Issue 846: Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C

issues
Status:open
Assigned To:Kaipo
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2021-11-11 by Brian Pratt
Changed:2021-11-11 by Brian Pratt
Resolved:
Resolution:
Closed:
2021-11-11 Brian Pratt
Title»Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C
Assigned To»Kaipo
Type»Defect
Area»Skyline
Priority»3
See user's point #2 of https://skyline.ms/announcements/home/support/thread.view?rowId=53519 (other points are split into other issues)

"If we export and choose Polarity = "All", it is exporting our entire list of transitions (that are designated as either [M-H] or [M+H] adducts in Skyline), but it is changing all of them to positive polarity while keeping the m/z values for positive and negative MRMs. Since this method has polarity-switching, we would have to individually search through the transitions and manually change those that are [M-H] back to negative polarity. If we choose Polarity = "Separated by polarity", it appropriately splits the transitions into a positive and negative method with the correct transitions and polarity in each, so we know that Skyline is able to decide the correct polarity based on the adduct. We only have this issue when trying to have both polarities in one method."

Probably should check with Agilent to verify this is actually supported.

2021-11-11 Brian Pratt
From what I can see, we do in fact pass the polarity information along but it looks like the Agilent-supplied executable fails to recognize it, and just claims everything as positive even when writing an all-negative list. Skyline, at any rate, is passing this kind of thing to our BuildAgilentMethod executable:

Compound Group,Compound Name,ISTD?,Precursor Ion,MS1 Res,Product Ion,MS2 Res,Dwell,Fragmentor,Collision Energy,Cell Accelerator Voltage,Polarity
Amino acids,Glycine.light,FALSE,76.039304,Unit,58.1,Unit,20,130,3.4,4,Positive
Amino acids,Glycine.light,FALSE,76.039304,Unit,53.5,Unit,20,130,3.4,4,Positive
Amino acids,L-Alanine.light,FALSE,90.054955,Unit,44.2,Unit,20,130,3.8,4,Positive
Amino acids,L-Alanine.light,FALSE,90.054955,Unit,29.3,Unit,20,130,3.8,4,Positive
Amino acids,L-Alanine.light,FALSE,90.054955,Unit,28.2,Unit,20,130,3.8,4,Positive
Amino acids,L-Alanine.light,FALSE,90.054955,Unit,27.3,Unit,20,130,3.8,4,Positive
Amino acids,L-Arginine.light,FALSE,173.1044,Unit,156.1,Unit,20,130,6.4,4,Negative
Amino acids,L-Arginine.light,FALSE,173.1044,Unit,131.1,Unit,20,130,6.4,4,Negative
Amino acids,L-Arginine.light,FALSE,173.1044,Unit,129.1,Unit,20,130,6.4,4,Negative
Amino acids,L-Arginine.light,FALSE,173.1044,Unit,85,Unit,20,130,6.4,4,Negative
(etc)