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Proteins in SDS-PAGE

A convenient, and easy to handle protein separation and isolation system is still the “old” SDS-PAGE technique; but which analysis can (still) be performed with the obtained protein bands?
One thing for sure, intact mass analysis is out of the question due to the many SDS molecules attached
to your protein, and suitable protocols to remove these SDS molecules are very cumbersome.
Protein identification by peptide mass fingerprinting, “PMF” (first choice) can be easily and
successfully performed, as well as N-terminal sequence analysis. The latter is only of importance if you need to know the N-terminal start of a certain protein band, information that can not be directly
obtained by PMF, or in case the protein might be a “novel” protein (see below). The PMF method has
the advantage that N-terminally blocked proteins can still be successfully identified.

N-terminal or internal sequence analysis can be performed on Coomassie stained protein bands,
and the latter is especially a good solution for “new” or unknown proteins if also the DNA sequences
of the organism from which the protein originates, is not available in the public data bases. After all,
PMF is based on identification using the peptide masses of known sequences. If you use electro-blotting onto PVDF as sample preparation for N-terminal sequence analysis, please see our technical /
background information sample preparation for N-terminal sequencing of PVDF samples.

Amino acid analysis can also be performed; we offer a special service: the protein isolation from gel, followed by suitable sample clean-up procedures prior to analysis. Important is to have also a good
blank piece of gel, for background correction. See also the more detailed AAA technical information.