You are better off replacing it with hydrogen. If you look at the chromatographic efficiency of nitrogen (Van Deemter curves) you will see that the optimum flow rate/optimum separation velocities for nitrogen are very limited. It takes special flow controllers and pressure regulators to use nitrogen effectively with GC-MS, especially since for many compounds the required head pressure is negative. 

It's a reasonable idea. I have actually done this, but with extensive modifications to the chromatograph.

You don't have the same issues with hydrogen - the curve is flatter than for helium, so it is much more tolerant of small changes in flow. Your pumping system (I am assuming turbo molecular pumps) will not be quite as efficient with hydrogen as with helium, and your tuning criteria will change, but many people have successfully changed over their systems to hydrogen.

Mark is right. There are kits available for some instrument for to mondify flow control. Unfortunately not for mine.

You can use hydrogen instead helium.

You can look for publication with this author's name "Varlet" from IML of lausanne who use such modification of GC-MS device in order to perform helium analysis in biological specimen in forensic context.

If you only want to save helium while the instrument is in standby then you can use any inert gas to replace the helium, but you first step needs to be to calculate how much money you will save, and how much you will lose waiting for the nitrogen to pump away when you want to use the MS. All modern mass spectrometers are optimized to work with helium, using anything else during an analysis will require major inputs to re-optimise your methods. Ion traps will only work with helium.

Thanks everyone for your answers.

Thanks Peter. If I have used nitrogen instead of helium by mistake without changing or optimizing methods. Will there by any impact on system performance?

The 240MS is an ion-trap. It will not work properly with nitrogen. 

Mark, Michael, Jean-Michel, Andreas, please read the question again.

The question is not about using nitrogen during analysis, the question is about using nitrogen when the GCMS system is IDLE.

Some new GCMS-systems have this option build-in, these systems switch automatically from helium to nitrogen when idle. When staring the system up again it will take about 30-60 minutes to flush the nitrogen out.

Regards, Alex

Thanks Alex. I feel you are getting me right. Unfortunately we don't have the automatic gas switching system. But I can change it manually.

However I am afraid that the nitrogen gas may cause some issue in MS because the GC is connected to MS. The model is Varian 450 GC and Varian 240 MS.

What should I do in such case? I have two options left

1. Turn off the system after use.

2. Keep the system always on with nitrogen gas during idle conditions which is cheaper than helium.

Thanks

To re-iterate. You can use nitrogen in standby. You cannot use nitrogen for analysis. In standby the nitrogen will have no bad effect on either the GC or the MS.