minimum pressure in stand-by mode

Built into MassHunter Acquisition are some GC Calculators. 

Using the Pressure/Flow Calculator, 15m column at 50°C and 1 ml/min, the inlet pressure required is only 1.1psi.  It is recommended to always have the inlet at >=5 psi for decent pressure regulation.  This is hard to do with a short column going to vacuum. 5psi needs the oven to be 100°C to be 1.22 ml/min.

The GCMS benefits by maintaining thermal equilibrium. If you have the ion source at 100°C standby and then want to run, it takes a little while for it to heat up to 230°C - but at least a couple of hours for decent stability.

I would suggest these parameters for standby.

Inlet temp = whatever is in your method - typically 250°C or so.
Inlet mode = split, 20ml/min total flow - do not go lower than this. The inlet needs flow to be able to maintain the inlet pressure which is the column flow.
Column flow = 1.2 ml/min - this is the optimum flow when running samples as well. The range with helium is 0.5 to 1.5 or so. Higher and lower change the way it works.
Oven temp = 111°C  --- I use this because it is over 100°C and I can see that 111 is different from across the room. 
Transferline temp = whatever is in your method - typically 250°C or so
Source = whatever is in your method - typically 230°C or so....but that's a good discussion topic. I like hotter ion source temps, like 265°C.
Quad = 150°C.  Never run the quad hotter than 150°C - there's no good reason for essentially all methods.

Keeping the oven >100°C helps reduce differential expansion differences with the brass transferline nut and the stainless steel transferline.  Leaving the oven cold often results in that nut loosening a bit and causing a leak.

Why a 15m x 250uM column?  You may want to explore alternative 30m x 250uM or a 20m x 180uM columns to allow you to run at higher inlet pressures.   

Thanks a lot for a detailed explanation.

About the oven temp.and differential expansion differences, the method I am using starts with a oven temp. 50degC and goes upto 280degC with a ramp of 20deg/C - could it cause the nut loosening and leak?

The transferline is very hot. If the oven sits cold, like <60 to 100°C  for many hours the brass MS transferline column nut and ferrule may get a bit colder than the transferline, contract, and leak.  Maybe.  It happens overnight or the weekend, typically. The first thing users do is crank down harder on the nut with a wrench to seal it again.  Some do this once or twice and it stops forever - with that column installation.  The better solution is to use the Self-Tightening Column nut and the required short vespel/graphite ferrule.  It has spring washers inside that hold the proper pressure on the ferrule and keep the seal no matter the temperature differential.   G3440-81013 | Agilent  

paulsalverda  Thanks a lot for explaining my query. We do have a self-tightening nut but yet to be installed. Till date, I have been using regular ferrule and nuts.

Make sure the ferrule on the MS transferline is the vespel/graphite one and not 100% graphite.   The 100% graphite ones are shiny.  The brass transferline nut uses the long ferrule and the self-tightening one uses the short ferrule.

 paulsalverda  Thanks a lot for explaining further. I believe the ferrule is not 100% graphite, but I will surely doublecheck on that. 

An off-topic query : It's mentioned in the 'Steps to Shutdown a system' booklet that to "open the vent valve ~1/2 turn counter clockwise" during the pump down of the MSD. I am wondering that it isn't said to turn it back clockwise afterwards -- why so?

Which booklet? A link or part number?  

It surely should say to turn it back!  Make sure that any cables are connected before turning on the power.   Open the vent valve ~1/2 turn.  Turn on the power to start the rough pump.  Hold the analyzer door closed.  When you hear vacuum sucking air in through the vent valve you know that the vacuum is working and the door is shut.  Turn the vent valve all the way closed clockwise.  Wait at least an hour before using the MS to ensure that the air is pumped away.

It's just metal pressing against an O ring-  the same as an injection port liner O ring -- so tightening it harder does not make it more leak-free.

Which booklet? A link or part number?  

It surely should say to turn it back!  Make sure that any cables are connected before turning on the power.   Open the vent valve ~1/2 turn.  Turn on the power to start the rough pump.  Hold the analyzer door closed.  When you hear vacuum sucking air in through the vent valve you know that the vacuum is working and the door is shut.  Turn the vent valve all the way closed clockwise.  Wait at least an hour before using the MS to ensure that the air is pumped away.

It's just metal pressing against an O ring-  the same as an injection port liner O ring -- so tightening it harder does not make it more leak-free.

Sharing the screenshot of the page

Oh!! can't believe I missed that phrase !! probably the "~1/2" caught my attention and was looking for the same afterwards!!

As I start venting the MS, the window shows "Turn off the MS transfer line and set the GC oven temperature to ambient". Is the correct sequence to cool down the transfer line and GC oven and then start venting the MS? 

Is 40 degC a convenient temperature for the transfer line and GC oven? Should I cool down the front inlet as well similar to the previous two?

40 is fine, lower than ambient or set to OFF is typical, though.  They don't need to be cooled down before you start venting as the turbo does take some time to spin down - or if it is a diffusion pump the fluid to cool down. I only cool down the inlet if I'm going to do inlet maintenance or I don't want to get burned by it.  If you're not going to change the septum or liner or cut the front of the column and reinstall with a new ferrule - as long as the helium still flows it can stay hot.  If the helium will be shut off or the column removed at all, cool it down at the same time.

Oxygen is the enemy of the inlet, liner, column, and into the ion source. Do everything you can to minimize oxygen entry when those parts are hot.

As I started venting the MS and this message popped up, although the venting cycle was complete in due time. I kept the system as it was overnight but the message did not go away. That's why I wonder if those parts need to be cooled down before venting. The helium flow is kept shut off for a while, so I cooled down the front inlet temperature as well and finally shut the valve of the He tank the next day. Hope this doesn't hurt the system and I am following the correct route.