Skip to main content
SpringerLink
Log in

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

  • Research Paper
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Rubakhin SS, Jurchen JC, Monroe EB, Sweedler JV (2005). Drug Discov Today 10(12):823. doi:10.1016/S1359-6446(05)03458-6

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  3. Niehoff AC, Kettling H, Pirkl A, Chiang YN, Dreisewerd K, Yew JY (2014) Anal Chem 86 (22):11086. doi:10.1021/ac503171f

    Article  CAS  Google Scholar 

  4. Khatib-Shahidi S, Andersson M, Herman JL, Gillespie TA, Caprioli RM (2006) Anal Chem 78 (18):6448. doi:10.1021/ac060788p

    Article  CAS  Google Scholar 

  5. Stoeckli M, Staab D, Schweitzer A (2007) Int J Mass Spectrom 260(2):195. doi:10.1016/j.ijms.2006.10.007

    Article  CAS  Google Scholar 

  6. Schober Y, Guenther S, Spengler B, Ro mpp A (2012) Anal Chem 84 (15):6293. doi:10.1021/ac301337h

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  8. Karas M, Hillenkamp F (1988) Anal Chem 60:2299. doi:10.1586/epr.11.53. 10.1021/ac00171a028

    Article  CAS  Google Scholar 

  9. Pachuta SJ, Cooks R (1987) Chem Rev 87(3):647. doi:10.1021/cr00079a009

    Article  CAS  Google Scholar 

  10. Cooks RG, Ouyang Z, Takats Z, Wiseman JM (2006) Science 311(5767):1566. doi:10.1126/science.1119426

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  12. Liu Q, Guo Z, He L (2007) Anal Chem 79(10):3535. doi:10.1021/ac0611465

    Article  CAS  Google Scholar 

  13. Hsieh Y, Chen J, Korfmacher WA, Pharmacol J (2007) Toxicol Methods 55(2):193. doi:10.1016/j.vascn.2006.06.004

    Article  CAS  Google Scholar 

  14. Sugiura Y, Setou M (2010) J Neuroimmune Pharmacol 5(1):31. doi:10.1007/s11481-009-9162-6

    Article  Google Scholar 

  15. Murphy RC, Hankin JA, Barkley RM (2009) J Lipid Res 50(Supplement):S317. doi:10.1194/jlr.R800051-JLR200

    Article  Google Scholar 

  16. Gode D, Volmer DA (2013) Analyst 138(5):1289. doi:10.1039/C2AN36337B

    Article  CAS  Google Scholar 

  17. Chaurand P, Stoeckli M, Caprioli RM (1999) Anal Chem 71(23):5263. doi:10.1021/ac990781q

    Article  CAS  Google Scholar 

  18. MacAleese L, Stauber J, Heeren R (2009) Proteomics 9(4):819. doi:10.1002/pmic.200800363

    Article  CAS  Google Scholar 

  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

    Article  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  22. Reyzer ML, Caprioli RM (2005) J Proteome Res 4(4):1138. doi:10.1021/pr050095+

    Article  CAS  Google Scholar 

  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

    Article  Google Scholar 

  24. Walch A, Rauser S, Deininger SO, Höfler H (2008) Histochem Cell Biol 130(3):421. doi:10.1007/s00418-008-0469-9

    Article  CAS  Google Scholar 

  25. Gross JH (2011) Mass spectrometry: a textbook, 2nd edn. Springer, New York

    Book  Google Scholar 

  26. Zhang J, Ma J, Zhang W, Xu C, Zhu Y, Xie H (2013) J Proteome Res 12(9):3857. doi:10.1021/pr400003a

    Article  CAS  Google Scholar 

  27. Webb K, Bristow T, Sargent M, Stein B (2004) Best practice guide. LGC Limited, Tddington, pp 1–8

    Google Scholar 

  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

    Article  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  31. Muddiman DC, Oberg AL (2005) Anal Chem 77(8):2406. doi:10.1021/ac048258l

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  33. Hoffmann Ed, Stroobant V (1996) Mass spectrometry: principles and applications, 3rd edn. John Wiley & Sons, Chichester

    Google Scholar 

  34. Chapman JR (1985) Practical organic mass spectrometry: a guide for chemical and biological analysis, 2nd edn. John Wiley & Sons Ltd, West Sussex

    Google Scholar 

  35. Greaves J, Roboz J (2013) Mass spectrometry for the novice. CRC Press Taylor & Francis Group, Boca Raton

    Google Scholar 

  36. Barry JA, Robichaud G, Muddiman DC (2013) J Am Soc Mass Spectrom 24 (7):1137. doi:10.1007/s13361-013-0659-0

    Article  CAS  Google Scholar 

  37. Kozhinov AN, Zhurov KO, Tsybin YO (2013) Anal Chem 85(13):6437. doi:10.1021/ac400972y

    Article  CAS  Google Scholar 

  38. Stravs MA, Schymanski EL, Singer HP, Hollender J (2013) J Mass Spectrom 48(1):89. doi:10.1002/jms.3131

    Article  CAS  Google Scholar 

  39. Gobom J, Mueller M, Egelhofer V, Theiss D, Lehrach H, Nordhoff E (2002) Anal Chem 74 (15):3915. doi:10.1021/ac011203o

    Article  CAS  Google Scholar 

  40. Wolski WE, Lalowski M, Jungblut P, Reinert K (2005) BMC Bioinf 6:203. doi:10.1186/1471-2105-6-203

    Article  Google Scholar 

  41. Cvaċka J, Svatoṡ A (2003) Rapid Commun Mass Spectrom 17(19):2203. doi:10.1002/rcm.1178

    Article  Google Scholar 

  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

    Article  CAS  Google Scholar 

  43. Böcker S, Mäkinen V (2008) IEEE/ACM Trans Comput Biol Bioinf 5(1):91. doi:10.1109/tcbb.2007.1077

    Article  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

  47. Gibb S, Strimmer K (2012) Bioinformatics 28(17):2270. doi:10.1093/bioinformatics/bts447

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Purva Kulkarni is supported by the International Max Planck Research School, Jena. The authors also wish to thank Sebastian Gibb for providing assistance in using the MALDIquant package. Financial support from Max Planck society is acknowledged.

Author information

Author notes

  1. Philipp Kynast

    Present address: Computational Biochemistry Group, ICS-6, Forschungszentrum Jülich, 52425, Jülich, Germany

Authors and Affiliations

  1. Lehrstuhl für Bioinformatik, Friedrich Schiller University, Ernst-Abbe-Platz 2, 07743, Jena, Germany

    Purva Kulkarni, Philipp Kynast & Sebastian Böcker

  2. Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany

    Purva Kulkarni, Filip Kaftan, Philipp Kynast & Aleš Svatoš

  3. Institute of Organic Chemistry and Biochemistry, ASCR, Flemingovo nám. 2, 16610, Prague, Czech Republic

    Aleš Svatoš

Authors
  1. Purva Kulkarni
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Filip Kaftan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Philipp Kynast
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Aleš Svatoš
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sebastian Böcker
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sebastian Böcker.

Additional information

Published in the topical collection Mass Spectrometry Imaging with guest editors Andreas Römpp and Uwe Karst.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(PDF 2.10 MB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kulkarni, P., Kaftan, F., Kynast, P. et al. Correcting mass shifts: A lock mass-free recalibration procedure for mass spectrometry imaging data. Anal Bioanal Chem 407, 7603–7613 (2015). https://doi.org/10.1007/s00216-015-8935-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-015-8935-4

Keywords

Search

Navigation