Dear Sir. Concerning your issue about the preliminary analytical techniques to find the nature of an antimicrobial compound whether it might be a protein or a non protein moeity. I think the following below links may help you in your analysis:

http://medcraveonline.com/JMEN/JMEN-01-00010.php

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492345/

https://www.sciencedirect.com/science/article/pii/S2095177915300150

http://www.scielo.br/pdf/bjm/v38n2/v38n2a34.pdf

Thanks

Dear Sir/

To ensure from that, easily incubate your substance with different proteases for 6h(protenase K,pronase E ..etc) at suitable concentration.After that measure the activity of the substance,if it is antimicrobial protein or no.or make rapidly polyacrylamide gel electrophoresis with suitable standard protein and compare between the protease treated and the control,you will know what you need.

Did you do any kind of partition?

Assuming your options are small molecule vs. protein you can try precipitating in 80% acetone. Simply add 4 volumes of 100% acetone to aqueous sample, mix well, incubate ON in -20C, centrifuge for 20 min, and test for activity. Make sure to dry the pellet and soup and re-suspend in water before you do the assay as acetone will be anti-microbial .