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add functions for mRNA analysis?

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add functions for mRNA analysis? zhijcao  2024-07-31 06:19
 

Hi Skyline team,
Thank you for your contributions to the proteomics community.
There is a growing interest using Mass Spectrometry for mRNA analysis in academic and pharm industry. I wonder if functions for mRNA analysis could be added to Skyline. Similar to protein analysis, mRNA sequence is digested into oligonucleotides with enzyme (such as T1), and the oligonucleotides of interest are quantified with MRM.

Thanks,
Zhijun
 
 
Brian Pratt responded:  2024-07-31 10:17

Hi Zhijun,

The answer is yes, but...

Skyline intimately understands protein digestion into peptides, and peptide fragmentation in a mass spec. For other kinds of molecules we make it possible to create closely integrated external tools to lend that kind of knowledge to Skyline. An excellent example of this is LipidCreator (https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=LipidCreator).

So, if anyone cares to create such a tool for mRNA analysis we'd be very happy, but it's not something our small team has the bandwidth to implement ourselves. But we're here to answer questions when someone does.

Thanks for using the Skyline Support Board!

Brian Pratt