Thanks for the input! We do want to add this kind of lookup capability for molecular ID standards but it may be a while before we get there.

Nearer-term, at least making it easier to track SMILES as we do with InChi, HMDB etc is feasible. We'd gotten the impression that users weren't interested in SMILES but if your workflow uses it then we should do what we can to support that.

Thanks for using the Skyline support board!

Brian Pratt

Hi,

WRT SMILES vs InChIKey or other identifiers, the advantage is that SMILES is a full structural representation and allows to do downstream CompChem work, like QSARs or for example MS2 prediction (see CFM-ID). InChIkey always requires online lookup and fails if the molecule is not in a DB. (InChICode itself, not InChIKey, is of course also a structural representation, but I rarely see it used anywhere...)

Just to be clear: my wish was that you could use SMILES in analogy to peptide sequences in "Insert Peptides", so it automatically calculates the masses.

I actually downloaded the code to see if I might contribute myself, but I guess I would need to invest quite a lot of time to understand the structure before I could contribute anything...

Re "track SMILES as we do with InChi, HMDB etc":

Hm, this is a feature I don't know, where is it used / how can I find it?

Understood, and agreed. Writing a SMILES parser hasn't made the top of the priority list yet, and haven't I found a suitably licensed open source implementation, unfortunately.

By "track" I mean import as a molecule attribute and include in spectral libraries, reports, etc. Though I find that these attributes are not yet readily accessible in Skyline reports, an oversight which I'll correct in the next Skyline-Daily or two.

Thanks for helping move Skyline forward!

Brian