Isolation in ion trap MS

[stefano]

WE face a problem using Ion Trap DECA XP Thermo

We found in the same analytical run that some molecules can be isolated for MS-MS experiment, while some others can not.
This fact happens only in negative acquisition mode. The same compounds can be isolated at 100% in positive

For example we can isolate (isolation width 1 amu) estradiol, estrone but not ibuprofen and ketoprofen (which are benzyl-acetic acids). Also Ultramark ions can not be isolated in negative (while can be isolated in positive)

We can recover signals if we apply a isolation width of more than 4-5 amu.

We want to know whether:
- It depends on the kind of molecules (and that case the Ion trap is not suitable to analyse these compounds and nobody told us)

or it is a problem of our instrument

[Mary Carson]

Some molecules appear to be "fragile" in an ion trap--they need a wider isolation width to see them at all. We had that experience in positive mode with some aminoglycosides.

[Kostas Petritis]

In the paper below, the authors fragment by using a LCQ ion-trap several structural analogues of the compounds that you mentioned (including iduprofen) in negative ion mode with an isolation with of 2 amu so probably there is something wrong with the way you are doing things (i.e. poor settings, poor calibration?). It is not easy to say, as you were succesful in isolating other compounds...

Rapid Commun. Mass Spectrom. 2006; 20: 3412–3420
Determination of fourteen non-steroidal anti-inflammatory drugs in animal serum and plasma by liquid chromatography/mass spectrometry
Floriana Vinci1, Serena Fabbrocino1, Maurizio Fiori2, Luigi Serpe1 and Pasquale Gallo