Molecular weight calculate from primary structure of my protein is 23121 but after MALDI-TOF i got 22908.90 a difference of approximately 213 dalton. Any suggestions for the observed mass difference.
Hi Mangesh Bawankar
How did you calculate the molecular weight of the protein; the calculated mass (23121 Da) - does it correspond to monoisotopic mass or average mass ?
Did you take into account the disulphide bonds ?
What is the mass accuracy of the instrument at this mass range (20,000 to 30,000 m/z) ?
Depending on that we may come to some sort of conclusion.
Mass increment in proteins (+) usually corresponds to modifications/ adducts; while mass decrement (-) may correspond to terminal amino acid loss (excision/ truncation).
you should keep in mind that MALDI MS shows you the distribution of different protein isoforms including potential splicing variants and PTMs. It is also common to see M+Na and M+K ions in MALDI spectra of small proteins.
compare the monoisotopic mass calculated and still if this difference exists, it means the end residues are deleted. Calculate by removing the end residues manually and compare whether it is making any sense. As pointed out by Saravanan, I hope you take into account the disulphide bonds?
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