Please reply with more information - autotune reports before and after the PM and chromatograms from before and after the PM will help narrow down the issues. Are you using an internal standard?
But often - operators run their system at tune electron multiplier voltage, 0V relative to the tune, and as the source gets contaminated by samples the tune EM goes up so the raw peak heights often go up, too. When the source is cleaned, like during a PM, the tune EM goes down, sometimes significantly, and the raw peak heights go down as well.
Please reply with more information - autotune reports before and after the PM and chromatograms from before and after the PM will help narrow down the issues. Are you using an internal standard?
But often - operators run their system at tune electron multiplier voltage, 0V relative to the tune, and as the source gets contaminated by samples the tune EM goes up so the raw peak heights often go up, too. When the source is cleaned, like during a PM, the tune EM goes down, sometimes significantly, and the raw peak heights go down as well.
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