Custom transition list data

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Custom transition list data B.C.M. van der Helm  2018-02-06 02:09
 
Dear all,
I am analysing lipid data with the skyline software. One of the problems i have is that the lipids can be separeted in classes and (total-) fattyacid chain lenght (2 groups). and i was wondering of it is possible to ad a function in edit>insert>transitionlist where you can select the annotition for an specific transition, so that when you export the data in a report, you also be able to sellect those data from you transition import. The note function won't work because those are multiple parameters. I see the annotion function back in the notion. But how can i add my data to those anotions by the import of an transitionlist?

The transitionlist is imported from an .CSV and combiend with the MS/MS data and exported to R/Excel for data analysis and now i have a "loss" of data between import and export of the transitionlist. Adding the data later is an pain in the ass because there are more than 1500 transitions and a typical batch has more than 100 samples masseured in duplo. Also there could appear an error in the recombining of the data.

I was wondering if you have anny idea's to help me with those problems?
I work in both skyline 4.1.0.11714 and skyline daily 4.1.1.11756
Bas
 
 
Brian Pratt responded:  2018-02-06 08:49
Hi Bas,

Can I see an example of your starting transition list so I can better understand what kind of information you are wanting to pass through? I completely agree that this needs to be possible. I'm a little surprised that the Note mechanism doesn't cover this need, as that was the intent.

Thanks,

Brian
 
B.C.M. van der Helm responded:  2018-02-07 01:37
I have my problem visualized in a PowerPoint and i also uploaded the zipped skyline method and a part of the database to make it easy to the file sharing

When i think now again about the problem, i have a "temporary" solution to combine the data to a text string with comma separation like
=A1&","&B1&","& etc. this wil result in xxxx,zzzz, etc. when you load it back to Excel you had to separate the textstrings back to diffrent columns this wil work as long you do not have to use those data within skyline and only to hold the data between the import and export, so you can stil used the data after skyline.

I hope you now better understending my problems,
Thanks,
Bas
 
Brian Pratt responded:  2018-02-07 09:34
Hi Bas,

OK, so it seems the Note mechanism is usable for pass-through, but not fine grained enough for use within Skyline.

One approach would be to recognize defined annotation types as additional import column types. Any annotation type defined as applying to proteins*, peptides*, precursors or transitions would appear in the column headers pick list. Of course the user would have to be careful not to use annotation names that are already understood import column header types, but that's probably not too much to ask.

What do you think?

Thanks

Brian

* Skyline's proteomics roots still show where we wish they didn't for small molecule work, we're working on generalizing the terminology. You can read "Molecule list group" and "Molecule" for protein and peptide in this context.
 
B.C.M. van der Helm responded:  2018-02-07 23:31
Hi Brian,

I think that your proposal will be very useful and will help a lot to ad custom information to the transition list for passing through the data.

in the main wile I will use a combined columns to a text string an use it than as a note. when the report is created I can extract those columns form this cell an than I can us the data in my statistical programs.

Thanks,
Bas