Question about method setting of data dependent NL-MS3
Posted: Fri Nov 16, 2018 4:23 am
Hi everyone,
I’m a user of Thermo Fisher LTQ-Oribitrap Elite.
Recently, I have some problems of method setting in data-dependent neutral loss MS3 (DD-NL-MS3) scan mode.
Since my research candidates are all have a great characteristic that is consecutive loss of two different moiety (R1 and R2) on their structure by CID in MS.
So that these two specific neutral loss mass (R1 and R2) can be used as feature for screening these candidates.
Firstly, we test a single compound that would consecutively neutral lose R1 and R2 moiety by CID.
We setting parent mass of this compound and turned off dynamic exclusion function to evaluate the method.
In our results, we found a lot of MS3 events were triggered for this compound, but they all came from same fragment ion (loss of R2).
However, the other fragment ion (loss of R1) can not be triggered the MS3 event since their intensity is always weak than other one (loss of R2).
The mass error and intensity were all satisfy data dependent criteria.
Detailed result and method parameters can be see as follows links.
(MS2 fragmentation spectrum)
https://drive.google.com/open?id=1yHHcf ... XDBWUmgFrT
(Chromatogram of MS1, MS2 and MS3)
https://drive.google.com/open?id=1oOAyZ ... DuHuZoPfBf
(Method parameters)
https://drive.google.com/open?id=18sErG ... IldPC724aE
Our ultimate goal is to see all candidates precursor that can be triggered MS3 scan twice for loss of R1 and R2, separately.
I’ll appreciate any comments and help.
Thank you all.
I’m a user of Thermo Fisher LTQ-Oribitrap Elite.
Recently, I have some problems of method setting in data-dependent neutral loss MS3 (DD-NL-MS3) scan mode.
Since my research candidates are all have a great characteristic that is consecutive loss of two different moiety (R1 and R2) on their structure by CID in MS.
So that these two specific neutral loss mass (R1 and R2) can be used as feature for screening these candidates.
Firstly, we test a single compound that would consecutively neutral lose R1 and R2 moiety by CID.
We setting parent mass of this compound and turned off dynamic exclusion function to evaluate the method.
In our results, we found a lot of MS3 events were triggered for this compound, but they all came from same fragment ion (loss of R2).
However, the other fragment ion (loss of R1) can not be triggered the MS3 event since their intensity is always weak than other one (loss of R2).
The mass error and intensity were all satisfy data dependent criteria.
Detailed result and method parameters can be see as follows links.
(MS2 fragmentation spectrum)
https://drive.google.com/open?id=1yHHcf ... XDBWUmgFrT
(Chromatogram of MS1, MS2 and MS3)
https://drive.google.com/open?id=1oOAyZ ... DuHuZoPfBf
(Method parameters)
https://drive.google.com/open?id=18sErG ... IldPC724aE
Our ultimate goal is to see all candidates precursor that can be triggered MS3 scan twice for loss of R1 and R2, separately.
I’ll appreciate any comments and help.
Thank you all.