Error message: Failure opening - "the file contains an error on line 13438 at column 9"

Error message: Failure opening - "the file contains an error on line 13438 at column 9" katherine wongtrakul-kish  2022-12-06 02:44

Hoping you can help me get back into my skyline file please... I added a new molecule to my transition list recently ( (HexNAc)2 (Deoxyhexose)1 (NeuAc)1 + (Man)3(GlcNAc)2 with m/z 876.8) by copying and modifying an existing one.

Usually this works alright if I'm copying and creating multiple entries for isomers, but on this occasion I modified the mass as well to make an entirely new glycan molecule -- which was perhaps where my mistake was?!

I managed to integrate peaks for the new glycan, but then at some point hit a clipboard error. When I closed and tried to re-open the file, I couldn't (error message in the attached screen shot).

I've also attached the SKYL file. Thanks for any advice you can give
Nick Shulman responded:  2022-12-06 06:53
Can you send me the .sky file (not .skyl) "Total"?

Skyline has a couple of bugs in it where it gets in a state where the value that Skyline has calculated for a molecule is a different number than what Skyline would have gotten if it were starting from scratch. Unfortunately, if you save your document when Skyline is in that state, you get this error when you try to open the document.

I will be able to quickly fix this file when you send it to me and I will send you back a fixed version of the file.

If the .sky file is less than 50MB you can attach it to this support request. You can upload larger files here:
-- Nick
katherine wongtrakul-kish responded:  2022-12-06 13:29
Thanks Nick, makes sense.
.sky file now attached...
Nick Shulman responded:  2022-12-06 13:40
That's the ".sky.view" file.
Can you attach the ".sky" file instead?

Windows Explorer sometimes makes it tricky to find the .sky file because Windows hides the filename extensions for most files.
Here is a page which describes how to turn off "Hide filename extensions for known file types":

-- Nick
katherine wongtrakul-kish responded:  2022-12-06 13:54
ok, trying again..
Nick Shulman responded:  2022-12-06 14:07
Here is a fixed version of that file.
You should save that file overtop of the file which you already have so that it will be in the same folder as all of the related files that it needs (the .skyd, .skyl, .sky.view, etc)
By the way, when you open the file in Skyline, you will get a warning that the Audit Log has detected that a change was made outside of Skyline, which you do not need to worry about.

-- Nick
katherine wongtrakul-kish responded:  2022-12-06 14:25
It worked! Can't thank you enough, Nick -- that file was several months of work in the making