Could not open the chromatogram file.

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Could not open the chromatogram file. Vineel  2019-02-07
 

Hi, I could not open the skyline chromatogram files. Showing error 3429 at column 7 for 1 file; error 10689 at column 7 for the second file and error 8379 at column 7 for the third file.
Please help.
Thank you.

 
 
Nick Shulman responded:  2019-02-07
Can you show us the whole error message? There's a copy button in the lower left corner of most Skyline message boxes, that will copy the text of the entire message to the Clipboard.

Those numbers are actually the line number where Skyline ran into a problem. If you send us your .sky files, we will probably be able to figure out what is wrong, and fix it.
If your .sky files are less than 50MB, you can attach them to this support request. Otherwise, you can upload them here:
https://skyline.ms/files.url

-- Nick
 
Vineel responded:  2019-02-07
Hi Nick,
Appreciate your quick response.
I have skyline version 4.2.0.... I could not open the file. Shows error.
My lab member have skyline version 4.1....installed on his computer. I could able to open the same file on the pervious version of skyline.
I have attached two files 1) error message screen shot and 2) file with error.

Please help.

Best Regards,
Vineel.
 
Vineel responded:  2019-02-07
Hi Nick,
After clicking submit button I saw error message. did you receive the attached files. Skyline file with error is more than 200 MB. Error message file is small.
Try to attach the files again.

Thanks.
Vineel.
 
Vineel responded:  2019-02-07
Hi Nick
Uploaded the file "file with error" at "https://skyline.ms/files.url".


Thank you

Vineel.
 
Vineel responded:  2019-02-07
please see the attached error message
 
Nick Shulman responded:  2019-02-07
The error your getting now is that you are trying to open the .skyd file, instead of the .sky file.
This is not the same error as you were getting before. If you try to open a .skyd file in Skyline, the error always happens on the first line, because Skyline is able to notice immediately that this is not the correct type of file.

This is different than the error that you were seeing before. The error that you were seeing before happened much later in the file. Can you get the original error message to happen?

(Also, the file that you uploaded also had the extension ".skyd". We need to see the file that has the extension ".sky" in order to diagnose this problem.)
-- Nick
 
Vineel responded:  2019-02-07
Hi Nick,
Got your point.
Please see the attached files.

Thank you.
Vineel.
 
Brian Pratt responded:  2019-02-07
Hi Veneel,

Thanks for providing the file. I'm glad you're updating from Skyline 3.7, our handling of non-proteomic data is much improved since then.

I will make sure that this files opens without any trouble in the next Skyline-Daily, but for now it's possible to make a simple change to the file in a text editor so that it will load.

If you change line 10330 from
          <precursor_mz>223.09162799999999</precursor_mz>
to
          <precursor_mz>223.091628</precursor_mz>

you should find that it loads. Skyline was confused by the implied amount of precision involved, and couldn't make the various labeled versions agree on a common parent molecule mass.

It sounds like you have other Skyline 3.7 documents that cause trouble like this, please let me know if you need help with those. I'm sure we can get them ready for Skyline 4.2 without difficulty.

Best Regards,

Brian Pratt
 
Vineel responded:  2019-02-07
Hi Brian,
Thank you for the quick response.
I have no idea how to do the change that you suggested. Can you please guide me how to do the change.

Thank you
Vineel.
 
Brian Pratt responded:  2019-02-07
Sorry - you can use any text editor, like Notepad. It's just XML text.

Cheers,

Brian
 
Vineel responded:  2019-02-07
Hi Brian,
I made the change that you suggested.
Please see the "attached images" of screen shots of error messages.
I could not see chromatograms.

Vineel.
 
Brian Pratt responded:  2019-02-07
It appears that you need to reimport the raw files, but they have been moved from where they were when originally imported.
 
Nick Shulman responded:  2019-02-07
Vineel,

You are probably seeing that error because your .sky file is not in the same directory as its .skyd file, or you changed the name of the .sky file when you saved it.

Extracted chromatograms are stored in the .skyd file. When Skyline opens a .sky file and sees that the .sky file is supposed to have chromatograms with it, Skyline looks for a file with the same name in the same directory, just with the .skyd file extension. If Skyline does not find that file, then Skyline tries to extract chromatograms again.

You probably don't want to extract chromatograms again, so just make sure that you .skyd file and .sky file are in the same place when you try to open the .sky file.
-- Nick