Import peak boundaries for small molecules

Import peak boundaries for small molecules jay kirkwood  2016-03-17
Hi Skyline team,

I am currently unable to import peak boundaries for small molecule data.
This ability would really streamline our metabolic flux efforts, where peak shape for several acidic, polar molecules is far from ideal.

Would it be possible to make this functional for small molecule data?

Thanks for all your help and support.

Brian Pratt responded:  2016-03-21
Hi Jay,

This is certainly something that's needed, but there are internal changes needed before we can make that happen, and some further design calls to be made. There's a common theme that runs through the areas that haven't yet been generalized from peptides to small molecules - a common question before we can drive it all forward: what's the ideal small molecule analog to the unique identifier (the "key", in software-speak) we use for peptides, namely the unlabeled amino acid sequence?

It's not as simple as molecular formula, though that's a good start. Structural information is needed to be truly unambiguous - how is that best represented (SMILES)? And of course this is not at all useful when users are dealing only with masses, which is not uncommon.

It's tempting to just use whatever name the user provides for the analyte as its key, but there's no standardization around that, and it seems like ambiguity could still creep in.

I'd be very curious to know your thoughts on the matter.


Brendan MacLean responded:  2016-03-21
Just a quick note that by "unlabeled amino acid sequence", we are talking about the Modified Sequence for the light form (no isotope labeling) of the peptide e.g.


which fairly uniquely identifies the structure of the peptide, but not the bare amino acid sequence without any modifications:


Which would not be very unique in the face of many potential structurally modifying PTMs.