Skip to main content
SpringerLink
Log in

A fast algorithm and software for analysis of FT-ICR data

  • Original Paper
  • Published:
Journal of Mathematical Chemistry Aims and scope Submit manuscript

Abstract

In this paper, we present and analyze a fast algorithm that determines the possible molecular formulae corresponding to the resolved peaks in the spectral data obtained from a mass analyzer like an FT-ICR-MS. In contrast to our approach, most known algorithms and software that attempt to solve this important problem are brute-force in nature and consequently, highly prone to combinatorial explosion when dealing with the volume of real data. We also present an object-oriented implementation of our algorithm in a general-purpose, user-friendly, interactive, and easily extensible software tool PG Compound Match Finder. A run-time performance analysis of our software shows that even when dealing with several billion theoretical possibilities matched against tens of thousands of resolved peaks, a complete analysis using today’s standard desktop machines can take only a few minutes.

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

Similar content being viewed by others

References

  1. Comisarow M.B., Marshall A.G.: Fourier transform ion cyclotron resonance spectrometry. Chem. Phys. Lett. 25, 282 (1974)

    Article  CAS  Google Scholar 

  2. Pulapaka H., Gibson D.R.: An efficient algorithm for chemical fingerprinting. J. Math. Chem. 44(1), 75–87 (2008)

    Article  CAS  Google Scholar 

  3. J. Bryant, T.J. Manning, D.R. Gibson, A.G. Marshall, R. Rogers, Comparing chemical fingerprints: is oil the product of bacterial production? 58th Southeast Regional Meeting of the Americal Chemical Society, Augusta, GA, United States, November 1–4 (2006), SRM06-704. Publisher: American Chemical Society, Washington, DC CODEN: 69INUY Conference; Meeting Abstract written in English. AN 2006:1191233 CAPLUS

  4. Seebass B., Pretsch E.: Automated compatibilty tests of the molecular formulas or structures of organic compounds with their mass spectra. J. Chem. Inf. Comput. Sci. 39(4), 713–717 (1999)

    CAS  Google Scholar 

  5. Lederberg J.: Rapid calculation of molecular formulas from mass values. J. Chem. Educ. 49(9), 613 (1972)

    Article  CAS  Google Scholar 

  6. Rockwood A.L., Haimi P.: Efficient calculation of accurate mass of isotopic peaks. J. Am. Soc. Mass. Spectr. 17(3), 415–419 (2006)

    Article  CAS  Google Scholar 

  7. Kind T., Fiehn O.: Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 7, 234 (2006)

    Article  Google Scholar 

  8. Kind T., Fiehn O.: Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8, 105 (2007)

    Article  Google Scholar 

  9. Senior J.K.: Partitions and their representative graphs. Am. J. Math. 73(3), 663–689 (1951)

    Article  Google Scholar 

  10. Morikawa T., Newbold B.T.: Analogous odd-even parities in mathematics and chemistry. Chemistry (Bulg. J. Chem. Educ.) 12(6), 445–450 (2003)

    CAS  Google Scholar 

  11. Weiss A.W.: Data Structures and Problem Solving Using Java. Addison Wesley, Reading, MA (2006)

    Google Scholar 

  12. Cormen T.H., Leiserson C.E., Rivest R.L.: Introduction to Algorithms. McGraw-Hill Publishing/MIT Press, NY/Cambridge (1990)

    Google Scholar 

  13. Tovey C.: Tutorial on computational complexity. Interfaces (INFORMS) 32(3), 30–61 (2002)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics and Computer Science, Valdosta State University, Valdosta, GA, 31698, USA

    David R. Gibson

  2. Department of Mathematics and Computer Science, Stetson University, DeLand, FL, 32723, USA

    Hari Pulapaka

Authors
  1. David R. Gibson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hari Pulapaka
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hari Pulapaka.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gibson, D.R., Pulapaka, H. A fast algorithm and software for analysis of FT-ICR data. J Math Chem 48, 381–394 (2010). https://doi.org/10.1007/s10910-010-9679-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10910-010-9679-1

Keywords

Search

Navigation