Raw files moved

Raw files moved ingo.wohlgemuth  2019-09-28 01:12


thanks for the great software.
I analyzed a larger DDA dataset with MS1filtering. Unfortunately, the external disk with the RAW files crashed. I still have the skyline file on my computer and a backup of the maxquant search plus raw files of the corresponding analysis. However, Skyline expects the original location of the raw files on the broken external memory.

  1. Is it possible to reimport the data in the skyline files from a new folder?
    or 2. is there another way to reconnect skyline analysis and raw data (plus maxquant search)?

Thanks in advance!


Nick Shulman responded:  2019-09-28 06:34
You can copy the .raw files into the same folder as your .sky file.

Whenever Skyline does not find a .raw file in its original location, Skyline then checks to see whether the .raw file is in the same folder as the .sky file.

warham responded:  2023-09-15 06:13
Hi Nick,

I have most of my data on large external SSD. When I attach them to the computer I'm using skyline they get the directory (D:, E:, F: . . . etc) assigned by windows. As I move these drives routinely between 3 computers to do the analysis, and they don't all have the same number of internal hard drives it would be convenient to be able to redirect a skyline file to its data either arbitrarily or at its drive level. Is this possible and I am just not seeing how to do it? I have been doing other work arounds but with $60 2TB drives being available I don't imagine I will be alone in my . . . data management approach.


PS: the data is on a drive assigned to the E directory on this computer, but the directory tree is otherwise identical
Nick Shulman responded:  2023-09-15 09:41
When you click on a point along a chromatogram curve, Skyline tries to show you the spectrum from the .raw file which contributed to that point in the extracted ion chromatogram.
The message box that you are seeing is Skyline telling you that it was not able to find the .raw file anymore.
The points that you can click along the chromatogram curve to bring up the spectrum viewer are very close to the places on the graph that you might click when zooming in or adjusting peak boundaries.
A lot of people who see that message box are not even aware that they clicked on the chromatogram curve, and think that Skyline needs the .raw file.
Skyline will work perfectly fine without those .raw files, so if you were not interested in looking at spectra from the .raw file, then you can ignore those messages when you accidentally trigger them while clicking on chromatogram graphs.

-- Nick
warham responded:  2023-09-15 10:11
Hi Nick,

I want skyline to be able to continue to access the .raw data, in particular I want to be able to click on the chromatogram and be able to update the full scan view of the spectra vs expected.