Tips for a long small molecule transition list?

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Tips for a long small molecule transition list? lparsons  2019-02-11
 

I am trying to insert a long (12,500) transition list of small molecule information into Skyline (4.2.0.19009). I have four columns in the list; m/z, rt, charge, rt window (in that order). If I insert a small portion of the list at a time (say 2,000) everything is fine. However if I try to import the entire list at once, it invariably crashes. The program itself gets killed off by Windows and never reports an error (windows simply says "Skyline has stopped working", and gives me no options but to close it).

If anyone has any suggestions on how to troubleshoot this, I would really appreciate it.

thank you!
Lee

 
 
Brian Pratt responded:  2019-02-11
Hi Lee,

Sorry you're having a hard time with this. If you can zip that up along with the Skyline document you're trying to populate and upload it to http://skyline.ms/files.url, I'd like to investigate.

Thanks for using the Skyline support board!

Brian Pratt
 
lparsons responded:  2019-02-11
Brian

I just uploaded the list itself. I'm trying to insert it into a blank skyline document currently (through Edit -> Insert -> Small Molecules). I can certainly upload a skyline file that shows the crashing behavior as well if you'd like.

thank you
Lee
 
lparsons responded:  2019-02-11
I went ahead and pasted the .sky file in as well, it is only 3kb. If there is anything else I can provide please let me know.

thank you!
Lee
 
Brian Pratt responded:  2019-02-11
Hi Lee,

I can't reproduce the crash you describe, but I suspect this isn't the actual file you're using since the column order is not as described, and it can't be imported with charges that aren't written as integers. Perhaps you can send me a different file?

Even so, when I do import it it's very slow. The problem is that Skyline is going through that long list and trying to understand whether these transitions have any relationship to each other - are they different charges of the same molecule, are they effectively the same transition when considering the mz match tolerance (0.055 in your file), etc. Skyline is struggling through the fact that it's software for targeted mass spec but it's not being given information about the targets.

I think that for what you're doing you should probably tell Skyline that each transition represents a different molecule by adding a column with a name for each like "mz555.3347" (Excel formula =CONCATENATE("mz",B2) ). This will speed up import by quite a bit. I will also do some work to optimize import of such large lists.

Best regards,

Brian
 
lparsons responded:  2019-02-11
Brian

The csv was the actual file that I had tried to import, I apologize if I reported the column order incorrectly (I always corrected it in import).

Your observation on the charge being floating numbers instead of integers was helpful, I should have considered it myself. I changed it to be only integer and the import went fine! I'll try adding molecule names as well like you suggest (though I suspect I'll may need to incorporate more than just m/z to make them unique; I might do "mz(m/z)_(rt)" instead just to be safe. For now though it works and I'll go with that and keep your suggestion in mind for down the road.

thank you!
Lee