Agilent QQQ 6460 Data import showing " chromatogram information unavaliable"

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Agilent QQQ 6460 Data import showing " chromatogram information unavaliable" xue shi  2021-07-29
 

Help! Help! Could you please help me out ?When I try to use skyline to process my Agilent QQQ 6460 LCMS data, It cannot show chromatogram correctly. When I click on the lysine or any other molecule, it cannot show chromatogram. I don't know what cause this.
I attached the screen shot for what I get from skyline and what I get from mass hunter.
I also attached my transition list.
Thank you,

 
 
Nick Shulman responded:  2021-07-29
Can you send us your Skyline document and one of your Agilent raw data (.d) directories?

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

If that .sky.zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

You should also zip up one of your .d folders with your Agilent data.

One reason that you might be seeing "Chromatogram Information Unavailable" would be that there really was no chromatogram in the raw data whose Q1 and Q3 values matched the precursor and product ion m/z's in the Skyline document.

After we see your Skyline document and raw data we will probably be able to tell you what is going wrong.
-- Nick
 
xue shi responded:  2021-07-29
Hi Nick,
Thank you for your response. Please find the attachment for the two raw data. (amino acid standards mixture with two different concentration). I can see the MRM Chromatograms in mass hunter. Could you help to find out?
Thank you so much,
Xue
 
xue shi responded:  2021-07-29
Hi Nick,
In Skyline you can use the menu item:
File > Share
to create a .sky.zip file containing your Skyline document and supporting files, including extracted chromatograms.

Do you mean the one which I created? Please find the attachment and let me know if you need more information.
I attached Agilent .d data here again.
Thank you,
Xue
 
Nick Shulman responded:  2021-07-29
Thank you for sending those files.

When you inserted your transition list into Skyline, Skyline did not understand that the "ms2" column was supposed to be interpreted as the Product m/z.
Instead, the transitions that you have in the Skyline document that you sent me are all the intact precursors. That is, the Precursor m/z and the Product m/z's in the Skyline document are all the same.

I have attached a different transition list that will work better with Skyline.
Some things to note:
1. I added a column "Product Charge". Skyline usually needs the product charge to be specified in addition to the product m/z
2. We recommend that you specify the same Precursor Name for the heavy and light versions of a molecule, and use the "Label Type" column to tell Skyline which is heavy.

I am also attaching the Skyline document "AminoAcids.sky.zip" which you will be able to open up in Skyline and see your chromatograms.
Note that the molecule "Glycine" is still missing its chromatogram. This is because your transition list specified the product m/z as 30.2, but what actually appears in your raw file is 29.996.
-- Nick