Help! Blocked N-terminus..

Philp Robin John mcbrp at
Tue Jan 24 00:13:39 EST 1995

Kang Ke-Won (kwkang at wrote:
: I have a problem on sequencing a purified protein. MW of the protein is 
: about 10kd and has thrombin inhibiting activity. While sequencing the protein,
: unusual amino acid peak appeared in first cycle and then no peak appeared there
: -after. I used TFA method to deblock the protein. After deblocking, same
: unknown peak was detected in first cycle and then many of peaks were detected.
: The protein was blotted to PVDF membrane and sequenced by automated sequencer.
: Is there a good method to deblock N-terminus without fragmentation?
: Please Help! 
Unfortunately the methods available to un-block (usually acetylated) 
proteins do give very clear data when subsequently sequenced. I would 
suggest carrying out an in-situ digestion of the protein on the PVDF 
membrane or alternatively an in-gel digestion of the stained gel. 
Following HPLC separation of the peptides you can obtain some great data 
from the sequence of the individual peptides. Both methods give excellent 
results. Please feel free to E-mail me if you need further info about 
these methods.Good luck.

Robin J. Philp
Protein Chemistry
Institute of Molecular and Cell Biology
National University of Singapore
E-mail: mcbrp at

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