (2007) Int J Mass Spectrom 260(2):195. doi:10.1016/j.ijms.2006.10.007 CrossRefGoogle Scholar
  6. 6.
    Schober Y, Guenther S, Spengler B, Ro mpp A (2012) Anal Chem 84 (15):6293. doi:10.1021/ac301337h CrossRefGoogle Scholar
  7. 7.
    Boggio KJ, Obasuyi E, Sugino K, Nelson SB, Agar NY, Agar JN (2011) Expert Rev Proteomics 8 (5):591. doi:10.1586/epr.11.53. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268336/pdf/nihms337735.pdf CrossRefGoogle Scholar
  8. 8.
    Karas M, Hillenkamp F (1988) Anal Chem 60:2299. doi:10.1586/epr.11.53. 10.1021/ac00171a028 CrossRefGoogle Scholar
  9. 9.
    Pachuta SJ, Cooks R (1987) Chem Rev 87(3):647. doi:10.1021/cr00079a009 CrossRefGoogle Scholar
  10. 10.
    Cooks RG, Ouyang Z, Takats Z, Wiseman JM (2006) Science 311(5767):1566. doi:10.1126/science.1119426 CrossRefGoogle Scholar
  11. 11.
    Ifa DR, Wiseman JM, Song Q, Cooks RG (2007) Int J Mass Spectrom 259 (1):8. doi:10.1016/j.ijms.2006.08.003 CrossRefGoogle Scholar
  12. 12.
    Liu Q, Guo Z, He L (2007) Anal Chem 79(10):3535. doi:10.1021/ac0611465 CrossRefGoogle Scholar
  13. 13.
    Hsieh Y, Chen J, Korfmacher WA, Pharmacol J (2007) Toxicol Methods 55(2):193. doi:10.1016/j.vascn.2006.06.004 CrossRefGoogle Scholar
  14. 14.
    Sugiura Y, Setou M (2010) J Neuroimmune Pharmacol 5(1):31. doi:10.1007/s11481-009-9162-6 CrossRefGoogle Scholar
  15. 15.
    Murphy RC, Hankin JA, Barkley RM (2009) J Lipid Res 50(Supplement):S317. doi:10.1194/jlr.R800051-JLR200 CrossRefGoogle Scholar
  16. 16.
    Gode D, Volmer DA (2013) Analyst 138(5):1289. doi:10.1039/C2AN36337B CrossRefGoogle Scholar
  17. 17.
    Chaurand P, Stoeckli M, Caprioli RM (1999) Anal Chem 71(23):5263. doi:10.1021/ac990781q CrossRefGoogle Scholar
  18. 18.
    MacAleese L, Stauber J, Heeren R (2009) Proteomics 9(4):819. doi:10.1002/pmic.200800363 CrossRefGoogle Scholar
  19. 19.
    Lalowski M, Magni F, Mainini V, Monogioudi E, Gotsopoulos A, Soliymani R, Chinello C, Baumann M (2013) Nephrol Dial Transplant 28(7):1648. doi:10.1093/ndt/gft008 CrossRefGoogle Scholar
  20. 20.
    Meding S, Nitsche U, Balluff B, Elsner M, Rauser S, Schöne C, Nipp M, Maak M, Feith M, Ebert MP, Friess H, Langer R, Höfler H, Zitzelsberger H, Rosenberg R, Walch A (2012) J Proteome Res 11(3):1996. doi:10.1021/pr200784p CrossRefGoogle Scholar
  21. 21.
    Cazares LH, Troyer DA, Wang B, Drake RR, Semmes OJ (2011) Anal Bioanal Chem 401(1):17. doi:10.1007/s00216-011-5003-6 CrossRefGoogle Scholar
  22. 22.
    Reyzer ML, Caprioli RM (2005) J Proteome Res 4(4):1138. doi:10.1021/pr050095+ CrossRefGoogle Scholar
  23. 23.
    Thiele H, Heldmann S, Trede D, Strehlow J, Wirtz S, Dreher W, Berger J, Oetjen J, Kobarg JH, Fischer B, Maass P (2013) Biochim Biophys Acta Proteins Proteomics 1844(1):117. doi:10.1016/j.bbapap.2013.01.040. http://www.sciencedirect.com/science/article/pii/S1570963913000599 CrossRefGoogle Scholar
  24. 24.
    Walch A, Rauser S, Deininger SO, Höfler H (2008) Histochem Cell Biol 130(3):421. doi:10.1007/s00418-008-0469-9 CrossRefGoogle Scholar
  25. 25.
    Gross JH (2011) Mass spectrometry: a textbook, 2nd edn. Springer, New YorkCrossRefGoogle Scholar
  26. 26.
    Zhang J, Ma J, Zhang W, Xu C, Zhu Y, Xie H (2013) J Proteome Res 12(9):3857. doi:10.1021/pr400003a CrossRefGoogle Scholar
  27. 27.
    Webb K, Bristow T, Sargent M, Stein B (2004) Best practice guide. LGC Limited, Tddington, pp 1–8Google Scholar
  28. 28.
