Chromatography Forum

We have been working on bringing a somewhat-neglected Agilent 5975c GCMS back to life. People in our lab would turn it on, use it for a month, then it would sit off for a while. Bare minimum maintenance to up-keep it. We have solved most issues by replacing He air filter (it was saturated!), changing pump oil, cleaning the ion source, replaced both filaments, replacing injector septum, liner & o-ring. Clipped column, new ferrules. However, we keep seeing water (18/69 = 3-14%) in our Air & Water leak checks. We have now separated the MS using a no-hole ferrule and still get water at the same abundance. Oddly enough, when we do a manual tune with the PFTBA valve CLOSED, we see almost no water or nitrogen (abundance around 300-500). When the valve opens, water abundance jumps to 20,000- 40,000+. An air and water check yesterday morning showed water at an abundance of 32,624 (18/69=12.44%), with barely any N (28/69=0.97%) or O (32/69=0.17%). Our first step was to replace the vent valve o-ring. We did so and not much change. We then checked the bulb & its o-ring. All looked fine. Ordered fresh PFTBA just in case, but haven't gotten it in yet.

Values from this morning show abundance of water at 25,880 (18/69=3.07%) and nitrogen 41,344 (28/69=4.90%) and oxygen 15,124 (32/69=1.79%) after purging the calibration valve. We did another 4min purge and the values are water 24,064 (18/69=4.06%), nitrogen 22,216 (3.75%), oxygen 5,215 (32/69=0.88%). Another 4 min purge shows water 10,035 (18/69=3.27%), nitrogen 5,559 (28/69=1.81%), and oxygen 1,611 (32/69=0.53%). However, when you let the MS sit for 10 minutes and DO NOT purge the calibration vial beforehand, the values from an air and water check now read: water abundance 28,368 (18/69=2.73%), nitrogen 56,152 (5.40%), oxygen 12,624 (32/69=1.22%).

We didn't see much nitrogen or oxygen before venting the MS and messing with the vent valve and calibration bulb but it seems to be venting out. Did a manual tune while spraying Argon and saw no signs of a leak. Given the low abundance of water (and N, O, etc.) during a manual tune with the PFTBA valve CLOSED, we believe the water is coming from the valve or bulb itself. Has anyone else experienced this? Any advice or recommendations? We are planning to replace the PFTBA with fresh stuff (it's probably never been changed... although it is at the correct height), but besides that we are puzzled on what to do next...

You pumped this down overnight and your water is at 3%? What's the problem?

Give the MSD interface nut a snug, tune, calibrate and run samples.

I sort of agree with the previous poster. 3% isn't too bad, and you're not gonna have it open when running samples anyway. But it would be nice to know if it's normal for the water and nitrogen to increase when the PFTBA valve is open, and if not, why it's happening to your instrument.