Hi Abla,
Skyline will always find raw data in the same folder as the document itself and also two parent folders up, since .sky.zip files create a subfolder when they are opened.

At present, this is the only method of reconnecting a Skyline document with its raw data: put the Skyline document in the same folder with the raw data or a subfolder no further than 2 away from the data.

I can see that it would be useful to allow users to specify a new path or paths to search for raw data in, ideally either relative or absolute. Maybe we can add this to the Document Settings soon.

https://skyline.ms/issues/home/issues/details.view?issueId=558

For now, though, the document will have to be put in the same folder, a child folder or a grand-child folder of the raw data folder.

--Brendan

Great, thanks for the info.
Sometimes I end up with more than 2 sub folders especially if I am running things through command line or importing data from different experiments.
Specifying the raw data path would be a very useful tool.
Thank you
Abla

Hi, I am also having the issue of reassigning raw files in my session. I used to put raw files in subfolders of my Skyline sessions. Do I read correctly that only parent folders are looked at? Another issue is if working on cloud folders: the absolute path on different devices is usually distinct, which renders the session unusable. Or maybe there is a workaround?

edit: best solution might be to also use relative paths in addition to prompt for an updated path with the raw files in case they were moved/renamed.

Thanks a lot,
best

skyfall,

There are only a couple of times when Skyline will try to look at the original raw files after you have extracted chromatograms.
1. If you click on a point along an extracted ion chromatogram, Skyline will try to show you the spectrum that contributed to that point. In this case, if Skyline does not find the raw file at its original location, Skyline will look in the folder that the .sky file is in, and then that parent folder.
2. If you use the "Reimport" button on the "Edit > Manage Results" dialog, if Skyline does not find the raw file in its original location, Skyline will look in the folder that the .sky file is in. After the Reimport has finished, Skyline will update the location of the files in the document so that they point to the place where the raw file was found (which is now either the original location, or the folder containing the .sky file).

What do you mean "renders the session unusable"? Are you referring to reimport, or clicking on points along the chromatogram to show spectra, or am I overlooking another place where the original location of the .raw files is important?
-- Nick

Hi,
thank you.
Yes, I frequently click on the chromatogram to get the spectrum. I do sort my session and rawfiles the other way around: sessions in the parent folder and the raw files in subfolders. When this is in a cloud folder and I store my session and open it on another PC the absolute path will be different (eg D:cloud.. vs C:cloud..). when I open my session there and want to see the spectrum, the only solution I found is to import the raw files as new files and remove the old files in that session. This way a lose all my assigned peaks etc and when going back to my other device, I'll have the problem again.

yes looking at relative subfolders would be fantastic