what is the best method to extract proteins from serum and tissue sample?
what is the best method to identify the signature protein/peptide between serum and tissue samples by using mass spectrometry?
Hi,
It would be helpful to get a bit more details of the background of your question, as it seems quite general.
First, there are a lot of ways to extract proteins from serum on the one hand, and tons of methods to extract proteins from tissue on the other hand.
If you're interested in a specific protein, it might be best to perform an affinity extraction using an antibody against your protein of interest.
Second, I'm not sure what you mean by 'signature protein', but a signature peptide that can be used for the selective and accurate quantitation of a protein of interest can be identified using an in silico approach, where you generate a theoretical digest of your protein of interest with a protease of choice and then assess which of the peptides generated is specific for that particular protein and not prone to post-translational modifications, for example not containing a methionine as that can be oxidized, which complicates your targeted quantitation.
Hope this helps, but again, a bit more details about your plans might aid the community with coming up with a useful answer!
Hi Eef Dirksen,
Thanks for your comment.
I have some serum and tissue samples from patients with a certain disease, and I want to identify signature proteins or peptides that can differentiate them from healthy controls. I am wondering what is the best method to extract and analyze (top down or bottom up) these biomarkers.We have a Q-Exactive mass spectrometer for this experiment. how to handle the data analysis and interpretation? Is there any specific software or tools to process and visualize the results?
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