Notes, HMDB etc in report henrik molina  2019-07-16
 

Dear Skyline Team,

For our analysis of polar metabolites we, in addition to names, composition RT, charge, also upload HMDB and KEGG info) [EDIT->INSERT->TRANSITIONS LIST].
However, we can not figure out how to get the HMDB and notes included when we export the report [FILE->EXPORT->REPORT].

Also, will it be possible to add a column for KEGG as well - so we can free up the 'Note' column (that we currently uses for KEGG).

Cheers, h

 
 
Brendan MacLean responded:  2019-07-16

Hi Henrik,
The Custom and Live Reports tutorial should be helpful:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

You should also look into custom annotations (which should be covered in the tutorial). These should allow you to store all kinds of data in columns associated with various elements in Skyline, without needing to use the "Note" field for anything but free-text comments, as was its intent.

The tutorial should also teach you how to customize reports to get exactly what you want exported in CSV format from Skyline.

Thanks for using Skyline in your research.

--Brendan

 
henrik molina responded:  2019-07-19

Thanks for answer. I have read through most of the manual you suggested and also the small molecule manual on the site.

I managed to define HMDB and KEGG in the report, but can not 'link' those terms with the 'Transition List' table to where I am uploading the information.
Also, I could not find any notes re. how to define new columns in the 'Transition List'.
Pls keep in mind that this is for Small Molecules!

cheers, h

 
Brendan MacLean responded:  2019-07-19

Hi Henrik,
You are right that there is currently no way to add custom annotations to the Edit > Insert > Transition List table. However, you should still be able to paste most of what you want into that table and then finish by pasting into the Document Grid, using a saved report template like a modified version of "Small Molecule Transition List". You need Edit > Insert > Transition List to create new targets in your document, but once you have those, you can further annotate them with the Document Grid. Furthermore, if you are worried about ordering, you can use a sort both in the Document Grid and in, say, Excel to make sure the values you have line up exactly with the rows you are pasting into in the Document Grid.

Hope this makes sense and allows you to achieve the annotations you want. It is unlikely that we can add custom annotations to Edit > Insert > Transitions quickly enough to satisfy your current need. So, this two-part solution is about all I can offer you. It should work, though.

--Brendan

 
henrik molina responded:  2019-07-19

Adding the info via 'DOCUMENT GRID' did the trick. Thx.
cheers, h

 
Brian Pratt responded:  2019-07-19

Hi Henrik,

I'll see about adding a KEGG column soon.

  • Brian Pratt