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Adding Peak Manually

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Adding Peak Manually Alok  2015-11-09 15:31
 
Hi Brendan,

I have been using Peak Picking algorithm and firstly I have to say it's very good in integrating correct peak.

However, when I used Q value cutoff of 0.001, some of the peaks are not integrated as expected (Please see attached file). The peptide (transitions) seem to be present in all except one sample. So I would prefer not to discard the peptide. Instead I would like to add the peak manually for that particular sample if possible. I am not sure how can I add a peak manually. I tried to search the manuals but can't find the answer. Can you tell me how can I add a peak in one particular chromatogram?

The alternative would be to use higher Q value cutoff. In that case even though it integrates peak for this particular sample but it compromises quality of overall data. So I would prefer not to do that.

Thanks,
Alok
 
 
Brendan MacLean responded:  2015-11-09 15:58
Hi Alok,
Th at is a really surprising outcome that Skyline is picking no peak at all in the case you highlight, despite the fact that it has clearly highlighted several peak options and one with very nice coelution, and very close to the predicted RT. This seems like it must be due to a bug to me. And I would be interested to see the data to see if we might be able to fix the problem.

In the meantime, you can certainly manually choose an peak with a retention time label, simply by clicking on the label, in this case "13.7". You will see the cursor change to a hand when you move it over the label.

Otherwise, you can also always set the integration to the retention time range of your choosing, even if Skyline has not labeled a potential peak in that range by clicking beneath the x-axis at one end of the desired range, and dragging to the other end of the desired range.

This is definitely covered in several of the tutorials, and I highly recommend the Processing Grouped Study Data tutorial for anyone interested in learning some of the most effective techniques for processing data quickly in Skyline, even if it is not grouped study data:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_grouped

Thanks for your post, and good luck with your research.

--Brendan
 
Alok responded:  2015-11-09 16:17
Hi Brendan,

Thank you for prompt response as usual.

I think it makes sense that Skyline did not select any peak. In fact it makes very easy to visualize peaks with Q value > set cutoff.

Meanwhile I figured out how to select the peak. I should have known this in first place considering I have been using Skyline since few years now.

I went through the tutorial to remind myself all options for batch processing.

Thanks,
Alok