Request to allow Skyline to handle 'special characters' in files

support
Request to allow Skyline to handle 'special characters' in files Tim McCubbin  2018-08-09 19:06
 

Dear Skyline team,

Apologies for the somewhat silly request but we have been sent raw files for analysis a number of times by people who insist on using the micro symbol in the file names (e.g. to specify the concentration or mass of protein in the sample or volume injected into the MS). This appears to create issues for Skyline, i.e. DDA files can't be imported via Import -> peptide search. We are also currently experiencing difficulties with DIA files with the micro symbol in the name; which import okay but peak quantification appears to fail; although we are yet to really demonstrate that this issue is caused by the 'micro' character. Simply renaming the files is not sufficient; it appears that raw files 'know' what they were originally called. We are looking into possible ways around this and would appreciate any suggestions if you already have some, such as converting the raw file to a file format we can possibly view and edit; but I thought I would raise this as a possible request as others might run into the same issue.

Obviously this is just poor file naming practice but once created, it does not appear to be trivial to correct.

Many thanks,

Tim

 
 
Nick Shulman responded:  2018-08-09 20:14
If you successfully imported peptide search results into Skyline (perhaps by renaming your search result files), then you can check what names Skyline thinks the .raw files are supposed to have by going to:
View > Spectral Libraries
If you press the "..." button next to the library name, you can see the list of files that Skyline thinks are in the library.
You might be able to rename your .raw files to whatever it says there.

I could imagine that when translating between UTF-8 and ASCII, the mu character could get replaced by:
¿╝
(ALT-206 ALT-188)

It might be best if you send us your files. You can upload them here:
https://skyline.ms/files.url

Or, if you have some other way of sending files such as Google Drive or DropBox, that works too.

I will try to figure out what can be done.
-- Nick