No peaks

You have a small air leak that should be fixed.

Did your peak's retention time move or just got really small but stayed in the right place?

Did you try squirting the sample from the syringe onto a KimWipe to make absolutely sure sample comes out?  Plugged syringes happen all the time as do worn out plungers.

How far is the column installed in the injection port? Into the MS?  How is your guard column connected to the analytical column? What happens if you install the analytical column direct into the inlet?

I found that our syringe plunger failed to withdraw sample. By replacing with a new syringe, the problem solved. So the sensitivity issue is resolved. thank you very much for your tip.
However, we have come across another issue - unusual features in the auto tune result that we have never had before; low ion focus (72 deg instead of 90.2), double humps in repeller. I also see gain factor and EM voltage increased a bit than early September. I switched to Filament 1 (as this is new) in manual tune parameter window, and ran auto tune, but it continued to tune using filament 2 which is old...During the troubleshooting last week, we had replaced the column with a dirtier one accidentally and got auto tune failed. Then we replaced back with the newer column, cleaned the ion source again and the tune came to normal, exept the two issues mentioned above. Can you please advise me regarding the low ion focus and double humps in repeller?

I found that our syringe plunger failed to withdraw sample. By replacing with a new syringe, the problem solved. So the sensitivity issue is resolved. thank you very much for your tip.
However, we have come across another issue - unusual features in the auto tune result that we have never had before; low ion focus (72 deg instead of 90.2), double humps in repeller. I also see gain factor and EM voltage increased a bit than early September. I switched to Filament 1 (as this is new) in manual tune parameter window, and ran auto tune, but it continued to tune using filament 2 which is old...During the troubleshooting last week, we had replaced the column with a dirtier one accidentally and got auto tune failed. Then we replaced back with the newer column, cleaned the ion source again and the tune came to normal, exept the two issues mentioned above. Can you please advise me regarding the low ion focus and double humps in repeller?

Switch to Filament 1 - then save the tune as atune.u ... and then tune again.

Sometimes it is necessary to replace both filaments with new ones at the same time. The opposite unused filament is not glowing, but the electrons still go there and are reflected back. The electrons bounce back and forth four or more times. 

Have the repeller insulators been replaced lately?  Are they pristine white beautiful ceramic?  What about the brown lens insulator, replaced sometime in the last couple of years?  How about the PM on the rough pump - how old is the pump itself?  What is the column flow into the MS during tune?   Pumping/vacuum issues can cause strange tuning and results.

And just for fun - how many runs are on that system?

6890:
Options
Diagnostics
Instrument Status

Thank you. I finally switched to Filament 1, and a lot of the tune issues went away - not really expected that they could get better with a new filament!
But, anyway now I've got lower gain factor by double, and no more two humps in repeller. Ion Focus rose a little, but still significantly lower than 90.2...
It's good know that all sorts of things can affect the tune results regarding repeller. Thank you for your comments. I'll keep it mind.
Foreline pump has been refurbished early this year, and column flow remained at 1.0 mL/min, 
One question is can I sonicate the repeller insulator? I sonicated 4min three times in different solvents during cleaning, which actually made it cleaner. Can that cause  unnoticeable breakage or crack in the insulator? The brown lens insulator is pretty expensive... Please let me know if there is a good way to clean this.
We've been using the system since 2017, and it's possible that it was a second hand instrument. 

The repeller insulators are ceramic. They're quite porous so sonicating in solvent doesn't help all that much. It won't hurt them but doesn't clean them enough.   If your lab has a muffle furnace, you could put them in a ceramic crucible and bake them hotter than 500°C...up to 1000° C is fine for them.  This cleans them well.  Slowly heat up and slowly cool down, too or the thermal shock can break them.

The brown lens insulator is vespel so maybe some careful use of a cotton tipped swab dipped in solvent will help, but the recommendation is to replace it somewhat regularly.  

It was originally sold in August 2007.

Thanks for the good tip for insulator cleaning. I'm going to order a repeller insulator spare.

Interesting that you found it!
What would be the shelf-lif of GCMS, especially MSD?

Much can be gleaned from serial numbers.  Yours was built in August 2007.  That means 4,013 work days since then. How many samples has it run? How many times has the source been cleaned? The column replaced? The pump PM'd?   5,915 calendar days - how many revolutions has the turbo pump, which spins at about 60,000 rpm, turned?  That's a fun calculation.... about 5,11 x 10^11 !

The 5975C end of production was 11/30/2013.  The End of Guaranteed Support was 12-31-2020.  There are some parts that are either at incredibly low stock worldwide or even unavailable.  There is no way to get new replacement electronic parts made for that model as those chip manufacturing processes are not even used anymore. The standard turbo pump TMH071 pump is obsolete - has it been replaced sometime by the Pfeiffer HiPace 80 (G3170-67000)-- about $9,000 USD of parts plus labor?    The detector - the older EM is no longer manufactured --- has it been replaced sometime by the Triple Axis Detector version using the G3392A kit - about $4,500 USD of parts plus labor?  

The upside is that there are still many of these out there running, but they are all coming up on at least ten years old.  Electric fans, turbo pumps, and rough pumps all spin and spinning devices fail eventually.  Sample residue deposits on all of the surfaces inside the vacuum chamber. They redistribute and dirty a freshly cleaned source faster the older the instrument gets.  That requires remedial cleaning.

So ...it's complicated.  The 5975C is at or quickly approaching the time where fixing it may not be economically feasible.

That's very useful to know in PM. I think the turbo pump and the foreline pump have been replaced, but not sure about the detector...
Thanks for all your support. I've learned a lot through this community and am having more fun in GCMS.