Chromatography Forum

Greetings, and thank you in advance for any advice.

I am trying to help get a GC-MS from PE functioning (Clarus 580 / SQ 8 S) in a new lab. It is hooked up to a PC Windows 7, using Turbomass software, and operating with He. The instrument was set up by a PE technician in January 2016, but no projects were ever ran on it. The issue I am facing is the following...

I can tune and calibrate the MS; I see clear peaks for the reference gas, and I checked ratios of masses 4, 18, 28, and 32 for no leaks. I take control of the instrument. I can build the MS method (2 min solvent delay, Scan for min 2 - 15). I can build the GC method (initial 50C, ramp to 250C). I put it all into the sample list, and then hit play. The auto-sampler activates and injects the sample, and the GC runs through the entire 15 min method ... BUT

1) The mass spec never displays any spectra. The lower right hand of the screen will change from Not Scanning to Waiting for Injection ... However, the file that is created at the end of the run is no spectrum, no baseline, and from -0.5 to +0.5 seconds.
2) The auto-sampler proceeds to then REINJECT the first sample! And if it finishes that 2nd injection ... it will do it again, and again. If the queue has multiple samples, it will just keep repeatedly reinjecting vial 1 and run through the full 15min method each time ... !!!???

I have read and searched the PE manuals! The problem is they assume everything is working and provide so little guidance on actual troubleshooting. My MS seems to work ... I can tune it. I see peaks when I tune it. My GC runs through the method as programmed. But it is like the GC never notifies the MS it is starting. And while the software on the screen says I submitted 1 of X samples, I can find nothing to justify the infinite loop. Was a COM port set up wrong? I don't want to waste huge money on a service call if it can be avoided. But I`ve been on this for three days now ... ANY thoughts are much appreciated!!! Thank you again.

IMHO
I haven't used the software before so I'm basing this on experience with other instrumentation and software.
I suggest dividing the problem into 3 parts.

1) Is the GC sending the start signal to the MS? disconnected the remote start signal cable and see if anything changes, if not, then an issue with the cable.

2) Can I get MS data?: setup the configuration so the software only thinks you have a MS, then create a sequence and run, the software should not acquire data until the MS has received start signal. The start signal may be a simple contact closure, or it may be complicated like a TTL going high briefly.
This will demonstrate if the remote signal to the MS is working.

3) Is the software faulty?: setup the configuration so the software only thinks you have a GC, and see if reinject issues go away. Demonstrates that software and GC are working.