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Best way to ID my protein

Best way to ID my protein - Proteomics Forum

Best way to ID my protein - Post Questions and Discuss Proteomics, Proteomic Bioinformatics, Proteomic Techniques such as 2-D, Mass Spec etc.


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Old 01-10-2009, 05:39 PM
Pipette Filler
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Default Best way to ID my protein



Hi guys

I Just wanted to try get a general conscious on what is the best approach I should take. Iím undertaking an industrial PhD were I am identifying novel enzymes, over the past year I have been quite successful and been able to purify and identify my protein using Maldi (as a related genome had already been sequenced it was relatively easy)

I am about to start work on a new enzyme from a different organism, as my work is part of a bigger project there is generally a strong emphasis on indentifying the protein ASAP so that I can work on making this enzyme a product. If I go down the same route I doubt I will be able to identify the protein by tryptic digestion (no similar genomes have been sequenced)
As far as I can figure out I have four options:

*Maldi -Post source decay sequencing, but been told very time consuming
*Send away for N-terminal sequencing then do degenerate PCR, but I believe this approach can be a bit hit a miss.
*Edman sequencing (limited to short aa lengths but can be done if protein digested, does anyone do a full protein service?)
*Get entire bacteria genome sequenced (I know it sounds daft but have read prices dropped dramatically to around US $1000 ) that way I could just do the relatively easy tryptic digest and use Maldi.

Given I need results ASAP (cant spend over a year trying to find the sequence of my protein) what approach would you guys take?

Are there any other ways I could identify my protein sequence?
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