May 4, 2009
This is a continuation of a series of posts that began here.
I learned an interesting lesson a few years ago when I was presenting our software on-site to a group of chemists. I began the demonstration by opening up an FID. The response from most of the room was a mix of confusion as well as horror! What is that squigly line you have up on the screen?
It was then I learned that most chemists don’t need fancy processing, nor go through the manual steps of FT, baseline correction, phasing, etc. Provided that the sample was prepared and acquired well, the chemist generally doesn’t need to do anything fancy to make their 1H NMR spectrum look reasonable.
This is why in many open access environments that I have visited, chemists are not required to process their data at all. No need to FT their data, nor baseline correct it, nor phase it.
This can be accomplished in a couple of different ways.
You can supply the chemists with processed data from the instrument. In Bruker-speak that’s the 1r file. In Varian-speak, it’s a phasefile. This is really useful for a chemist because it saves them the additional mouse-clicks for processing data every single time. The only drawback of this approach is that the integrals are usually not all that nice. So a standard workflow for this, is deleting the integrals and re-cutting them a small price to pay, in my opinion. And of course there are always going to be some cases where the phasing is off, or the spectrum will need some additional baseline correction.
Some other ways, for example, in our software, is to use macros to automatically process the data with one button click. Essentially, you need only create a macro with all the steps set to your liking. Once complete, you can use this macro on all your data. Simply import the FID and click the button. Of course you can also import processed Bruker or Varian files and work with them straightaway in the software. Finally, one of the things we added in the software back in version 10 was Shortcut Mode. With this mode, when you import or drop an FID into the software, it will auto-execute a set of pre-defined processing steps. For example FT, phasing, baseline correction, weighting functions, etc.
All in all, there are a variety of ways to greatly simplify the software interaction for a chemist. I recommend if you are a chemist, or the NMR person responsible for setting up the instrument, that you investigate the possibility of getting direct access to processed data. From there, it’s just a matter of cutting integrals, and you’re away!