Re: why there are fragments in MS when using ESI or APCI /MS

APCI is not a non-energetic process. When an analyte molecule is protonated,
the difference in the proton affinity of the analyte and the reagent gas
results in an energy transfer to the protonated molecule of an analyte. The
proton affinity of methane is 132 kcal/mol. The proton affinity of ammonia
is 204 kcal/mol. When an amine reacts with a gas-phase CH5+ ion, more energy
is transferred to the protonated molecule than when the same gas-phase amine
reacts with an NH4+ ion. Both mass spectra exhibit a protonated molecule
peak. However, the CH4 CI mass spectrum will exhibit a lot more
fragmentation than the mass spectrum obtained with NH3-CI. This is because
the proton affinity of NH3 is closer to the proton affinity of the analyte
than the proton affinity of the CH4 is to that of the analyte.

In addition to proton affinity energy differences that can result in
fragmentation of protonated molecules formed in APCI, all atmospheric
techniques such as APCI and ES require that ions pass from a reduced region
of atmospheric pressure to a pressure region of about 10^-6 Torr. During
this transfer, ions can experience inelastic collision with inert molecules
of nitrogen. This will result in collisional activation of the ions. The
collisionally activated ions will then fragment. You can help to reduce this
phenomenon by reducing the voltage on the mass spectrometer's component used
to transport the ions (transfer voltage). The interface temperature can
sometimes be a factor. You can reduce the temperature as a means of possibly
reducing fragmentation.

You have stated that you are using a quadrupole ion trap mass spectrometer.
The pressure in the ion analyzer portion of these instruments is 10^-3 Torr
rather than the normal 10^-6 Torr or lower experienced in other types of m/z
analyzers. This high pressure is necessary to cool the ions so that they
will remain in concentric orbitals according to their individual
mass-to-charge ratios. Because these ions are in motion and they can come in
contact with He atoms, they can become collisionally activated and fragment.
This may be the reason for some of the fragmentation you are observing.
There are ways specific to each manufacturer's instrument to reduce the
amount of other energy being put into the ions as they are stored in the
trap. Making these adjustments can sometimes help in reducing the amount of
fragmentation.

You should put your name on your post.

Regards


-- 
O. David Sparkman
Consultant-At-Large
[EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote in message news:[EMAIL PROTECTED]
}
} In my experiment, there are many fragments in MS,especially when APCI
} is used.  why there are fragments in MS when using ESI or APCI /MS(not
} using MS/MS) , and  how to reduce them,thank you.
}