Hi Parviz,
The degree of fragmentation for CID is dependent on these two factors on the 4800.
1. CE voltage - 1KV for normal fragmentation and 2KV for harder to fragment peptides. Will have to test on which of the voltages would be better by swaping the acquisition method
2. CAD gas pressure and type - High value would means more gas thus more fragments. Change the gas type from nitrogen (or air) to Argon (need to connect new), will improve the fragmentation pattern as well.
The aim is to improve the number of visible Y & B ions for better interpretation by the de novo explorer.
Hopes this helps!
Best,
Jason
Dear Jason,
Thanks for useful answer.
As you know there are two aqusition method for MS/MS (1KV and 2KV). I did both of them but not handy for my protein and peptides. It is noteworthy that, I always use air as CID gas. Thus, I will change gas and again use 2 methods.
Many Thanks again.
Best Regards,
Parviz
Dear Parviz,
The most important factor is - your sample is able to produce a strong signal. Are your samples from Coomassie Blue gels?
From our experience, if you would like to achieve 50% accuracy in de novo peptide sequencing - the given MS precursor peptide should have at least a S/N greater than 400 to 500.
If you are to perform the de novo peptide sequencing using AB Sciex's software DeNovo Explorer - you can refer to this paper, which has quite detail description:
https://www.hindawi.com/journals/ecam/2011/471020/
Good luck!
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