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Protein identification from bands with same molecular weight but different intensity

Posted: Mon Oct 20, 2014 10:18 pm
by Fazilah
Hi All,
This is probably a very basic question, but I want to confirm if protein bands (from 1D gel) with similar molecular weight but
different intensity will end up to be the same set of proteins after LC/MS analysis? or is it possible to be different?

Thank you!

Posted: Wed Oct 22, 2014 7:21 am
by Infinity
It is not clear. What do you mean by saying "the same set of proteins"???

Posted: Wed Oct 22, 2014 5:17 pm
by Fazilah
Hi Infinity,
Sorry if i don't explained clearly.
I plan to cut bands from a gel and identify the protein using LCMS.
If i have one band (let say sample 1) with a specific molecular weight, but low intensity, and another band (sample 2) with similar intensity but more intense, will I end up with the same proteins from these two samples? or should expect more proteins from more intense band?

Thank you!

Posted: Thu Oct 23, 2014 2:29 am
by Biomarker
In principal yes more protein IDs with intense band. But they may be same set or different proteins..

Posted: Thu Oct 23, 2014 4:42 am
by Infinity
Nope, It doesn't mean anything. For example you might have very intense band but 99% of this intensity will be attributed to some high-abundant protein (albumin, keratin, etc.) - so you end up having many peptides for one protein. In an opposite way you might see almost nothing on a gel because many low-abundant proteins with similar mass and you end up having much more protein IDs.