How to create a file with default settings and how to see the precises signal intensity?

How to create a file with default settings and how to see the precises signal intensity? t j f m voermans  2019-03-27


I was wondering if there is a way to create a new file with default settings, like when you created your first file after installing Skyline. I am asking because I get different signal intensities for a peptide between two files while the same results where imported. So I must have done something with the settings that changed the signal intensity. I tried to create a new file, but I still didn't get the same signal intensity as the first file I created.

Also, is there a way to see the exact signal intensity? Above the peak, I only see the retention time and the ppm difference. I tried various options provided by the right mouse button, but nothing seems to give me some numbers.



Brendan MacLean responded:  2019-03-27

Hi Tim,
You can use Settings > Default to get the default settings Skyline uses when you first install it.

If I were trying to figure out what was different in the settings of two files, I might consider saving and exporting two settings files (.skys) and then using a visual diff tool like WinMerge or TortoiseMerge to see how the XML text differs between the two. You can use Settings > Save Current to save the settings of any document you like, and then Settings > Share to save a .skys file, which will express the settings in XML text.

There is not a way to put either the peak height or peak area text on the chromatogram graph. The best way to get access to the exact values would be the Results Grid.

Thanks for using Skyline.


t j f m voermans responded:  2019-03-27

Hi Brendan,

Thank you for your answer. It was of great use. I found the Results Grid tutorial which helped me to get the information I was looking for. (I only can't find a way to get the same information I get in my 'Report' and 'Results Grid'. For example, when going to the 'Results Grid' --> 'Views' --> 'Customize View' I don't get 'Precursors' and 'Precursor results summary' option which I do have when creating a new report. But I am guessing this information will be in the tutorial as well).

I have never heard of a program like WinMerge and I am looking forward to comparing the two files. Thank you!

Kind regards,

Tim Voermans

Brendan MacLean responded:  2019-03-27

Note that what is available in the Results Grid (unlike the Document Grid) depends on what you have selected, if you want to see precursor and precursor results options, you must first select a precursor in the Targets view. Hope this helps.