DNA and mRNA oligonucleotide mapping using Skyline

DNA and mRNA oligonucleotide mapping using Skyline Alok  2022-05-16

Hello Skyline Team,

In addition to protein/peptide therapeutics, there is a quite a lot going on with regards to DNA and mRNA therapeutic development. As far as I am aware, one can analyse a small number of DNA or mRNA using 'molecule interface' of Skyline. However, this is not possible when a long DNA (e.g. full length plasmid DNA) or mRNA need to be studied using mass spectrometry based workflows. Similar to bottom-up proteomics, the long DNA or mRNA needs to be digested by endonuclease(s) followed by either MS1 based mass fingerprinting or MS2 based sequencing analysis. I wonder if these kind of full length DNA or mRNA MS-based analysis features are available on Skyline. If not, then is there any plan to develop such features in future?