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SpinAssign

Title(optional):
Query peaks: ¹³C-HSQC Format: ¹HPPM <tab or spaces> ¹³CPPM<newline> ¹HPPM <tab or spaces> ¹³CPPM<newline> ¹HPPM <tab or spaces> ¹³CPPM<newline> ... (multiple lines are acceptable) 1D Format: PPM<newline> PPM<newline> PPM<newline> ... (multiple lines are acceptable)

¹H tolerance (ppm):
¹³C tolerance (ppm):
Solvent:
	Consider aliased peaks with the ¹³C spectrum width of ppm
Spectrum type:

	takes minutes if longer query lines. Push the button only once.

A web browser with fast JavaScript such as Google Chrome is recommended.

Release Notes

July 10, 2018. InterSpin update.
SpinAssign was completely re-implemented and connected to the new SpinLIMS database to run within InterSpin.

About SpinAssign

SpinAssign provides batch-annotations of a large number of metabolites against user NMR peaks based on our original ¹H and ¹³C chemical shift database. The database collected chemical shifts under accurately standardized measurement conditions, thus adequate for batch-annotations. Mathematical indices called p-values are implemented to assess SpinAssign results.

Introduction

Metabolomics, which involves the identification and pathway analysis of all measurable metabolites, is becoming one of the most popular areas of research in the post-genomics and proteomics era. NMR-based metabolomics has emerged as an important discipline that offers the advantage of reproducible, non-invasive (i.e., in vitro experiments are not required), atomic-level measurements to support research such as metabolic flux analysis. Our strategy aims to annotate a number of metabolites as many as possible from user ¹³C-HSQC spectrum peaks in a batch manner. That is omics-oriented rather than targeted. To support this research, we developed a ¹H and ¹³C standard chemical shift database of metabolites and SpinAssign, a batch-annotation system for 2D user ¹³C-HSQC query peaks to annotate metabolites.

Method

Figure 1 shows the method we have used to develop the chemical shift database and how to annotate metabolites using SpinAssign.

Figure 1. (A) Standard chemical compounds in metabolic pathways are selected for standard chemical shift database accumlation. (B) A ¹³C-HSQC is recorded for each of the selected chemical compounds and the peaks are accumulated in a standard chemical shift database. (C) The chemical shifts of the standard database on the ¹³C HSQC plane. (D) A ¹³C-HSQC spectrum is prepared for a user biological sample. (E) The ¹³C-HSQC peaks are used as a query and annotated by SpinAssign using the standard chemical shift database. (The image in (A) was obtained from ExPASy Biochemical Pathways.)

Related references

E. Chikayama, Y. Sekiyama, M. Okamoto, Y. Nakanishi, Y. Tsuboi, K. Akiyama, K. Saito, K. Shinozaki, and J. Kikuchi, "Statistical Indices for Simultaneous Large-Scale Metabolite Detections for a Single NMR Spectrum", Analytical Chemistry, 82, 1653-1658 (2010)[PubMed]

Y. Sekiyama, E. Chikayama, and J. Kikuchi "Profiling polar and semi-polar plant metabolites throughout extraction processes using combined solution-state and HR-MAS NMR approach" Analytical Chemistry, 82, 1643-1652 (2010)[PubMed]

E. Chikayama, M. Suto, T. Nishihara, K. Shinozaki, T. Hirayama, and J. Kikuchi ,"Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways" , PLoS ONE 3: e3805 (2008)[PubMed]

Kikuchi, J. and Hirayama, T. , "Practical aspects of stable isotope labeling of higher plants for a hetero-nuclear multi-dimentional NMR-based metabolomics" , Methods Mol Biol., 358, 273-86 (2006)[PubMed].

Kikuchi, J., Shinozaki, K. and Hirayama, T. , "Stable isotope labeling of Arabidopsis thaliana for an NMR-based metabolomics approach" , Plant Cell Physiol., 45, 1099-1104 (2004)[PubMed].

Tools

Peak filter for setting up a simplified SpinAssign query from an nmrDraw-formatted peak file written in a Perl script [download]

This eliminates the peaks possibly caused of decoupling sidebands by regarding tiny peaks (the fraction of less than 8%) that reside within the strip of + or - 0.08 ppm in ¹³C axis from a sideband-generating peak as sidebands. Note that this is over-eliminating candidate peaks. This reads from the standard input and write to the standard output. You might need edit the line 1 in this script to the appropriate path to a perl program.

Usage: gomifilter_HSQC

We recommend the use of as following:

[hostname]$ gomifilter_HSQC < nmrDraw_saved_peak_file > output_result_file