Chromatogram information unavailable

Chromatogram information unavailable davis  2019-08-08

Hello Skyline team,

I am using skyline daily. However, when import my .raw file, there is no signal and "chromatogram information unavailable" is displayed. This is only the case for the files I generated as of today. My previous files (072419) have been imported and are visualized.

I appreciate for all of your help.
Best regards


Nick Shulman responded:  2019-08-08
This is an SRM experiment, right?
It appears that your raw file "20190807_KEY_ATP_MS Exp2_ATPase_Neg_052.raw" does not contain chromatograms that mass the molecules in your Skyline document.

The file "20190807_KEY_ATP_MS Exp2_ATPase_Neg_052.raw" has chromatograms with precursor (Q1) m/z values -121.3, -346, -350, -426, -431.1, and -506

whereas the file "20190724_SD_20190724_ATPase pilot experiment 001_Membrane_ATPase_Neg_022.raw" has all of those (except -350) but additionally has chromatograms with precursors -361, -430.1, and -510.1.

-- Nick
davis responded:  2019-08-08
Hi Nick,

Thank you for assisting me with this.
Yes, this is an SRM experiment. Precursors -361, -430.1, and -510.1 should also be included in the data file 20190807_KEY_ATP_MS Exp2_ATPase_Neg_052.raw. I am able to extract these ions (please see attachment) for this file in MassLynx.
Nick Shulman responded:  2019-08-08
Can you send us that file "20190807_KEY_ATP_MS Exp2_ATPase_Neg_052.raw"?

If that file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

I will try to figure out why Skyline is not seeing those chromatograms.
-- Nick
davis responded:  2019-08-08
I have uploaded the file to the provided link.

Best! Sonnet
Nick Shulman responded:  2019-08-08
Thanks for sending that file.

Skyline is ignoring those chromatograms because they do not overlap in time with the Explicit Retention Time that you have specified for your molecules.
The Explicit Retention Time for AMP is set to 3.1 minutes, but the chromatogram ends at 2.8 minutes.

You can get Skyline to import those chromatograms if you blank out the Explicit Retention Time for your molecules.

You can change the Explicit Retention Time for your molecules in the Document Grid using the report called "Molecules".
-- Nick
davis responded:  2019-08-08
Thanks so much Nick for your help!
Best! S