Skip to main content
SpringerLink
Log in

The Short and Long of it: Shorter Chromatographic Analysis Suffice for Sample Classification During UHPLC-MS-Based Metabolic Fingerprinting

  • Original
  • Published:
Chromatographia Aims and scope Submit manuscript

Abstract

Ultra high-performance liquid chromatography hyphenated to mass spectrometry (UHPLC-MS) technologies has been widely applied in metabolomics, and the high resolution and peak capacity thereof are only some of the key aspects that are exploited in such and related fields. In the current study, we investigated if low resolution chromatography, with the aid of multivariate data analyses, could be sufficient for a metabolic fingerprinting study that aims at discriminating between samples of different biological status or origin. UHPLC-MS data from chemically-treated Arabidopsis thaliana plants were used and chromatograms with different gradient lengths were compared. MarkerLynx™ technology was employed for data mining, followed by principal component analysis (PCA) and orthogonal projections to latent structure discriminant analysis (OPLS-DA) as multivariate statistical interpretations. The results showed that, despite the congestion in low resolution chromatograms (of 5 and 10 min), samples could be classified based on their respective biological background in a similar manner as when using chromatograms with better resolution (of 20 and 40 min). This paper thus underlines that, in a metabolic fingerprinting study, low resolution chromatography together with multivariate data analyses suffice for biological classification of samples. The results also suggest that, depending on the initial objective of the undertaken study, optimisation in chromatographic resolution prior to full scale metabolomics studies is mandatory.

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

Similar content being viewed by others

References

  1. Hall RD (2005) New Phytol 169:453–468

    Article  Google Scholar 

  2. Oksman-Caldentey K-M, Saito K (2005) Curr Opin Biotechnol 16:174–179

    Article  CAS  Google Scholar 

  3. Verpoorte R, Choi YH, Mustafa NR, Kim HK (2008) Phytochem Rev 7:525–539

    Article  CAS  Google Scholar 

  4. Lu X, Zhao X, Bai C, Zhao C, Lu G, Xu G (2008) J Chromatogr B 866:64–76

    Article  CAS  Google Scholar 

  5. Winder CL, Dunn WB, Goodacre R (2011) Trends Microbiol 19:315–322

    Article  CAS  Google Scholar 

  6. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, Willmitzer L (2000) Nat Biotechnol 18:1157–1161

    Article  CAS  Google Scholar 

  7. Sumner LW, Mendes P, Dixon RA (2003) Phytochemistry 62:817–836

    Article  CAS  Google Scholar 

  8. Dunn WB, Ellis DI (2005) Trends Anal Chem 24:285–294

    Article  CAS  Google Scholar 

  9. Fukusaki E, Kobayashi A (2005) J Biosci Bioeng 100:347–354

    Article  CAS  Google Scholar 

  10. Idborg H, Zamani L, Edlund P-O, Schuppe-Koistinen I, Jacobsson SP (2005) J Chromatogr B 828:9–13

    Article  CAS  Google Scholar 

  11. García-Pérez I, Vallejo M, García A, Legido-Quigley C, Barbas C (2008) J Chromatogr A 1204:130–139

    Article  Google Scholar 

  12. Zeng M, Liang Y, Li H, Wang M, Wang B, Chen X, Zhou N, Cao D, Wu J (2010) J Pharm Biomed Anal 52:265–272

    Article  CAS  Google Scholar 

  13. Ellis DI, Dunn WB, Griffin JL, Allwood JW, Goodacre R (2007) Pharmacogenomics 8:1243–1266

    Article  CAS  Google Scholar 

  14. Samra T, Sharma S, Pawar M (2011) J Clin Monitor Comp 25:49–150

    Google Scholar 

  15. Xiao JF, Zhou B, Ressom HW (2012) Trends Anal Chem 32:1–14

    Article  Google Scholar 

  16. Wilson ID, Nicholson JK, Castro-Perez J, Granger JH, Johnson KA, Smith BW, Plumb RS (2005) J Proteome Res 4:591–598

    Article  CAS  Google Scholar 

  17. Plumb RS, Granger JH, Stumpf CL, Johnson KA, Smith BW, Gaulitz S, Wilson ID, Castro- Perez J (2005) Analyst 130:844–849

