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**Unable to view small molecules analysed in ESI negative mode**

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**Unable to view small molecules analysed in ESI negative mode** ejg29  2025-08-14 07:39
 

Hi,

I am currently analysing some small molecule data (WATERS .raw) on the Skyline software however when i import my transition list and then import the data, i am only able to view the chromatograms of the analytes run in ESI positive and not the ones run in ESI negative mode.
Please can you help.

Kind regards,
Elliot.
 
 
Nick Shulman responded:  2025-08-14 07:58
Can you send us your Skyline document and your Waters .raw folders?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

The Share Document dialog gives you the option to include the Waters .raw folders in the .zip file. Alternatively, you can zip those .raw folders up yourself and send them to us separately.
Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick
 
Brian Pratt responded:  2025-08-14 08:09
It's likely that we will also end up wanting to see whatever artifact (transition list etc) you imported into Skyline to specify the molecules and adducts of interest. Its often the case that people forget to specify negative charges along with positive.

Best Regards,
Brian Pratt
 
ejg29 responded:  2025-08-14 08:44
Hi Nick and Brian,

Please the requested attached, thank you!

Kind regards,
Elliot.
 
Brian Pratt responded:  2025-08-14 09:53
I can see from the .sky.zip that as I suspected it looks like you just haven't told Skyline that you're interested in negative ion mode.

That other file doesn't appear to be a transition list (I was thinking something human readable), but in essence for every [M+] target transition you need to add an [M-].

Best regards,

Brian