The tune report gives an indication of the condition of the mass spectrometer. It is independant of the GC as long as the column flow is the same each time the tune report is made. The condition of GC and MS together can be checked with injection of a liquid sample (like OFN or HCB). And a reference sample run through the P&T will give you an indication of the whole system. If you check the MS first and find no problem, then a problem in the GC and MS combined has to be the GC. Likewise if the GC and MX combined are OK, but the problem occurs when you bring in the sampler, the problem is with the sampler.
And do not neglect to tune (or optimize) the instrument on a regular basis. Some like daily, others weekly. But I've seen an instrument go for three months without being tuned. Sensitivity returned dramatically after the instrument was tuned... (It apparently was a surprise to the operator. Story for a different day...)
First make sure all the PM stuff is up to date (inlet liners, septa, leak check the column, etc.) Then, look to see what is not running to spec. With the instrument known to be in good shape, look at things like peak shape in the chromatography. Narrower peaks give better signal to noise values than short, fat peaks -- even if they have the same area. Look at injection conditions. Again, the narrower the sample band on the column, the narrower the peak and the better the signal to noise. Adjustments of the chromatography are low cost or no cost. Look at sampling rate to be sure that you are properly sampling the chromatographic peak - undersampling or oversampling will affect peak RSD's - and detection limits. After you have looked at all of those parameters, look at detector voltage. Increase it to obtain the detection limits you need. Just understand that this is not a no-cost adjustment. Higher detector voltages shorten the life of the detector - so use the "no cost" changes first.
