SMILES peptide sequence entry into skyline

SMILES peptide sequence entry into skyline faizanzubair2  2018-11-14

Dear Skyline Team,

Thank you for the amazing piece of software that has made a tremendous influence in biomarker research!

I am trying to develop automated MRM methods using skyline for heavily modified peptides (containing methylation, lipid chains, non-natural amino acids). Due to number of these peptides, entering them and modifying them individually in Skyline is very tedious. I have list of sequences in SMILES format-- can those be inputted directly into Skyline? Alternatively, is there a converter that converts SMILES format into skyline compatible sequences?

Thank you so much!


Brendan MacLean responded:  2018-11-15

Hi Faizan,
When the peptide support in Skyline fails to serve more exotic needs in peptide-related measurements, such as cross-linking and probably the application you are describing, people have been turning to our new "small molecule" support, which may be more accurately described as "all molecule" support.

So, I recommend you have a look at the small molecule tutorials which describe how to add target transitions to Skyline by chemical formula and even raw m/z, and where a SMILES column is also supported. Though, there is no direct conversion from SMILES to even chemical formula and certainly not peptide sequence.

Hope this will work for you as well as we have heard reported for cross-linking applications.


faizanzubair2 responded:  2018-11-16

Thanks Brendan! I will check out the small molecule support videos.

Brian Pratt responded:  2018-11-16

Just to amplify what Brendan has said about how we work with SMILES: we can associate a SMILES description with a molecule but we don't (yet?) accept SMILES directly as a means of defining the molecule. That is to say, we don't have any code for parsing SMILES that would give the molecular formula, so we need that defined separately.

  • Brian Pratt