I wonder if Skyline will join MS-based RNomic and DNomic studies?

I wonder if Skyline will join MS-based RNomic and DNomic studies? licky lck  2022-07-18
Dear Skyline team,

I really appreciate the massive contribution of Skyline to the proteomics community, and it is one of the most important software I used during all of my proteomic studies. Recently, researchers from epigenetics, biology and pharmacy are trying to "borrow" the bottom-up concept from proteomics to study modifications in oligonucleotides (from DNA and RNA) using MS-based methods. So I wonder if the Skyline team would consider joining the party?

I have been using Skyline to study site-specific protein modifications on peptides using the manual peptide insert function, and it would be absolutely a game changer if a similar function is available for nucleotide study in Skyline for epigenetics-related studies as there is still a blank in the study of DNA (or RNA) modifications site-specifically. I will be working in this field in the coming years, and I would love to hear if Skyline is also interested in working with DNA and/or RNA. Thank you very much for your time and patience.

Best regards,
Brian Pratt responded:  2022-07-18
Hi Chengkang,

Skyline, as you know, has built in domain knowledge for proteomics - understands the way proteins and peptides fragment - but other classes of molecules have entirely different behaviors. So while Skyline can also deal with generalized molecules ("smALL molecules", as some say), there can be a lot of domain knowledge needed to make a truly useful tool for specific kinds of molecules.

Happily, Skyline's external tools interface enables others to bring their domain knowledge to Skyline. LipidCreator is an excellent example of this, a very nice front end for describing lipids and feeding that information into Skyline, written by Skyline users with only a very tiny bit of help from the Skyline team.

Perhaps you're interested in doing something like that for your field?

Best Regards,

Brian Pratt
licky lck responded:  2022-07-19
Dear Brian,

That is a good suggestion, thank you very much.

Best regards,