You could resolve the issue?

It could be internal turbo pump issues/ break down or transfer line leak issue!

There are many possibilities. Could be a seal on the point of breaking, the turbo pump, leaks etc. Start by isolating from the GC by blanking the transfer line. If you are able to obtain and maintain vacuum now, then it may be a connection or the column on the verge I would replace all nuts, ferrules, and columns between inlet and transfer line.

If you still have the issue, I would contact tech support as they likely have protocols to troubleshoot and identify the source of error.

Too many possible reasons to list in a free forum like this one (including, as mentioned, a problem with the vacuum pump, or something simple such as the column has not been properly connected). Follow basic troubleshooting steps.

As you are a student at a school, please contact your teacher or the person in charge of maintaining and training people in the use of the specific GC-MS system that your school has. Utilize their expertise. Anyone local with practical experience in using the GC-MS system will be able to assist you troubleshoot the vacuum leak. Vacuum leaks are somewhat common, so experience and training are required for anyone planing on using or maintaining any GC-MS system.

To detect leaks the better is to start to check part to part the equipment starting from the MS an later move to the GC. From your description it only happen when you are running a sequence? Are you sure? without using it check the vacuum. It that it is the problem that means that from the GC something allow to enter air time to time. Normally when it change the temperature inside the oven. For that reason you have to fit all the connection at room temperature and a little more in hot. I don´t know if you are an authorized operator but take in care that when you are doing this, the filament must be off and don't use the Pirani vacuum control when you are working in the equipment because any quick loose of vacuum could break the filament of the MS or the Pirani vacuum sensor!! If you didn´t know all these call the service.

Most probably, it could be due to some leakage in the system. It could be from the column connection point or even from the door of the ion source. You need to find out the source of leakage by checking all the possible points. If you are not able to detect it yourself, take the help of a service engineer from the service provider.

1- Check the pump itself for the correct rpm

2- if the source chamber dosen't leak(screw tightened) , check the O RING on the closing side of the chamber

3- verify column is not broken

4- check for the inlet side ferrule( over tightening might crush the ferrule )

5- check liner / septa for any possible leaks.

I agree mostly with the answer given by @ Eleuterio Umpierrez . Check point for point and do it in a systematic way. 1- injector fittings 2-column-in nuts 3-column-outlet nuts 4-checking the fittings of an eventual "make-up gas". If the leak is very small, even then you will have trouble in recording mass spectra. You will receive just peaks for 28, 32, 40, 44 ... (N2, O2, argon, CO2 ...).

You did not tell what kind of GC-MS and what GC method You use. This knowledge would be helpful to solve the problem. But a view general remarks:

Especially if you inject splitless it might be the case that the injected solvent leads to a shutdown of your vacuum system if your cut time is not chosen the right way. The presence of impurities like DEHP (an ubiquitous phthalate) may also lead to vacuum problems during the elution time of DEHP. Some GC-MS have two separate high vacuum gauges (at source and analyzer). If it is set to source during the measurement You might observe problems with your vacuum system, also.

Thank you very much for your answers. I am grateful for that. I will take note for the future.