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I am not planning to do these types of experiments but I would like to know the order of magnitude of the time it takes to run an LC-MS/MS experiment. Let's assume that I have the sample prep (protein) finished and I just need to load the sample into the LC. How long would I need to wait before I would get MS/MS data?

I know that for a typical HPLC experiment, the sample takes around 20 minutes to go through the column.

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    $\begingroup$ The LC is the rate-limiting step. That can take anywhere from a couple of minutes to hours, depending on what you're eluting. The MS-MS part should be a breeze. $\endgroup$
    – CHM
    May 15 '12 at 17:45
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The MSMS part is the detection of the LC in this case (nb. you don't need to do LC-MSMS, you can do direct infusion quite happily if you don't need to separate anything), so the actual experiment wouldn't need to take much longer than any other LC (as CHM says).

However, calibration + set-up of these things, and extensive cleaning afterwards, can make it a day's job to run just a few samples (even direct infusion). If you don't have much information on the system already, you may also find that you need to do a 'sighting' run, to work out which ions you need to examine more closely (MSMS). And then there is data processing.....

All in all: quick, if you know exactly what you want, and someone is running everything for you. If you want to argue that it is an easy job, you can, but be aware that this is not always gong to be the case.

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You can adjust your run times to your preference, based on your conditions. For example, I am doing LC-MS/MS on steroids (low molecular weight compounds) extracted from human urine samples through a liquid-liquid extraction. It only takes me 10 min per sample from the time the run starts until the very end of it.

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    $\begingroup$ May you share details on your column and eluent? This would be a nice addition to show how different elution conditions can affect separation time. $\endgroup$
    – CHM
    May 17 '12 at 1:24

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