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Different retention times on identical instruments

Posted: Sat Mar 01, 2025 2:01 am
by foodtesterchemist
Hello,

My company has two laboratories with identical Shimadzu/Sciex LC-MS/MS triple quad instruments and identical LC columns. There is a test we run for a set of two analytes, and at the two laboratories, we find different retention times for these analytes. At lab 1, we have retention times of 1.75 mins and 2.75 mins; at lab 2, we have retention times of 2.5 mins and 3.0 mins, respectively.

Is this just a matter of e.g. different lengths of tubing between the LC and the MS, etc.? Or are these retention time differences indicative of some deeper discrepancy between the labs?

Thank you for any advice you can provide!

Re: Different retention times on identical instruments

Posted: Sat Mar 01, 2025 2:47 pm
by Consumer Products Guy
I'm assuming that these two labs are in different cities; if not, I'd take the column over to the other lab and see what happens when I installed that there.

Otherwise, the usual suspects are:
columns of different lots/age/usage/history
lab temperature if units are not temperature controlled
different tubing lengths and/or internal diameters

So what would I do if I encountered similar when I was working? I'd purchase two brand-new columns from the same lot number from my supplier, and run both at my R&D lab. If same performance, I'd send one column to lab #2 to try there, before I made a "hands-on" trip there.

Re: Different retention times on identical instruments

Posted: Sat Mar 01, 2025 7:34 pm
by foodtesterchemist
This is helpful, thank you! I agree that columns and temperatures are good possibilities to explore.

As far as the lengths of tubing, would that be expected to create a consistent offset in elution times between the two labs (e.g. all peaks shifted by X minutes) or might the different peaks shift in their elution times by different amounts? I would think the latter is more likely to be a column and/or temperature difference, but maybe that's not true.