ion source and column

1.  It depends on the system and ion source type, SQ, TQ, or QTOF, Electron Ionization orthogonal or axial ion source, or Chemical Ionization.   The source is already contaminated before the tune changes dramatically, too. A few small adjustments by the autotune algorithm may be missed by the operator and tuning is definitely a dance with many partners.  One simple way to determine it is to have a known stable sample that you can inject and evaluate peak height, area, and the peak's spectrum.  As the spectral tilt changes, the higher masses typically get lower as the source gets coated with the adhered organic layer, and the response changes, you can see the reduction in response and choose when to clean the source. An injected sample can also prove that the inlet and column are still working, too.   

In fact it could replace tuning so often. Run the sample and evaluate the results. If it's within typical limits, run samples.  If it's not, then run autotune.  If you inject the smallest volume of the lowest concentration of the cleanest samples you can, GCMSs don't change all that quickly. There are operators running clean drinking water samples that only need to tune once every six months or so.

2.  Are the columns damaged from oxygen exposure?  Once the spine of the crosslinking of the phase to the walls starts and the column bleed shows, the bleed can be reduced but the column damage cannot be repaired necessarily.  Or are the columns contaminated with sample matrix, dirty solvents, or bad gas?   Agilent sells a column rinsing apparatus but I've never heard of anyone who used it. (Capillary Column Rinse Kit for GC | Agilent)  .

thanks for your answer.
Regarding the ion source (EI): it happens that in a relatively new column, the abundance of the peaks of the same control that I had been injecting almost 3 weeks ago, has decreased from 5 x10^5 to almost 1x10^4. I tried injecting a new control, change the liner, septa, etc. and there were no changes. Reviewing the autotune report, I see that the GF is outside the recommended range (1.3228), and that's why I was asking. Also, it's been almost 6 months since the last cleaning.

Exact. Regarding the column, I think they are contaminated with sample matrix. It turns out that I have a method in wastewater that works through SPE. And I say with sample matrix, because I have always had to change the column for the same reason: it happens that once I have run n samples the chromatography starts to fail, which I can only solve by installing a new column. And I say alone, because none of the common treatments that I do work. For example: heat treatment, cutting, etc.
So I conclude that my columns are saturated preventing their proper functioning. From what I was looking for, I found the alternative of washing with solvent, but I see that it is not a widely used technique.

thanks for your answer.
Regarding the ion source (EI): it happens that in a relatively new column, the abundance of the peaks of the same control that I had been injecting almost 3 weeks ago, has decreased from 5 x10^5 to almost 1x10^4. I tried injecting a new control, change the liner, septa, etc. and there were no changes. Reviewing the autotune report, I see that the GF is outside the recommended range (1.3228), and that's why I was asking. Also, it's been almost 6 months since the last cleaning.

Exact. Regarding the column, I think they are contaminated with sample matrix. It turns out that I have a method in wastewater that works through SPE. And I say with sample matrix, because I have always had to change the column for the same reason: it happens that once I have run n samples the chromatography starts to fail, which I can only solve by installing a new column. And I say alone, because none of the common treatments that I do work. For example: heat treatment, cutting, etc.
So I conclude that my columns are saturated preventing their proper functioning. From what I was looking for, I found the alternative of washing with solvent, but I see that it is not a widely used technique.