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SMILES peptide sequence entry into skyline

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SMILES peptide sequence entry into skyline faizanzubair2  2018-11-14 15:56
 

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!

Faizan
 
 
Brendan MacLean responded:  2018-11-15 00:36

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.

http://skyline.ms/tutorials.url#small-mol

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

--Brendan
 
faizanzubair2 responded:  2018-11-16 09:49

Thanks Brendan! I will check out the small molecule support videos.
 
Brian Pratt responded:  2018-11-16 10:11

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