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eDR Full Scan Data wes rogers  2025-07-02 13:10
 

Hi Skyline team,

I am trying to extract MS1 information from an enhanced dynamic range (eDR) full scan on the Orbitrap Excedion Pro. This scan is multiplexed at the MS1 level and combines 2 Orbitrap subscans to form a single full scan. The ion packets have variable injection times. I am getting the following error when trying to import the data…

[SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=1": [SpectrumList_Thermo::getMultiFillTImes()] Unexpected fill time format: IT=25;35;22;4;3.6;0.21;IT=28;28;28;7.2;0.96;0.72

I am using the latest version of Skyline daily (v. 25.1.1.174). Is this type of data, eDR full scan, data supported yet?

I will upload the .raw file. Please let me know if you need any more information. Thanks!

Thank you,

Wes
 
 
Matt Chambers responded:  2025-08-05 13:44

Hi Wes,

Thanks for the raw file and sorry for the delay responding. This is an interesting case because in your file the EDR MS1 scans are marked as "MSX". Previous our MSX handling code assumed that MSX = multiple precursors, but that's clearly not correct for MS1 scans. :) Can you also get EDR scans for MS2+? I'm wondering if those would have similar IT= fill format that we can't handle.

-Matt
 
wes rogers responded:  2025-08-06 07:25

Hi Matt,

No worries. Thanks for your help on this! It is weird in that it is multiplexed at the MS1 level but not in the traditional sense with multiple precursors with small isolation windows (1-2 m/z). The isolation windows are much wider (in this experiment, ~ 90 m/z isolation windows with overlap) and then are stitched together to make a "full scan". Here are the isolation windows for this eDR full scan covering 100 - 1,000 m/z: 1st Orbitrap subscan (836.4 - 926.4; 689.1 - 779.1; 541.8 - 631.8; 394.5 - 484.5; 247.3 - 337.3; 100.0 - 190.0); 2nd Orbitrap subscan (910.0 - 1000.0; 762.7 - 852.7; 615.5 - 705.5; 468.2 - 558.2; 320.9 - 410.9; 173.6 - 263.3). I have attached a PDF showing the scan information pulled from Freestyle and a little more information regarding eDR.

I have not seen any eDR for MS2 so I'm not sure on this. Please let me know if you need any additional information. Thanks!

Thank you,

Wes
 
wes rogers responded:  2025-09-18 06:04

Hi Matt,

I tried this out in the latest daily build (25.1.1.258) and it appears to be working now. Thanks for working on this!

Thank you,

Wes