    Article  CAS  Google Scholar 

  18. Gika HG, Theodoridis G, Extance J, Edge AM, Wilson ID (2008) J Chromatogr B 871:279–287

    Article  CAS  Google Scholar 

  19. Shaaban H, Górecki T (2011) Chromatographia 74:9–17

    Article  CAS  Google Scholar 

  20. Knox JH, Scott HP (1983) J Chromatogr A 282:297–313

    Article  CAS  Google Scholar 

  21. Usher KM, Simmons CR, Dorsey JD (2008) J Chromatogr A 1200:122–128

    Article  CAS  Google Scholar 

  22. Fiehn O (2002) Plant Mol Biol 48:155–171

    Article  CAS  Google Scholar 

  23. Van den Berg RA, Rubingh CM, Westerhuis JA, van der Werf MJ, Smilde AK (2009) Anal Chim Acta 651:173–181

    Article  Google Scholar 

  24. Jansen JJ, Smit S, Hoefsloot HCJ, Smilde AK (2010) Phytochem Anal 21:48–60

    Article  CAS  Google Scholar 

  25. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Trends Biotechnol 22:245–252

    Article  CAS  Google Scholar 

  26. Van den Berg RA, Hoefsloot HCJ, Westerhuis JA, Smilde AK, van der Werf MJ (2006) BMC Genom 7:1–15

    Article  Google Scholar 

  27. Trygg J, Holmes E, Lundstedt T (2007) J Proteome Res 6:469–479

    Article  CAS  Google Scholar 

  28. Yamamoto H, Yamaji H, Abe Y, Harada K, Waluyo D, Fukusaki E, Kondo A, Ohno H, Fukuda H (2009) Chemometr Intell Lab Syst 98:136–142

    Article  CAS  Google Scholar 

  29. Fonville JM, Bylesjö M, Coen M, Nicholson JK, Holmes E, Lindon JC, Rantalainen M (2011) Anal Chim Acta 705:72–80

    Article  CAS  Google Scholar 

  30. Wiklund S, Johansson E, Sjöström L, Mellerowicz EJ, Edlund U, Shockcor JP, Gottfries J, Moritz T, Trygg J (2008) Anal Chem 80:115–122

    Article  CAS  Google Scholar 

  31. Sieber M, Wagner S, Rached E, Amberg A, Mally A, Dekant W (2009) Chem Res Toxicol 22:1221–1231

    Article  CAS  Google Scholar 

  32. Dubery IA, Louw AE, van Heerden FR (1999) Phytochemistry 50:983–989

    Article  CAS  Google Scholar 

  33. http://bioinfogp.cnb.csic.es/tools/venny/index.html. Accessed 20 Jun 2012

  34. Aliferis KA, Jabaji S (2010) Metabolomics 6:96–108

    Article  CAS  Google Scholar 

  35. Safer S, Cicek SS, Pieri V, Schwaiger S, Schneider P, Wissemann V, Stuppner H (2011) Phytochemistry 72:1379–1389

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The South African National Research Foundation (NRF) and the University of Johannesburg are thanked for financial support.

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa

    Ntakadzeni E. Madala, Fidele Tugizimana, Paul A. Steenkamp, Lizelle A. Piater & Ian A. Dubery

  2. CSIR Biosciences, Pretoria, 0001, South Africa

    Paul A. Steenkamp

Authors
  1. Ntakadzeni E. Madala
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fidele Tugizimana
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paul A. Steenkamp
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lizelle A. Piater
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ian A. Dubery
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ian A. Dubery.

Additional information

Published in the topical collection Chemometrics in Chromatography with guest editors B. Jančić-Stojanović and Y. Dotsikas.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 5118 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Madala, N.E., Tugizimana, F., Steenkamp, P.A. et al. The Short and Long of it: Shorter Chromatographic Analysis Suffice for Sample Classification During UHPLC-MS-Based Metabolic Fingerprinting. Chromatographia 76, 279–285 (2013). https://doi.org/10.1007/s10337-012-2336-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10337-012-2336-z

Keywords

Search

Navigation