Hi Mostafa,
There's something amiss here, certainly - Skyline issues these warnings:
"Error on line 3: Precursor m/z 386.3263 does not agree with value 364.3439 as calculated from ion formula and charge state (delta = -21.98243, Transition Settings | Instrument | Method match tolerance m/z = 0.055). Correct the m/z value in the table, or leave it blank and Skyline will calculate it for you."
and
"Error on line 4: Precursor m/z 610.5403 does not agree with value 588.5579 as calculated from ion formula and charge state (delta = -21.98241, Transition Settings | Instrument | Method match tolerance m/z = 0.055). Correct the m/z value in the table, or leave it blank and Skyline will calculate it for you."
Working back upstream to understand this mismatch in formula and reported m/z in whatever tool produced the transition list will probably clear things up.
Cheers
Brian |
Hey Brian,
So yes I see those, its because of the precursor formula which needs to be changed as these are Na adducts. I usually fix these before submitting the transition list. Once all is ok, then I upload the raw files, and the rest u can see that I was unable to see chromatograms.
Mostafa |
Hi Mostafa,
All you need to do, then, is declare the adduct in the transition list. This works fine, for example:
Molecule List Name,Precursor Name,Precursor Formula,Precursor Adduct,Precursor Charge,Product Charge,Precursor m/z,Product m/z
15:0-18:1(d7) PC,15:0-18:1(d7) PC,C41H73 H'7 NO8 P,[M+H],1,1,753.6125,184.0725
15:0-18:1(d7) PE,15:0-18:1(d7) PE,C38H67H'7NO8P,[M+H],1,1,711.5657,570.5507
18:1(d7) MG,18:1(d7) MG,C21H33 H'7O4,[M+Na],1,1,386.3263,303.7459
15:0-18:1(d7) DG,15:0-18:1(d7) DG,C36H61H'7O5,[M+Na],1,1,610.5403,368.3149
Let me know if that helps.
Brian |