Most GC-MS vacuum systems comprise of a two-stage pumping arrangement - an initial low-vacuum, high capacity stage consisting of a rotary oil pump or diaphragm pump; and a second high stage, low capacity vacuum pump such as a diffusion or turbo-molecular pump.  The first stage or low-vacuum pump requires maintenance to ensure optimum pumping performance.  Two aspects that are often overlooked are the use of the ballast valve on the vacuum pump and replacement of the pump oil at the correct intervals.

Knowing where your gas cylinders are located and regularly checking the contents is very important for any gas chromatographer when troubleshooting an instrument. People responsible for the cylinders go on holiday or leave and the first the instrument operators knows about it is when they run out of gas and then it is a major panic!
 
Unfortunately, many problems have already occurred by then.
 

Splitless injections are used to transfer all of the injected analytes onto the analytical column for separation and detection and are therefore used for low concentration samples. Opening the split exit too early causes any remaining analytes in the inlet to be flushed out of the split exit and lost. Opening it too late (or not at all) leads to a long, tailing solvent peak which can interfere with the separation and detection of early eluting analytes and provides a higher baseline well into the chromatogram.

Sample introduction or the GC inlet parameters are very often overlooked when developing a GC or GC-MS method, but these parameters are so powerful that they can result in success or total failure of an application and as a result are also the main area for troubleshooting and maintenance within the GC system.