Hello,
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Mike Here. I've seen the exact same problem you're dealing with - a mass spec with a tiny charge coming back.
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Firstly, the mass spec had a gating grid to shut off the incoming particles during except for the time in which you sampled.
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Next, the the resulting signal had to be processed close to the cup. Run it through a cable and the tribolectric noise will be an issue. In this case, the signal was conditioned by an integrator which was mounted in the vacuum.
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Finally, the integrator was a major piece of work. It had a JFET input amp with a glass capacitor for the feedback and an external reed relay that did the reset. Ah, the glory of yesteryear...
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If I were you, I'd look into the Burr-Brown/Ti ACF2101 sample and hold / integrator. Working off-die, you won't get less charge injection with a semiconductor device. Mount it right off your seal, reset and start it integrating before your peak is expected.
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As for wanting to look at a particular portion of the wave, I'd use two sample and holds. One to grab the value from the integrator before and then another for immeadiately after the event. Take the difference of those sample holds, and either grab it quick with a long time constant sample hold, or catch it with a fast A/D. Be sure to make a dry run before each trial. That will give you a baseline to subtract the offsets and charge injection.
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With 18-20 bits readily available, most folks just leave the A/D streaming the output of the integrator, and get the transition using math.
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. Best Wishes and Good Luck, I wish you well with your experiments,
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. - Mike