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Skyline m/z tolerance window not work with Altis files

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Skyline m/z tolerance window not work with Altis files Lian  2018-01-26 18:14
 
Hi dear Skyline developer,

I have an issue with the m/z tolerance window when using skyline 3.7.1 to analyze Altis raw data files. Sometimes, Altis automatically changes the parent m/z by 0.001 when importing more than 10 transitions for the same compound (e.g. change parent m/z from 852.233 to 852.234). I am assuming Altis is relying on Skyline to still recognize it since the smallest isolation window of Q1 and Q3 is 0.2 but skyline does not. When the resulted raw data file is imported into skyline, skyline does not recognize the transitions with parent m/z changed by 0.001. This issue still exists when I changed the method mass tolerance m/z to 0.6 in transition settings/instrument in skyline.

I heard that this issue is resolved previously but probably the raw data from the new version TSQ-Altis is still not compatible. Could you please fix it?

Thanks

Emma
 
 
Brian Pratt responded:  2018-01-29 13:34
Hi Emma,

This will be easier to help with if you can provide the data.

Please use Skyline's File | Share menu item (choose "Complete" if asked), which prepares a single zip file with your document and all the needed supporting files in it. Then upload that .sky.zip file to the Uploads page http://skyline.ms/files.url . The actual raw data files are also needed, those will need to be zipped up and uploaded separately.

Thanks

Brian Pratt
 
Lian responded:  2018-01-29 18:42
Hi Brian,

I have uploaded my skyline files and raw data. Please take a look! Thanks

E
 
Lian responded:  2018-01-29 18:44
Sorry, did not mention the file names. The raw data file name is raw and skyline file is skyline mz tolerance window.
 
Brian Pratt responded:  2018-01-30 13:39
Hi Emma,

Thanks for sending the data. I see what you mean about the parent mz changing, but I agree that with your settings it seems like Skyline should have been able to match it. I have some other work that needs doing in the SRM area, I'll make sure to address this when I do. For now, though, all I can do is thank you for bringing it to our attention.

Thanks,

Brian