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MS TIP No. 8 - Tuning a Finnigan 5100 to Meet BFB or DFTPP Criteria


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Author: Dennis Beauchamp

Affiliation: Roy F. Weston


It is best to reproduce the same conditions for tuning every time you tune. For best results I always make sure that the GC is at the same temperature every time I look at FC43, usually the initial temperature of the GC program used to direct inject the BFB or DFTPP. Also the system should be under vacuum for at least 8 hours. Although the exact ratios required from the FC43 spectrum may differ slightly from instrument to instrument, the required ratios are approximately the same. Once the desired FC43 ratios are determined for a given instrument, they will provide reproducible results for EPA abundance criteria. This is a very important point and will help to maintain Five Point Initial Calibrations for extended periods of time.

In Manual Tune the following values are good to use as a starting point.

Ion Energy 2.75 Ion Program 4.50

Lens 50 Extractor 0.00

High Res. 128 Low Res. 128

The EM Voltage and Electrometer Zero vary greatly from instrument to instrument, the Em can range anywhere from 500 volts to 3500 volts but normally will be between 1000 to 2000 volts. The Electrometer Zero can be from +6.00 to -6.00, putting the EZ at 0.00 is usually the best place to start.

The first thing to do before Tuning is to dip the RF Generator. In Manual Tune set SW on; FM800, and MRO measure the null voltage at TP 3 and 4. This is a DC voltage. It should be below 1 volt dc. A good adjustment is around .75vdc. Once the RF generator is dipped never move the knob.

The next thing to do is to create a new Caltab. This will provide correct mass assignment. In Manual Tune verify that no Ion is saturated (32,760 counts), adjust the EM voltage to achieve this. I usually try to adjust the EM for around 28,000 counts. Leaving the EM, Filament and CalGas on, exit Mtune and run a CA from the MSDS prompt (>). Now you should have a relatively good calibration and final tuning can be done.

In order to properly tune for BFB or DFTPP it is handy to have MID descriptors with specific ions of interest. I've called one "BF" and one "DF".


The approximate FC43 ratios for DFTPP are:

M/Z 69 100% M/Z 131 and M/Z 219 should be equal to each other and about 40% of M/Z 69

M/Z 414 should be 2% of M/Z 69

M/Z 502 should be 1 to 2% of M/Z 69

After direct injection of DFTPP adjust the 131/219 ratio depending on the M/Z 127 in the DFTPP. If it is too low (below 40% of 198) adjust the parameters to make 131 bigger than 219, if M/Z 127 is too high (above 60% of 198) adjust the parameters to make 219 bigger than 131. I usually start with the Lens voltage and ramp it from 10 to 200 volts. It will display this wide range in ten equal intervals. Somewhere over this range the 131/219 ratio should "FLIP." 131 will be bigger then 219, then they should be equal and then 219 will bigger then 131, depending on what is required you can narrow down the ramp to a narrower range. No matter what range is displayed it is always in ten equal intervals. After adjusting the Lens voltage, next adjust the Ion Energy. The Ion Energy is adjustable from 0 to 20 volts but the normal range is from 2 to 4 volts. After adjusting the Ion Energy, next adjust the Ion Program. It is adjustable from 0 to 20 volts but the normal range is from 3 to 10 volts. The key to the Ion Program adjustment is to always keep it at least equal to or higher than the Ion Energy. Never have the Ion Program voltage lower than the Ion Energy voltage, this will lead to unstable tunes.

After each adjustment in Manual Tune, shoot another DFTPP tune and check the ratios. Go back and forth between MTune and direct injection of DFTPP until satisfactory Tune is met. Then after successful tune go back into MTune and hardcopy what Ion ratios were necessary for the DFTPP Tune. This will give a good reference for future tuning.



The approximate FC43 ratios for BFB are: M/Z 69 100%

M/Z 131 and M/Z 219 should be equal to each other and about 40% of M/Z 69. M/Z 219 ratio is related to the Bromoform Response Factor and sometimes slightly increase 219 to 69 ratio 50% or better will increase Bromoform response.

After initial injection of BFB you want to adjust this 219 to 69 ratio so M/Z 174 in BFB is approximately 65 to 80% of the M/Z 95 base peak. Its a good thing to have your M/Z 173 and 1,4-Diflourobenzene M/Z 114 and help maintain the correct response factor.

The tuning method that I use is the same as in DFTPP tuning. I start with the Lens voltage, then Ion energy, then Ion program and then with the standard Ion Source, the Extractor can be ramped from 0 to 6 volts.

After a successful BFB tune it is a good idea to go back into MTune and hardcopy what Ion Ratios were necessary to achieve the tune. This will be a good reference for future tuning.


If M/Z 365 is below 1%, turn up the Electrometer zero in MTune. Increasing the zero will increase system noise and increase the 365. A zero that is too high will cause too much disk space to be used. If M/Z 365 is over 2.5% it would be a good idea to lower the Electrometer zero somewhat.

If M/Z 51 is below 30%, turn up Resolution Low. Be careful, Resolution Low affects the whole mass range so if you turn up the Resolution Low and then find M/Z 443 below 17% then turn Resolution High down.

If M/Z 127 is below 40%, make sure 131 is equal or bigger than 219. Adjust parameters as necessary.


If M/Z 174 is base peak instead of 95, then try raising Ion energy and seeing if it helps.

If M/Z 174 is below 50%, try lowering Ion energy and seeing if it helps

If M/Z 175 is below 5%, usually lowering Resolution Low will bring this in.

If M/Z 96 is below 5%, usually lowering Resolution Low also will bring this in. Also raising Electrometer Zero will sometimes be of help for this problem.

Always keep a copy of a tune file when your instrument was running well. Keep the mass listings, spectra and chromatogram. Also a copy of the file parameters is helpful to have. Then you can use this as a reference the next time you have tuning problems.