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Peak picking

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Peak picking Yasin  2018-08-02 11:55
 

Dear Skyline Team,

I hope you can help me with some questions.

I have a targeted method for about 100 different small molecules (high resolution instrument) and would like to screen for each of them for about 20 different adducts. For most of those compounds I know already the retention time. Via the explicit retention time column in the transition list I can now force skyline to pick the peak closest to this retention time.

So I have the following questions:
However, how can I prevent skyline from picking a peak with a different retention time if no peak with the expected RT is present?
And also: Is it possible to prevent skyline from picking spikes (consisting of only 1 to 3 data points as peaks?
Moreover, it would be nice to be able to tell skyline to just integrate from e.g. 14.4 to 14.6 ignoring if there are spikes, a peak or nothing at all in that range.

Thank you a lot in advance!

Yasin
 
 
Yasin responded:  2018-08-10 07:13

Hello again,

I just wanted to try again and ask if there is some way to do those things in Skyline or if there is a chance of implementing it. Although I like many aspects of Skyline I do not really like to use it at the moment due the enormous amount of time I have to put in correcting the peak picking. It would help a lot if you would implement some of the mentioned things.
Thank you a lot for your time and effort!

Yasin
 
Nick Shulman responded:  2018-08-10 16:18
I don't think we have a good answer for this, but if you send us your data, maybe we can come up with something.

In Skyline you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise you can upload it here:
https://skyline.ms/files.url

It might help if you sent us a few of your raw files too.