Hello!
Yesterday I had a problem with Skyline and this problem remains today.
I imported the results of the alignment run but the info about iRT peptides was not seen: "chromatogram unavailable". The run itself was OK, I could open it in Excalibur and all peptides were at place. Moreover, it seems that the Skyline had SOME info about the run because it allowed export transition lists based on THIS particular alignment run. But I don't see iRT peptides.
Today I imported results of the real run, import was OK since I have seen the chromatogram import process. Moreover,the chromatogram originally was seen! However, when I clicked another peptides in the target pane, again the chromatogram picture disappeared, and I see nothing. The pane Targets shows green spots but no picture available.
Skyline or computer re-starts did not help.
Please advice what to do.
Technical info:
I recently updated to Skyline (64-bit) 3.7.0.10940
The SRM runs were performed with TSQ Vantage (Thermo)
Whatever else info you need, inform, I will act ASAP
Best regards
Natalia |
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| natbat responded: |
2017-09-08 01:20 |
Hello again
I will upload the Skyline file, alignment run and the result run to the URL that you indicated for other requests, maybe it will help. Files are:
natbat.sky.zip
170907_alignment.raw
170907_Mix4_heavy.raw |
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| Nick Shulman responded: |
2017-09-08 13:52 |
Thank you for sending us your files.
It looks like Skyline is getting confused by the fact that you have both SRM and PRM data files in the same document.
The PRM chromatograms are stored in the .skyd file with the exact precursor m/z and peptide sequence associated with them (e.g. 1054.525039 and "APPGATVSTPQGTNT[+80]QIQPTPASSASPLTAPK").
The SRM chromatograms are stored with whatever m/z is was found in the .raw file (e.g. 1054.525).
Skyline is supposed to be able to find the "1054.525" chromatogram and show it to you, however, because Skyline also found an exact match ("1054.525039" albeit for a different file), Skyline is unable to ever find you the SRM chromatogram.
You are able to see the chromatogram for a brief moment after you first imported the SRM results, because, for a short while that chromatogram lived in a temporary .skyd file.
Until we fix this bug, the best workaround would be to have separate documents for your SRM and PRM data files. |
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Problem with Skyline-Chromatogram unavailable.png