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Incorrect retention time window

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Incorrect retention time window rocketjishao  2018-09-06 02:40
 

Dear Skyline developers,

I have used Skyline for about one year, but I am still confused about the incorrect rentention time windows that Skyline occasionally gives me.
As you can see in the attachment. The retention time window is cut by Skyline, resulting in a loss of peptide information.
I have ever tried modifying the parameters in peptide settings and transition settings, but the problem still could not be solved, which is really headaching.
Could you please give me some suggestions to resolve the issue?
Thanks a lot.
 
 
Nick Shulman responded:  2018-09-06 07:08
It looks like you might need to use a larger number of minutes in the setting at:
Settings > Transition Settings > Full Scan > Retention Time Filtering
(or change it to "Use all matching scans")

If that does not help, then you should send us your Skyline document.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.
If that .zip file is less than 50MB then you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url
-- Nick
 
rocketjishao responded:  2018-09-06 07:19
Dear Nick,

Thank you for your response.
I did select "Use all mataching scans", but the problem still exits.

I have attached the skyline document in the attachment.
Hope you can figure it out, thx a lot.
 
rocketjishao responded:  2018-09-06 07:22
Dear Nick,

Thank you for your response.
I did select "Use all mataching scans", but the problem still exits.

I have attached the skyline document in the attachment.
Hope you can figure it out, thx a lot.
 
Nick Shulman responded:  2018-09-06 22:31
Thank you for sending us your files.
The problem is that you are trying to extract MS2 chromatograms from DDA data.
The area under MS2 chromatograms extracted from DDA data are not meaningful, because any particular precursor does not get selected for fragmentation on any sort of predictable schedule.
Also, whenever you have MS2 and MS1 chromatograms, Skyline truncates the MS1 chromatograms down to the same retention time length as the MS2 chromatograms. This is the correct thing for Skyline to do in a scheduled PRM experiment, but results in the truncated chromatograms like you see.

We have some plans to add a new acquisition type "DDA" that you will be able to choose on:
Settings > Transition Settings > Full Scan > MS/MS Filtering Acquisition Method

For now, if you have DDA data, you should choose "None" for MS/MS Filtering Acquisition Method
 
rocketjishao responded:  2018-09-08 01:01
Dear Nick,
Thank you so much for your suggestion. It really helps a lot for processing of DDA data.

In fact, previously I have also encountered the incorrect retention time issue by using the method (selecting "MS/MS Filtering Acquisition Method") to analyze some PRM data.
I am wondering what other parameters we could change to eliminate that.
The detailed information is shown in the attachment.

Thank you.
 
rocketjishao responded:  2018-09-08 01:10
Dear Nick,
Thank you so much for your suggestion. It really helps a lot for processing of DDA data.

In fact, previously I have also encountered the incorrect retention time issue by using the method (selecting "MS/MS Filtering Acquisition Method") to analyze some PRM data. The detailed information is shown in the attachment.
I am wondering what other parameters we could change to eliminate that.

Thank you.