LC-MS charactering short RNAs with 50-100nt

[Yankee IT]

Our lab starts working on short RNAs with 50-100 nt long and ~10 ng , and we want to use LC-MS for characterization.

Which LC-MS platform will be the most suitable for analyze these RNA? Do anybody have these instruments that we can first try on to see if they work for our RNA?

Thank you

[Johte]

Unfortunately you're not going to find the documentation that someone in proteomics would. I'm still fussing with AGC, isolation, etc.

When you say platform are you asking about source information as well or is that predetermined by what is available to you?

Personally, I run NH4OAc / ACN gradients on C18, trying to get good enough separation without ion-pairing such that I don't have to clean my source as frequently. Which is ESI by the way.

Anyway, best of luck with 50-100mers. Not to say it can't be done but it's outside ideal fragmentation range.