I am trying to develop an experiment in a teaching lab on MS/MS but do not have too much experience with 2-D Mass Spec. Can anyone recommend a set of conditions to see the main fragments in order to sequence or partially sequence the CCK-4 peptide ? We have an MD-Sciex 3000 (This small peptide is inexpensive and I do see an analysis in the literature - but it is with an Orbitrap, but the voltages etc. might be different on that). Thank you.
There are no "universal" values to use. Every system is different. The flow rate, mobile phase composition used and of course the sample selected may change the settings used to obtain valid data (and a MS system will always output data, even if it is 100% wrong and invalid).
- Settings must be determined experimentally for every sample and method.
When sample is plentiful, we usually start with an infusion first, under the proposed method conditions (i.e. flow rate, mobile phase composition, voltages, etc). This allows us to: try out different MS settings, in real-time, to find the best ionization settings AND also try out different mobile phases and/or additives to identify settings and method conditions which may be used.
I absolutely second @William Letter's comments above. Perhaps start by drawing on the experience of other users of your MS facility (somebody must have run peptide samples), or looking for Sciex application notes. However, you will ultimately have to roll up your sleeves and experiment!
I suggest that you improve your experiment by expending it in a kind of ERMS (energy resolved MS). During your tests, after finding the spray conditions to get a good molecular signal, you may try several collision energies. Then you could select 5-10 energies for your lab work, to plot relative intensities against collision energies, and show indeed the importance of this parameter.
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