Many proteins have multiple GO terms for biological function.

I want to take these other functions into account when analysing functional changes between two stages of bacterial cell growth.

The changes I am looking for may be subtle or then again they might be quite obvious.

i.e. if i have identified proteins with GO biological functions as below

Protein X: quantity 12, (GO 1234), (GO 5678),(GO 9101112)

Protein Y: quantity 3, (GO 3456), (GO 78910)

Protein Z: quantity 56, (GO 78910), (GO 3456)

Protein A: quantity 38, (GO 9999), (GO 1234)

I can consolidate these figures with the main GO functional designation

(GO 78910), quantity 56

(GO 9999), quantity 38

(GO 1234), quantity 12

(GO 3456), quantity 3

but if i want to compare how often any particular function occurs from sample to sample, I am worried I might miss some information.

If I use the quantification figure for each protein and apply it to each function, I can also obtain

(GO 78910) 59

(GO 3456) 59

(GO 1234) 50

(GO 9999) 38

(GO 5678) 12

(GO 9101112) 12

Although this does not represent the functional ratios within a sample, can it be used to compare the abundance of the functional protein from sample to sample ? With this comparison I might be able to assess other seemingly underrepresented functions .