Peak boundaries for small molecule shotgun lipidomics

Peak boundaries for small molecule shotgun lipidomics bharat  2017-07-19

I am interested in using skyline instead of Analyst for processing data from shotgun lipidomics. These runs are generated without a column, so all we're interested is an area under the curve from a start time to an end time. After these raw areas are generated, all other work on deconvolution, quantitation, etc are done externally. So, all we would need is for the integration to be done somewhat robotically from start time t1 to end time t2. I've been very successful, thanks to the good documentation, in getting all the transitions in (>140) and the integrations done. But, I can' get to the final step, which is this automatic peak boundary picking. So, you can see from the attachment that sometimes we get the good, and sometimes the needs adjustment. I've tried the "import peak boundaries" option, but that doesn't seem to work for me for small molecules. Anything I'm missing here?


Brian Pratt responded:  2017-07-19
Hi Bharat,

It's possible that the Import Peak Boundaries feature hasn't been adapted to small molecules yet - may I see your Skyline document (use the Skyline "File | Share" menu for that, please), the raw file, and the file you're using with Import Peak Boundaries? Hopefully we can get something working for you - I'll contact you privately about sending the files.

Thanks for using the Skyline support board!

Brian Pratt
Brian Pratt responded:  2017-07-21
Just leaving a note here for anyone that might be interested: we determined that this works fine for small molecules, but it's important to set up your transition list such that the "peptides" (molecules) names match the boundary file you're importing. In this case the "proteins" (molecule groups) were getting the name instead.