Skip to main content
SpringerLink
Log in

LipidomeDB Data Calculation Environment: Online Processing of Direct-Infusion Mass Spectral Data for Lipid Profiles

  • Methods
  • Published:
Lipids

Abstract

LipidomeDB Data Calculation Environment (DCE) is a web application to quantify complex lipids by processing data acquired after direct infusion of a lipid-containing biological extract, to which a cocktail of internal standards has been added, into an electrospray source of a triple quadrupole mass spectrometer. LipidomeDB DCE is located on the public Internet at http://lipidome.bcf.ku.edu:9000/Lipidomics. LipidomeDB DCE supports targeted analyses; analyte information can be entered, or pre-formulated lists of typical plant or animal polar lipid analytes can be selected. LipidomeDB DCE performs isotopic deconvolution and quantification in comparison to internal standard spectral peaks. Multiple precursor or neutral loss spectra from up to 35 samples may be processed simultaneously with data input as Excel files and output as tables viewable on the web and exportable in Excel. The pre-formulated compound lists and web access, used with direct-infusion mass spectrometry, provide a simple approach to lipidomic analysis, particularly for new users.

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

Abbreviations

DCE:

Data Calculation Environment

m/z :

Mass/charge

MS:

Mass spectrometry

QqQ:

Triple quadrupole

References

  1. Brügger B, Erben G, Sandhoff R, Wieland FT, Lehmann WD (1997) Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass spectrometry. Proc Natl Acad Sci USA 94:2339–2344

    Article  PubMed  Google Scholar 

  2. Kurvinen J-P, Aaltonen J, Kuksis A, Kallio H (2002) Software algorithm for automatic interpretation of mass spectra of glycerolipids. Rapid Commun Mass Spectrom 16:1812–1820

    Article  PubMed  CAS  Google Scholar 

  3. Haimi P, Uphoff A, Hermansson M, Somerharju P (2006) Software tools for analysis of mass spectrometric lipidome data. Anal Chem 78:8324–8331

    Article  PubMed  CAS  Google Scholar 

  4. Haimi P, Chaithanya K, Kainu V, Hermansson M, Somerharju P (2009) Instrument-independent software tools for the analysis of MS-MS and LC-MS lipidomics data. In: Armstrong D (ed) Lipidomics, methods in molecular biology, vol 580. Humana Press, Totowa, pp 285–294

    Google Scholar 

  5. Ejsing CS, Duchoslav E, Sampaio J, Simons K, Bonner R, Thiele C, Ekroos K, Shevchenko A (2006) Automated identification and quantification of glycerolipid molecular species by multiple precursor scanning. Anal Chem 76:6202–6214

    Article  Google Scholar 

  6. Song H, Hsu F-F, Ladenson J, Turk J (2007) Algorithm for processing raw mass spectrometric data to identify and quantitate complex lipid molecular species in mixtures by data-dependent scanning and fragment ion database searching. J Am Soc Mass Spectrom 18:1848–1858

    Article  PubMed  CAS  Google Scholar 

  7. Yang K, Cheng H, Gross RW, Han X (2009) Automated lipid identification and quantification by multi-dimensional mass spectrometry-based shotgun lipidomics. Anal Chem 81:4356–4368

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Dr. Susan Brown for helping us start the LipidomeDB project and obtain financial support for it. We are also grateful to Dr. Youping Deng for his efforts to initiate a lipidomics database and to Drs. Todd Williams and Xuemin Wang for helping us initiate lipidomics work. We appreciate Emily Archer Slone, Byron Sparkes and Dr. Sherry Fleming for allowing us to use their data as example data. We also wish to thank members of the Welti and Visvanathan groups, who provided helpful suggestions. Funding for development of LipidomeDB Data Calculation Environment was from Kansas IDeA Networks of Biomedical Research Excellence (National Institutes of Health grant P20 RR16475 from the National Center for Research Resources). Mass spectrometer acquisition and mass spectrometry method development were supported by National Science Foundation grants MCB 0455318, MCB 0920663 and DBI 0521587, Kansas National Science Foundation EPSCoR grant EPS-0236913, Kansas Technology Enterprise Corp. and Kansas State University. Contribution no. 11-295-J from the Kansas Agricultural Experiment Station.

Author information

Author notes

  1. Liangjiang Wang

    Present address: Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA

Authors and Affiliations

  1. K-INBRE Bioinformatics Core Facility, University of Kansas, 2121 Simons Drive, Lawrence, KS, 66047, USA

    Zhenguo Zhou, Shantan Reddy Marepally, Daya Sagar Nune, Gerald H. Lushington & Mahesh Visvanathan

  2. Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Ackert Hall, Manhattan, KS, 66506-4901, USA

    Prashanth Pallakollu, Gail Ragan, Mary R. Roth & Ruth Welti

  3. Division of Biology, Kansas State University, Manhattan, KS, 66506, USA

    Liangjiang Wang

Authors
  1. Zhenguo Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shantan Reddy Marepally
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Daya Sagar Nune
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Prashanth Pallakollu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gail Ragan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mary R. Roth
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Liangjiang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Gerald H. Lushington
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Mahesh Visvanathan
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Ruth Welti
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Mahesh Visvanathan or Ruth Welti.

Additional information

Z. Zhou and S. R. Marepally contributed equally.

About this article

Cite this article

Zhou, Z., Marepally, S.R., Nune, D.S. et al. LipidomeDB Data Calculation Environment: Online Processing of Direct-Infusion Mass Spectral Data for Lipid Profiles. Lipids 46, 879–884 (2011). https://doi.org/10.1007/s11745-011-3575-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11745-011-3575-8

Keywords

Search

Navigation