Skip to main content
SpringerLink
Log in

Peakmatch: a simple and robust method for peak list matching

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

Peak lists are commonly used in NMR as input data for various software tools such as automatic assignment and structure calculation programs. Inconsistencies of chemical shift referencing among different peak lists or between peak and chemical shift lists can cause severe problems during peak assignment. Here we present a simple and robust tool to achieve self-consistency of the chemical shift referencing among a set of peak lists. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned. The chemical shift referencing offset between two peak lists is determined by optimizing an assignment-free match score function using either a complete grid search or downhill simplex optimization. It is shown that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. Using a simulated peak list, the Peakmatch algorithm can also be used to obtain the optimal agreement between a chemical shift list and experimental peak lists. Combining these features makes Peakmatch a useful tool that can be applied routinely before automatic assignment or structure calculation in order to obtain an optimized input data set.

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
Fig. 6

Similar content being viewed by others

References

  • Aeschbacher T, Schubert M, Allain FHT (2012) A procedure to validate and correct the 13C chemical shift calibration of RNA datasets. J Biomol NMR 52:179–190

    Article  Google Scholar 

  • Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541–3555

    Article  Google Scholar 

  • Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10

    Article  Google Scholar 

  • Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT—a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149

    Article  Google Scholar 

  • Ginzinger SW, Gerick F, Coles M, Heun V (2007) CheckShift: automatic correction of inconsistent chemical shift referencing. J Biomol NMR 39:223–227

    Article  Google Scholar 

  • Guerry P, Herrmann T (2011) Advances in automated NMR protein structure determination. Q Rev Biophys 44:257–309

    Article  Google Scholar 

  • Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J 38:129–143

    Article  Google Scholar 

  • Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298

    Article  Google Scholar 

  • Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189

    Article  Google Scholar 

  • Ikeya T, Takeda M, Yoshida H, Terauchi T, Jee J, Kainosho M, Güntert P (2009) Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. J Biomol NMR 44:261–272

    Article  Google Scholar 

  • Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Meth Mol Biol 278:313–352

    Google Scholar 

  • Kainosho M, Güntert P (2009) SAIL—stereo-array isotope labeling. Q Rev Biophys 42:247–300

    Article  Google Scholar 

  • Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52–57

    Article  ADS  Google Scholar 

  • López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112–13122

    Article  Google Scholar 

  • López-Méndez B, Pantoja-Uceda D, Tomizawa T, Koshiba S, Kigawa T, Shirouzu M, Terada T, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Hirota H, Yoshida M, Tanaka A, Osanai T, Seki M, Shinozaki K, Yokoyama S, Güntert P (2004) NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana. J Biomol NMR 29:205–206

    Article  Google Scholar 

  • Nelder JA, Mead R (1965) A simplex method for function minimization. Comput J 7:308–313

    Article  MATH  Google Scholar 

  • Pantoja-Uceda D, López-Méndez B, Koshiba S, Kigawa T, Shirouzu M, Terada T, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Hirota H, Yoshida M, Tanaka A, Osanai T, Seki M, Shinozaki K, Yokoyama S, Güntert P (2004) NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana. J Biomol NMR 29:207–208

    Article  Google Scholar 

  • Pantoja-Uceda D, López-Méndez B, Koshiba S, Inoue M, Kigawa T, Terada T, Shirouzu M, Tanaka A, Seki M, Shinozaki K, Yokoyama S, Güntert P (2005) Solution structure of the rhodanese homology domain At4g01050(175–295) from Arabidopsis thaliana. Protein Sci 14:224–230

    Article  Google Scholar 

  • Schmidt E, Güntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817–12829

    Article  Google Scholar 

  • Schmucki R, Yokoyama S, Güntert P (2009) Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm. J Biomol NMR 43:97–109

    Article  Google Scholar 

  • Scott A, Pantoja-Uceda D, Koshiba S, Inoue M, Kigawa T, Terada T, Shirouzu M, Tanaka A, Sugano S, Yokoyama S, Güntert P (2004) NMR assignment of the SH2 domain from the human feline sarcoma oncogene FES. J Biomol NMR 30:463–464

    Article  Google Scholar 

  • Scott A, Pantoja-Uceda D, Koshiba S, Inoue M, Kigawa T, Terada T, Shirouzu M, Tanaka A, Sugano S, Yokoyama S, Güntert P (2005) Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes. J Biomol NMR 31:357–361

    Article  Google Scholar 

  • Wang YJ, Wishart DS (2005) A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins. J Biomol NMR 31:143–148

    Article  MATH  Google Scholar 

  • Wang LY, Eghbalnia HR, Bahrami A, Markley JL (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications. J Biomol NMR 32:13–22

    Article  Google Scholar 

  • Williamson MP, Craven CJ (2009) Automated protein structure calculation from NMR data. J Biomol NMR 43:131–143

    Article  Google Scholar 

Download references

Acknowledgments

We thank Dr. T. Ikeya, Dr. M. Takeda, and Prof. M. Kainosho for the DsbA peak lists. We gratefully acknowledge financial support by the Lichtenberg program of the Volkswagen Foundation, the Deutsche Forschungsgemeinschaft (DFG), and the Bio-NMR project of the European Commission.

Author information

Authors and Affiliations

  1. Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany

    Lena Buchner, Elena Schmidt & Peter Güntert

Authors
  1. Lena Buchner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elena Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter Güntert
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Peter Güntert.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 8111 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Buchner, L., Schmidt, E. & Güntert, P. Peakmatch: a simple and robust method for peak list matching. J Biomol NMR 55, 267–277 (2013). https://doi.org/10.1007/s10858-013-9708-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-013-9708-z

Keywords

Search

Navigation