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Use of Zip Tips for proteins digested with trypsin before LCMS


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Our interest is in LC/MS of the peptides, and we plan to work in water/acetonitrile/formic acid.  We found a number of protocols for C-18 on line (I can provide links to these), and we are focusing on those protocols that specify formic acid (not TFA).  Our Zip Tips use C-18.  (1) Are Zip Tips necessary?  (2) Given their capacity, does one obtain enough for material for one or for several LC/MS runs?  (3) Are Zip Tips reusable? (4) Does anyone have a paper or protocol that is especially informative?  Thank you very much.

Edited by BabcockHall
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1) they are not necessary, but depending on t quality of your sample prep it can help reduce contamination, and improve signal quality however,

2) depending on the volume of your zip tips (10 vs 100 ul, for example) and the sensitivity of your instrument as well as you should have enough to see something. But if whether you see enough depends on your sample and application. Generally I see significant loss of protein digests (up to 70%) and that may or may not be an issue for you. You often also lose e.g. very hydrophilic or very hydrophobic peptides along the way. If you have a very well defined and/or low complexity sample, I would use them, especially in conjunction with a nano-LC to keep your system happy. If purity is an issue, I would also use them. However, if sample loss is the dominant issue, then it may not be the best way.

3) I would not do it. Theoretically you could try to regenerate the material, but you will like get cross-contamination and the capacity might degrade.

4) can't think of any papers off the top of my head. Most that describe their use have some weird modifications which presumably help with sample prep, but in real applications rarely had any impact (in my experience).

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