Small molecule: Skyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the run

Small molecule: Skyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the run ayson  2020-03-26

We have acquired HILIC data in Agilent QQQ with diverter valve to waste from 0-0.2 mins. From 0.2 to 5 mins, mass spec was turned on. When I analyze the data in Skyline, I am only seeing the chromatogram from 0-0.2 mins but never 0.2 to 5 mins. The data looks fine in Masshunter Quant but not in skyline. I have sent you more detailed report in the attached word document.

It is vital that skyline can process these types of data because more small molecules will be diverter their initial flow to waste to protect mass spec instrument. Thank you so much!!!

Best regards,

Nick Shulman responded:  2020-03-26

Can you send us your Skyline document and one of your raw data files?
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.

You should also zip up one of your Agilent .d folders containing the raw mass spec run.

If those .zip files are less than 50MB, you can attach them to this support request.

Otherwise, you can upload them here:

-- Nick
ayson responded:  2020-03-26
Thanks, Nick! I have attached the following:

1. another word doc for more info on our method used.
2. zipped skyline file
3. transition list
4. zipped .d file

Please let me know if you need anything else. I am super excited to seeing this fixed. This will help analyze future small molecules. Keep safe!

Nick Shulman responded:  2020-03-26

You can use the "Explicit Retention Time" to tell Skyline at what time to expect your molecule to elute.
If you right-click on the molecule "Phenylalanine" in the Targets tree, there is a menu item "Modify" which brings up the Modify Molecule dialog.
In that dialog, you should set that to some number of minutes like "3" that is in the middle of your desired chromatogram.

When your raw file contains multiple chromatograms with the same Q1 and Q3 m/z values, Skyline will use the Explicit Retention Time to decide which chromatogram to use.

-- Nick
ayson responded:  2020-03-26
Wow! This is a quick fix. Thank you, Nick! I added the explicit RT and also explicit RT window to my transition list and I see the peaks. =)

I appreciate you getting back to me so soon. Thanks again. Take care and keep safe.