Monday, November 06, 2006

JCAMP-DX criticism

The JCAMP-DX protocol is a pair of articles, republished as scanned images. This fact alone, compared to the XML protocol says it all: with no money, you cannot be elegant and good-looking. The fact that the protocol looks so old, combined with the sentence: The commitment of three leading NMR spectrometer manufacturers at the Sixth INUM Conference in Italy 1990 to implement the standard when finished... makes me feel like an historical character, like if I had been at the Yalta Conference. I was indeed a registered attendee of the 6th INUM Conference, and I cannot forget it because it was my first time in the lovely Stresa. I was a completely passive attendee, of course, and it was also the first time I heard about the JCAMP standard, which seemed to me a wonderful idea. I hoped for a universal format for all spectra and easy connection of all spectrometers to PCs. The second hope has materialized after many years. The first hope soon faded away and had no reason to exist in the first place. Now that I am a player in the field I know that it's plainly impossible nor desirable. Then I was young and hopeful. The mere fact to be there, as the representative of a multinational corporation, was an accomplishment. Now it seems a dream. I really wonder if it was all true. Enough for the personal considerations. Back to the file format.
If you read the article you can't understand the protocol, because it is described elsewhere, in the infrared section. This is only the first fault: the protocol had to be contained into a single document. Let's count them all.

  1. The lack of a single reference text. Each new version should have completely substituted the old ones (like the pharmacopeia).
  2. Definitions are not complete. A sentence like: "FIDs will be handled differently depending on whether they originate from a spectrometer with a single detector and analog-to-digital converter (ADC) or with twin detectors and a single ADC." is clear but doesn't really help. How is the FIDs to be handled? How digital instruments enter into this picture?
  3. It was probably OK for IR, but when extended to 1D NMR it was not so great. Extension to 2D is questionable. They had to go from the general to the particular, but they went the other way.
  4. Let's not forget that today we have XML.
  5. JCAMP-DX, when it works, is simply a mean for data exchange, not for archival. It is not considered by regulatory agencies.
  6. It allows the creation of too many flavors of files.
  7. There is no validator.
  8. Existing programs both write and read (without warnings) files that are not completely compliant with the published guidelines.
  9. Numbers are rounded so, whatever the article says, the conversion into JCAMP-DX generates a small loss of information. This loss is highly variable.
  10. The only thing that the existing file formats had in common, is that they only store the intensity values. JCAMP-DX is the only NMR file format that stores the abscissa values.
  11. It is not popular.
  12. They forgot that NMR is not limited to chemicals. Spectra of living beings are not considered.

Creating an NMR standard is difficult and unpleasant. It was a dirty job and somebody did it and it even works (some times). I am not able to do any better. The good news is that nobody cares, therefore: why should we care?


At 9:57 PM, Anonymous Anonymous said...

Hi there,
I have a rather strange query for you. Is it possible to convert JPEG/BMP/TIFF files to JCAMP-DX? My NMR spectra is available ONLY as a scanned/hard copy and I am unable to make correct deductions regarding the structure of my compound. Is there any way to help me out? My thesis is stuck on this:(
Hoping for some help.

Thank you,

At 10:05 PM, Blogger old swan said...

Dear Fatima,
in theory it is possible to write a software to convert a very high-quality picture into JCAMP-DX. It's like with OCR (optical character recognition). The quality of the resulting spectrum, however, cannot be higher than the original. From what you say the quality of the original IS the problem... You should find a partial solution for a partial problem. What's your problem: extracting the frequencies of the peaks or measuring the integrals?

At 12:01 PM, Anonymous Anonymous said...

Hi again,

As I mentioned in my earlier post, I have the NMR spetra but am unable to read it as in which chemical shift belongs to which functional group..the splitting of signals etc..I have tried to make some assignments but wouldnt know whether they are correct or not. Do you know of any website that would help me tell whether the assignments are right or wrong? Thanks,


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