About the export the information of Internal Standard Type from the Skyline file

About the export the information of Internal Standard Type from the Skyline file yin lu  2018-10-29

Dear Skyline team,
I'm working on the SRM targeted proteomics data from CPTAC Assay Portal. My goal is to access and export the information in the *.sky file using the SkylineCmd.exe. For now, I could export some column information, such as, Protein Name, Peptide Modified Sequence, Isotope Label Type, Product Charge, Replicate, MultiplicationFactor, Concentration, SampleGroup and so on, by means of creating report template. However, I can't find one attribute named "Internal Standard Type" from there.
I found that I could find an item named "Internal Standard Type". I could find it by opening the *.sky file in Skyline GUI: On the Setting menu and Peptide Setting. How can I export the information of "Internal Standard Type" from *.sky files using the command line tool SkylineCmd.exe?
Thank you.


Brendan MacLean responded:  2018-11-20

Hi Yin,
There is no easy way to get that value. If you are up for writing code to read XML, you could pull it directly from the .sky file which is all XML. You could come up with a way to derive it from exporting report values. For instance the PrecursorResult.TotalAreaRatio will only have a value for precursors which are not the internal standard type (e.g. heavy). The precursors of the internal standard type will have #N/A for this value.

Certainly, if you expect the Assay Portal documents to have either "light" or "heavy" as the Isotope Label Type, it would be trivial to figure out which one is set through the PrecursorResult.TotalAreaRatio values. If you want to allow for custom Isotope Label Types like "All 15N" or something else, then it gets a bit more complicated.

The original assumption of SkylineCmd was that you would start with a .sky file that you knew something about. We could probably do some settings export features pretty easily. Any thoughts on the format that would be simplest for you to use, if we were to export settings values? We could export the settings only as XML, as we do when you use Settings > Share in the Skyline UI, to a .skys file. I am sure we could also come up with JSON, Java .properties, SQLite, but I am not sure what you would want. Let us know. I can't promise we can get to it right away, but I am interested.

Thanks for your feedback.