Customs Adducts // GC MS Agilent import

Customs Adducts // GC MS Agilent import Christina lucas  2020-01-06

I try to import GC MS Data (SingleQuad) to skyline, as I really like the software. The approach presented by Pawel Sadowski for Shimadzu and Thermo does not work for Agilent Data.

So far my I was to create different adducts for the basepeak molecule, but this is not possible if you just want to create a mass additon that is not in the adduct list.
I tried [M(-5.0)+H] or likewise, it does not work with the actual version.

If I try to add more than one precurser, skyline starts to label them

I attach a file of the agilent data, maybe that makes it aesier to solve the problem...

Brian Pratt responded:  2020-01-06

Hi Christina,

I was able to construct a transition list from your excel sheet without too much difficulty. For example:

"Precursor Name" "Precursor Adduct" "Explicit Retention Time" "Precursor Charge" "Explicit Retention Time Window" "Precursor m/z"
C10:0 [M+] 4.683 1 0.1 186.2
C10:0 [M(-112.1)+] 4.683 1 0.1 74.1
C10:0 [M(-99.1)+] 4.683 1 0.1 87.1
C10:0 [M(-43.1)+] 4.683 1 0.1 143.1
C10:0 [M(-131.1)+] 4.683 1 0.1 55.1
C10:0 [M(-31.1)+] 4.683 1 0.1 155.1

It was necessary to add that first line "C10:0 [M+] 4.683 1 0.1 186.2" to establish the mass of the no-losses precursor.
I constructed the adducts for the other lines using the formula =CONCATENATE("[M(",F3-I3,")+]") where column F is your "Product Ion" and column I is your "Molecular Ion".

Let me know how that works out for you!

Thanks for using the Skyline support board,

Brian Pratt

Christina lucas responded:  2020-01-08

Hi Brian,

thank you, that worked well !

I tried the losses, but I was not aware to put in the non loss precuser first :) Thanks for the hint!