"chromatogram information unavailable"

"chromatogram information unavailable" luzalonsodasques  2024-06-10 08:31

Good afternoon,

I am writing you because I cannot view the chromatograms after importing the files.

The message that i see is: Chromatogram information unavailable.

I tried to change in settings -> Transition list -> instrument -> Method match tolerance m/z ... but it didn' t work.

I also tried in edit -> modify molecule -> Explicit values -> RT window ... but it didn't work

I am using Skyline (64-bit) (e59d0dc56)

Waiting for your answer,

Thank you in advance,

Luz Alonso Dasques.

Nick Shulman responded:  2024-06-10 08:41
It looks like you have made a lot of changes to your document since the last time that you told Skyline to import results.
Skyline does not automatically reimport results when you add things to the Targets tree, so after you do something like that you should go to:
Edit > Manage Results
select all of the replicates and push the "Reimport" button.

If that does not result in your molecules getting chromatograms, then the problem might be that there really are no SRM chromatograms in your Agilent .d folders whose Q1 and Q3 values match the precursor and product m/z of the transitions in your document.

If you like, you could zip up and send us a few of your .d folders (e.g. "M1_MIDD_5uL_01.d") and we could tell you more about what is going wrong.
Files which are less than 50MB can be attached to this support request. You can always upload larger files here:
-- Nick
luzalonsodasques responded:  2024-06-10 09:22

Good afternoon,

I already tried to reimport the files any time i do any chage.

I am sending you some raw file/ .d folders (e.g. "M1_MIDD_5uL_01.d") in case you could tell me more about what is going wrong.


Luz Alonso Dasques.

Nick Shulman responded:  2024-06-10 09:50
Thank you for sending those .d folders.

The problem is that the "Explicit Retention Time" on some of your molecules has been set to a number which is outside of the time range of the SRM chromatogram that was acquired.
Skyline always discards SRM chromatograms that do not overlap with the Explicit Retention Time of their associated molecule. In Skyline-daily you get a warning about this, but in Skyline 23.1 it does this without telling you.
You should use the "Molecules" report in the Document Grid and set the Explicit Retention Time values for your molecules to blank, and then reimport the results.

-- Nick