When I want to autoclave pipette tip boxes, I would place these boxes at higher level during autoclave. Placing these boxes (or other materials) near to the perforated platform just above the autoclave water would invite the "dirty" autoclave water (sometimes we tend to change the water once every two days or more) from seeping into the tip boxes. The brownish (probably due to spilt media) water will seep into the boxes and when dried, the tips will have a yellowish to brown stain covering them later.
The dirty water might contain impurities that will inhibit sensitive reactions or worst, contaminate stock solutions, enzymes, and expensive reagents.
Not all labs would use commercially packed filtered tips and we do use sterilized tips for dispensing expensive reagents. It is very important to properly autoclave tip boxes so that no contamination from the autoclave water will occur.
I had my fair share of dirty tips due to the above type of autoclave machine.
Just to share.
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