If someone told me “I honestly believe, the instrument is calibrated, it seemed okay last year when I checked it last time. It looks like the mobile phase is a bit old, I am pretty sure I replaced it 3 months ago when a spider fell into the bottle, so it should work. It is recommended to clean the ion source daily, but who has time, let’s hope it is not too dirty. I’m just going to run your samples and see what happens. Fingers crossed!” chances are, I would take my samples to be analyzed elsewhere.
So when I hear “We used old reagents, but they should still work, right? I found this old trypsin in our lab, I hope it is still okay. I am pretty sure the protein is still there, but it might have degraded. We bought new co-IP beads and are unsure how much protein we have loaded, but fingers crossed – everything worked!” I lose my mojo. If crossing fingers is a part of the experimental design, how are we going to troubleshoot when something goes wrong? Was it old trypsin or was the hypothesis no good?
Good news! There is a way to check if the old reagents still work and if the beads have the expected capacity – run a pilot experiment using something that always works; run a control experiment (or two) in parallel with the real experiment. Carry your control through the same procedure as your unknown. Check every step in the protocol: did it work? Our facility loves controls so much that there is no additional charge for analyzing them. So go ahead, bring as many controls as you think are necessary and you won’t have to cross your fingers!