    Römpp A, Guenther S, Schober Y, Schulz O, Takats Z, Kummer W, Spengler B (2010) Angew Chem Int Ed Engl 49(22):3834. doi:10.1002/anie.200905559 CrossRefGoogle Scholar
  29. 29.
    Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME, Dabney AR, Qian WJ, Camp DGI, Smith RD (2008) Anal Chem 80(3):693. doi:10.1021/ac701863d CrossRefGoogle Scholar
  30. 30.
    Norris JL, Cornett DS, Mobley JA, Andersson M, Seeley EH, Chaurand P, Caprioli RM (2007) Int J Mass Spectrom 260(2):212. doi:10.1016/j.ijms.2006.10.005 CrossRefGoogle Scholar
  31. 31.
    Muddiman DC, Oberg AL (2005) Anal Chem 77(8):2406. doi:10.1021/ac048258l CrossRefGoogle Scholar
  32. 32.
    Staes A, Vandenbussche J, Demol H, Goethals M, Yilmaz Su, Hulstaert N, Degroeve S, Kelchtermans P, Martens L, Gevaert K (2013) Anal Chem 85(22):11054. doi:10.1021/ac4027093 CrossRefGoogle Scholar
  33. 33.
    Hoffmann Ed, Stroobant V (1996) Mass spectrometry: principles and applications, 3rd edn. John Wiley & Sons, ChichesterGoogle Scholar
  34. 34.
    Chapman JR (1985) Practical organic mass spectrometry: a guide for chemical and biological analysis, 2nd edn. John Wiley & Sons Ltd, West SussexGoogle Scholar
  35. 35.
    Greaves J, Roboz J (2013) Mass spectrometry for the novice. CRC Press Taylor & Francis Group, Boca RatonGoogle Scholar
  36. 36.
    Barry JA, Robichaud G, Muddiman DC (2013) J Am Soc Mass Spectrom 24 (7):1137. doi:10.1007/s13361-013-0659-0 CrossRefGoogle Scholar
  37. 37.
    Kozhinov AN, Zhurov KO, Tsybin YO (2013) Anal Chem 85(13):6437. doi:10.1021/ac400972y CrossRefGoogle Scholar
  38. 38.
    Stravs MA, Schymanski EL, Singer HP, Hollender J (2013) J Mass Spectrom 48(1):89. doi:10.1002/jms.3131 CrossRefGoogle Scholar
  39. 39.
    Gobom J, Mueller M, Egelhofer V, Theiss D, Lehrach H, Nordhoff E (2002) Anal Chem 74 (15):3915. doi:10.1021/ac011203o CrossRefGoogle Scholar
  40. 40.
    Wolski WE, Lalowski M, Jungblut P, Reinert K (2005) BMC Bioinf 6:203. doi:10.1186/1471-2105-6-203 CrossRefGoogle Scholar
  41. 41.
    Cvaċka J, Svatoṡ A (2003) Rapid Commun Mass Spectrom 17(19):2203. doi:10.1002/rcm.1178 CrossRefGoogle Scholar
  42. 42.
    Alexandrov T, Becker M, Deininger SO, Ernst Gn, Wehder L, Grasmair M, von Eggeling F, Thiele H, Maass P (2010) J Proteome Res 9(12):6535. doi:10.1021/pr100734z CrossRefGoogle Scholar
  43. 43.
    Böcker S, Mäkinen V (2008) IEEE/ACM Trans Comput Biol Bioinf 5(1):91. doi:10.1109/tcbb.2007.1077 CrossRefGoogle Scholar
  44. 44.
    Yew JY, Dreisewerd K, Luftmann H, Müthing J, Pohlentz G, Kravitz EA (2009) Curr Biol 19(15):1245. doi:10.1016/j.cub.2009.06.037. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726907/pdf/nihms128270.pdf CrossRefGoogle Scholar
  45. 45.
    Bartelt RJ, Schaner AM, Jackson LL, Chem J (1985) Ecology 11(12):1747. doi:10.1007/BF01012124. http://link.springer.com/article/10.1007 Google Scholar
  46. 46.
    Hammad LA, Cooper BS, Fisher NP, Montooth KL, Karty JA (2011) Rapid Commun Mass Spectrom 25(19):2959. doi:10.1002/rcm.5187/full CrossRefGoogle Scholar
  47. 47.
    Gibb S, Strimmer K (2012) Bioinformatics 28(17):2270. doi:10.1093/bioinformatics/bts447 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Purva Kulkarni
    • 1
    • 2
  • Filip Kaftan
    • 2
  • Philipp Kynast
    • 1
    • 2
    • 4
  • Aleš Svatoš
    • 2
    • 3
  • Sebastian Böcker
    • 1
  1. 1.Lehrstuhl für BioinformatikFriedrich Schiller UniversityJenaGermany
  2. 2.Research Group Mass SpectrometryMax Planck Institute for Chemical EcologyJenaGermany
  3. 3.Institute of Organic Chemistry and Biochemistry, ASCRPragueCzech Republic
  4. 4.Computational Biochemistry Group, ICS-6Forschungszentrum JülichJülichGermany

Personalised recommendations