Failure opening ...\ - error on line X at column Y

Failure opening ...\ - error on line X at column Y lilybirx  2021-06-21


I am trying to open a file and keep getting the same error message - 'The file contains an error on line 4299 at column 10'

When I go to the line and column in notepad, I see the following (start at line 4298), line 4299 is the second line from top

    <transition fragment_type="precursor">
        <neutral_loss modification_name="Tmem5_take2" loss_index="9" />
    <transition fragment_type="custom" measured_ion_name="HexNAc Oxonium" product_charge="1">

Any help recovering this file would be greatly appreciated, thanks in advance!

Nick Shulman responded:  2021-06-21
That error is usually caused by a bug in Skyline where Skyline is now calculating a different m/z value from the molecule than when Skyline saved out the document.
Sometimes this happens because of the way that the molecule was inserted into the document, and changes were later made to the molecule, and the way that Skyline ended up applying those changes caused Skyline to calculate a different mass than if Skyline were to calculate everything again from scratch.

If you send us your .sky file, we can send you back a fixed version of that file which you will be able to open without error. After that, we might have some follow up questions to try to figure out why Skyline was making this mistake.

If your .sky file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

-- Nick
lilybirx responded:  2021-06-21
Attached is the sky file, thank you!
Nick Shulman responded:  2021-06-21
Here is a fixed version of that file. You should be able to open it without error in Skyline.

It looks like Skyline probably has a bug in it where if you change the definition of the neutral losses of a modification, transitions that are already in the document and which are using those losses will be saved with m/z values which are not consistent with the new neutral loss definition.

I will try to fix this in a future version of Skyline. Until this bug is fixed, I would recommend that you not change the neutral loss definitions of modifications if there are any transitions currently in the document that are using those neutral losses.

Thank you for reporting this bug, and feel free to send us any other documents that you need fixed.

If you want to fix documents like this yourself, the "More Info" button on that error message does give you enough information to know what to change in the .sky file. In this case, the more info message included the text "error reading mz values - declared mz value 974.142669 does not match calculated value 1082.87622082333". You can then open the .sky file up in a text editor and replace "974.142669" with "1082.87622082333" and then Skyline will be able to open that file. If you run into this sort of error with other documents, the numbers that need changing will probably be slightly different.

-- Nick