I bought a new LCMS column that is very long as I require of a very good analyte separation. Just realised the column doesn't physically fit inside the LCMS instrument slot but I would swear I've seen other HPLC/LCMS columns that don't fit inside LCMS instruments used and just left hanging outisde the LCMS. Can I use it?
It should be no problem to have the column outside the LCMS unless you were planning on running the column at a temperature higher (or lower) than ambient. Back in the early days of HPLC there were no column ovens and the HPLC column was just hanging on the tubing between the injector and detector. You could wrap the column in some insulating material if you are worried about keeping it at a constant temperature over a long period of time. Keep in mind the columns operating temperature will also be determined by the temperature of the solvents supplied to it.
Alternatively, you can have an external column oven that is cheap to buy and then you can fit your column and control the temperature that way.
Is the "instrument slot" the same as the system's thermostatted column compartment or just an ambient compartment or open area? *That is the question which must be asked to answer your question.
If the HPLC method is utilizing column temperature (outside of ambient) as a method parameter (controlled temp), then you will need to use a column that fits in the compartment (or as Dalila notes, use an external column compartment to achieve the required column temperature). If ambient temperature is specified for the HPLC method, then you can place the column just as Bruce mentioned, hanging outside it, but please keep the connection capillaries between the injector, column and detector inlet as short as possible.
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