I have the following experimental setup: Protein A is capable of cutting protein B in small fragments. The small fragments are identified and the nature of the last amino acid in each fragment is counted. Thus, in one experiment it is possible to detect all 20 amino acids but with a different total count. The total count depends on the nature of Protein A and the conditions of the experiment. At the end, for the two conditions tested I end up with a table like this:
Amino-acid Exp1 Exp2 A 0 3 R 20 12 G 10 15 H 14 22 E 5 0
with entries for all 20 amino acids and I also know the total number of fragments from Protein B that were identified in each condition.
The question I need to answer is: Are the amino acids total counts significantly different under the two experimental conditions?
First I thought to use a chi-square test since with the chi-square test I can take into account the different number of fragments that were identified in the two conditions. But inevitably I will end up with expected values being 0 and thus I cannot use the chi-square test.
What test can be used in this case?