Posted by: tvasailor | May 1, 2011

Magnetic Accurate Mass Data vs. TOF Data

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We previously employed magnetic sector instrumentation (VG70 and Autospec) to acquire solid probe and GC-MS accurate mass results.  We no longer have that instrumentation.  They were difficult to use, the sources easily fouled, and the tuning was very time consuming.  They were replaced in the last few years by accurate mass TOF instrumentation: Waters GCT, Waters LCT, and Agilent 6550 i-Funnel Q-TOF.

I had collected data that compared our accurate mass results primarily obtained by GC-MS on our magnetic instruments to that noted in the Journal of Organic Chemistry.  Our data compared reasonably well to the literature values.  Some day when we get time, we need to collect data that shows the accuracy and precision of our current instrumentation.  I suspect that the Waters LCT and GCT have a standard deviation of approximately +/-5 ppm.  The Agilent QTOF system is probably round +/- 1 ppm.  Normally for our searches using the Waters systems, we use an error window of around 15-20 ppm and for the Agilent QTOF an error window of 3-5 ppm for determing the identification of unknowns.

In the following graph, I compiled our accurate mass data from our magnetic instruments.  There were 181 points and the standard deviation was 5.4 ppm.


In the next graph, I plotted the data I collected from the Journal of Organic Chemistry (197 different mass spectrometry libraries, 1280 points).  The standard deviation was 6.4 ppm which made me feel reasonably good about our results.  Many of their results were obtained by peak matching which should yield better results than our data.  Ours were primarily obtained by GC-MS with the data system which yields less precise data than peak matching with a magnetic instrument.


The raw data for the comparison of our data to the journal data is available in the following zip file in Excel Format.


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  1. Thank you for posting this very interesting result James. Out of curiosity, is the precision data you showed for the HRMS obtained with lock-mass?

  2. yes on LCT with infusion of a lock mass, we now have a LC-Orbitrap, so the data that i show here is somewhat obsolete

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