AMDIS is AMDAWESOME

As a follow-up to this earlier post I think its important to note that I have discovered how to search the entire NIST library from AMDIS! It is odd but this doesn’t seem to be well described in the manual so maybe I can help other GC-MS ninjas to get the most out of their data by describing it here.

The first thing you have to do after loading a results file, is to analyse it. You don’t need to use any particular library to do this, you just need AMDIS to identify all the component scans in the sample. Any identities assigned to targets in this step will be overwritten in the following one.

Next you have to select the “Search NIST Library…” option from the “Analyze” [sic] menu.

AMDIS11

This will give you a bunch of familiar options. If you haven’t set any reasonably stringent conditions in your earlier analysis step then you might want to specify a threshold to the intensity of the spectra it searches in the highlighted box in the image below. This will save you quite a lot of time. Just make sure you’ve got the mainlib selected in the drop-down box at the bottom left.

AMDIS22

I’ve tried this before and it just gave me an error message so I assumed it was a bug. Analytical software tends to be ridden with bugs and bits of it often just don’t work. As long as you try it on a file that’s already been analysed it will work though.

The output is exactly the same as that from any other AMDIS analysis. The only difference that I can see is that there is no way to automate this process,for batches of results files, unlike when using a custom library. At this stage I am prepared to accept this trade off for the extra hits you get from being able to exploit the ENTIRE NIST LIBRARY.

AMDIS33

You can see here that I’ve had identities returned for 57 targets, using the filters mentioned above. This particular sample is giant squid ink that has been derivatised with MCF*. When I analyse it using the custom library for MCF derivatives I get 114 targets identified. This is pretty good for MCF derv, but when I use the full NIST library to search for matches for all 2592 components I get 192 target matches!

I haven’t done any robust investigations of the accuracy of the full NIST results but they seem superficially relevant. I’m confident the results will at least compliment the MCF-specific results. Watch this space for more detail.

*How awesome is that?

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