My peptide is not getting fragmented by ESI-MS. The peptide mass is below 1kDa. I have already checked for Cys residue. I have not pretreated my sample with enzyme or 6 N HCl. Is there any specific sample preparation procedure before doing mass spectrometry?
What makes you think the peptide is cyclic? Do you have any evidence, or is it just that you're not seeing any fragmentation? I assume you've tried a range of collision energies?
Two older papers that sequence cyclic peptides are below;
C. Govaerts, J. Rozenski, J. Orwa, E. Roets, and A. Van Schepdael. Mass spectrometric fragmentation of cyclic peptides belonging to the polymyxin and colistin antibiotics studied by ion trap and quadrupole/orthogonal-accelerated time-of-flight technology. Rapid Commun.Mass Spectrom 16:823-833, 2002.
L. C. M. Ngoka and M. L. Gross. Multistep tandem mass spectrometry for sequencing cyclic peptides in an ion-trap mass spectrometer. J.Am.Soc.Mass Spectrom. 10 (8):732-746, 1999.
I'm sure I've seen some more recent work, a quick literature search will find them.
Good luck,
Peter
I think peptide is cyclic because it did n't show any spot with ninhydrin reagent but after hydrolysis with 6 N HCl I observed a purple spot. Also MALDI mass spectra shows loss of water molecule and oxygen. Lastly, this peptide is from plant source and only after hydrolysis it got fragmented . Yes we tried range of collision energies.
http://msr.dom.wustl.edu/Publications/pdf_files/2002Julia_Gross_Abstract.pdf
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