What’s the first thing you’ll do when back in the mass spec lab?

Posted on 4th June, 2020

Whilst being desperate to get back into the lab and continuing with my research, I can’t say I’m looking forward to the time when the LC system and mass spec are first switched back on. Since we still have a little time before that is likely to happen, I thought it might be worth jotting down a few ideas so that I have a plan at least for Day One – Please feel free to comment and add any further suggestions below (all constructive comments are VERY welcome)….

Firstly, as our mass spec (triple quad) is no longer under vacuum, a source clean seems like a good place to start. No need to rush this, a few extra hours is neither here nor there. Plus, due to social distancing, there should be plenty of bench space to spread out on.

While the source is in bits and undergoing a clean (sonication etc), time to check the nitrogen supply. Let’s get some clean, dry nitrogen pumping through the system – assuming the generator turns on, that is. Think I’ll disconnect the nitrogen line from the instrument for the first few minutes just in case there is anything in the line which may cause a problem. Over cautious? Maybe, but let’s not tempt fate.

As well as the N2 the LC will need some TLC. Fresh solvents throughout is an obvious first step. What about piston seals? It’s possible that these may have become stuck to the pistons. Careful removal, inspection and lubrication seems prudent. Next, starting with low flow and high organic, switch on the pumps, gradually building up both flow rate and aqueous content. Finally, it’s a case of running multiple blank gradients over the column (to waste) before trying some system suitability standards. Keep a close eye on the back-pressure here just in case!

Mass spectrometer and LC performance need to be checked independently if possible. We use the supplied calibrant solution to infuse directly into the MS to decouple the LC. This can be compared to historical data to determine performance once the masses have been brought back into calibration.

For LC performance, we have a freezer full of six protein mix digests (all from the same stock) for checking sensitivity and peak shape on a weekly basis, so we need to compare performance to that prior to the shutdown.

Finally, a serum digest sample, which is representative of our real samples is used as one final check. All being well we should now be ready to begin analysing live samples as before.


Good luck everyone.

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