Skyline Document Setup for MAM

Skyline Document Setup for MAM david schmidt  2021-10-26 02:09:26

thank you very much for this excellent piece of software!

I'm trying to monitor PTMs within a MAM Folder.
Could you tell me whether this is possible with MS1 Full-Scan Filtering (DDA) and with DIA (all-ion) MS2-based quantification? In your example it seems that only precursors were used.

Upon import of my Skyline document, the %modified column of the PTM report remains empty. Also the Peptide Mapping report is completely empty. Do I need to specify certain parameters in the Skyline results or Document grid?

best wishes,


david schmidt responded:  2021-10-26 17:33:58

Hi David,

Thanks for your post. I'd expect Panorama's MAM reporting to show data for your scenario.

As an admin, I was able to check the Skyline file that you uploaded to the server earlier today. I'm seeing 18 rows in the PTM report, and 38 rows in the Peptide Map report. Have you applied any filters to the grids?

If you're still seeing no data rows, feel free to send me an email at and we can figure out what's happening. I don't want to share anything about the content of your file here on the public support forum unless you say it's OK.


jeckels responded:  2021-10-26 17:43:04

My apologies - I was still impersonating you, David, when I replied (an admin capability that lets me make sure I'm seeing the same thing you're seeing). Here's a followup post as myself.