Hi, Brendan:
Thank you very much for developing this user friendly useful software for MRM experiments. After learning the skyline tutorial, I am trying to import some of my data from TSQ ultra into skyline 0.7.0 in windows.My files contains MRM analysis for 7 peptides with 2 transitions for each peptide. I also include one full mass scan besides the MRM scans.
The raw files seem to be imported. But only a part of transitions are used to reconstruct mass chromatograms. Because I use two transtiions, only one transition is used to reconstruct the ion chromatogram. No chromatograms was reconstructed for some of the peptides at all. Could you please tell me why this happened? Thank you very much.
Ting |
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| Brendan responded: |
2010-12-22 11:14 |
Hi Ting,
Were the data acquired from a method you created using a Skyline exported transition list?
If you entered the transitions yourself, the masses may not be accurate enough with the current settings.
I would suggest exporting a transition list from Skyline and then opening it in Excel. On another page of the worksheet, you can paste the transition list from your acquisition method, and then sort both by precursor and product m/z values. This should make it fairly easy to check for inconsistencies.
You may find that the m/z values are not quite right, or perhaps you have the wrong ions or charge states in some cases. If the m/z values are only slightly different from what Skyline expects, you can often alter the "m/z match tolerance" in the Instrument tab of the Transition Settings.
For a thorough treatment of working with experiments begun without Skyline, you can refer to the "Existing and Quantitative Experiments" tutorial:
https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_existing_quant
Once you have the transition list you used and the one Skyline proposes matching closely, you should be able to import your data and analyze your results using Skyline.
Good luck. Thanks for your interest.
--Brendan |
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| zhaot3 responded: |
2010-12-22 12:05 |
Thanks much for your prompt reply.
You are right. I did enter my transitions without using skyline.
The mass tolerance setting filtered out some peptide transitions.
It worked for me after I changed the mass tolerance.
Thanks a lot.
Merry Christmas and Happy New Year!
Best regards,
Ting |
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