These are cerebellar granule neuron precur cell lysates. Antibody used was ab24170 from Abcam. I always get one band around 80-90 kDa, but not as expected the 44 kDa band or the glycosylated 120 kDa band. Any idea why?
Is that possible that this band might represent some proteolytic degradation fragment of 120 kDa glycosylated protein ? It looks like highly glycosylated protein. Did you use freshly prepared protease inhibitors cocktail in your buffer just before the cells lysis ?
Yes, I did. And I was told by other people that they see the same phenomenon in human hippocampus lysates using a different lamp1 ab, but also did not know why.
According to the literature I read, the molecular weight you are seeing is consistent with a less glycosylated precursor of about 92 kDa. It may be that in the particular cell type you are studying, that is as far as the glycosylation gets. Another possibility is that there is alternative splicing of the mRNA in that cell type, leading to a shorter protein. Some useful methodology to study the question may be found in this paper:
http://www.ncbi.nlm.nih.gov/pubmed/3101702
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