LCMS Start of end of the day routines?

[KevinBe]

Hi All,

First of all, I'm really sorry for all the stupid questions I will be asking but I am far from a specialist...

We are a typical organic chem lab and we just got our very first own HPLC PDA/MS (a bit of a luxury I guess).

We would "just" be running samples to follow reactions, identify unknown compounds and maybe do a bit of quantification.

Usual conditions would be C18 RP, using A- H2O/0.1% Formic acid B- CH3CN with 0.1% formic acid.

The usual ramp from 95A/5B to 5A/95B.

And my questions were:

1- At the end of the day, how do you store your column for the night? Do you flush it with 95A/5B? Or do you want to avoid the formic acid and flush it with H2O/MeCN without formic acid?

2- At the start of the day, do you flow a lot of 95A/5B before starting? Or do you start right away?

Thanks a lot,

K

[James_Ball]

Unless it is one of the "aqueous" columns, which are specially made for high aqueous mobile phases then I would not store it with 95% aqueous mobile phase. It is better for most columns to store with at least 50% organic, and I would just store with the final 5% aqueous 95% organic mixture if storing overnight or longer.

In the morning, flush with the 95A/5B for 15-20 minutes. I normally set mine to flow this while I am getting everything else ready and preparing my samples and putting the sequence into the software, then make a blank injection or a wakeup injection of the check standard to see if the peaks are where they should be and have good shapes, if so then the column is equilibrated and ready to go.

[lmh]

I'd store in 70-80% organic, 20-30% water, no formic acid or other additives. You only need to flush a few column-volumes through. You can have a method set up to do this, added to the end of your last batch.

I don't bother doing any special start-up procedure.

If you're in a chemistry lab, with multiple users, the biggest risk you face is chemists who think that a dilute sample means 20mM. Or more likely, they think that a dilute sample means about this much stuff in that much solvent ("this much" meaning a spatula-full scraped off the bottom of a round-bottom flask from the rotary evaporator, and "that much" meaning a squirt from whatever pipette happened to be handy). These chemists will block up your desorbation line. Then they will get no signal, so they will assume they haven't injected enough, and they'll make up a more concentrated sample. They will also be adamant that they must use a more concentrated sample, because "otherwise they can't see anything". You only need one chemist like this to foul up the entire enterprise. Fortunately the vast majority of chemists are lovely people who don't work like that, but I don't have a strategy to deal with the one who causes catastrophe...

If your system has a way to divert to waste, you may also want to use it, if you have chemists running samples with good retention of the analyte, but salts and buffers from a reaction still hanging around. To be fair, this is more the crime of the Biologist, who forgets that their sample was grown in 0.5M sucrose. At least it smells nice in the spray chamber...