It depends on your protein isoform. Is it a splice variant, glyco-variant, or other PTMs? Assuming that you are working with mass spec databases, what you require is to then know exactly what peptides distinguishes/identifies between your 2 or more protein variants, and then compare the relative abundance of those peptides, either by AUC or spectral counting. If you are only targeting 1 protein, then manually doing this is actually easier than using some tools. If its for multiple proteins, then I wish you luck.

You must remember that the bacteria eating the protien must be measured before and after consumption and destruction that also destroies the cellular mitocondria, and completely changes the amino acid double helix.  You have a lot of work ahead of you as you'll have to consult with serveral surgeons to find ways to get the protien bioptsyd before and after the bacterological destruction that begins with the glucose.  You have two different protiens to target - 1 before the bacteria eats the glucose - and the one after - that will always be living in a reduced state of oxygen - or cancerious.

@Edward Moh - I am looking at genomic databases not protein databases. so I want to quantify the amount of spliced isoform based on their unique exon-exon junctions.