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Histogram

 

NUTS Help

HI – Histogram

This is a new tool for reducing or digesting (also referred to as “binning” or “bucketing”) a complicated spectrum for input into software that performs principal component analysis.

Background

Spectra such as 1H spectra of biofluids are so complex that it is not possible to assign all peaks, yet they still contain valuable information.  The spectra must be reduced to a simpler form that is more tractable to enable comparison of spectra and identification of correlations.

This is done by segmenting the spectrum into narrow frequency regions, usually 0.04 ppm wide, and summing all points in each region.  Each region is thereby reduced to a single number, called a descriptor.  This not only reduces the number of data points to a more manageable number, but also allows for small differences in chemical shifts, such as might be caused by variations in pH.

It may be desirable to eliminate some descriptors (such as the residual water peak, which varies from spectrum to spectrum).   The values are normalized, to allow comparison of different spectra.  The resulting data are output as an ascii text file consisting of 2 columns of numbers, chemical shift and intensity.  This data can then be analyzed by other software.

Using the HI command in NUTS

6/19/2002
HI
– (or equivalent, non-2-letter command  histogram)  This command generates a text file which is a list of intensity descriptors. The first item in each line of the descriptor file is the PPM value of the start of the descriptor.  The second item is a relative sum of the intensity in the descriptor PPM range, which by default is 0.04 PPM wide. The descriptor file has the following characteristics:

All negative sums are zeroed
The sum of all descriptors is 1.0

By default, the size of each descriptor is 0.04 PPM. By default the total spectrum is used for the descriptor file and all data points in the file are used.  It is possible to customize this by having NUTS read a file containing the relevant information.  This is done with NUTS in the non-2-letter command mode.  The command will take an argument which is the file name for this descriptor properties template file. A sample file is shown here:

Histogram_Template
Descriptor_Size 0.1
Include 10.0 0.0
Eliminate 9.50 9.0
Eliminate 5.00 4.00

The ends of the spectrum can be ignored by specifying a region to be digested, with the “Include” line.  The regions specified by “Eliminate” are excluded from the descriptor file.

References

Metabolic profiling of chronic cadmium exposure in the rat, Griffin JL, Walker LA, Shore RF, Nicholson JK, CHEMICAL RESEARCH IN TOXICOLOGY, 14 (10): 1428-1434, Oct 2001

An NMR-based metabonomic approach to the investigation of coelomic fluid biochemistry in earthworms under toxic stress, Bundy JG, Osborn D, Weeks JM, Lindon JC, Nicholson JK, FEBS LETTERS, 500 (1-2): 31-35, Jun 29, 2001

Metabonomics: Metabolic processes studied by NMR spectroscopy of biofluids, Lindon JC, Nicholson JK, Holmes E, Everett JR, CONCEPTS IN MAGNETIC RESONANCE, 12 (5): 289-320, 2000

Pattern recognition methods and applications in biomedical magnetic resonance, Lindon JC, Holmes E, Nicholson JK, PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 39 (1): 1-40 Jul 2, 2001

 


Last updated:  12/04/2002