generally incubation at RT with strong reducing agents as DTT or TCEP (i do not like so much BME) at mM concentrations are able to broke disulfides, the problem is that if you are not working in anaerobic enviroment the SH can be reoxidezied and for S-S in short time once you remove the reducing agent.
Jusy a question: How do you monitor the disulfide integrity?
You can treat the small molecule with DTT or TCEP for couples of hours at room temperature or for 12-hrs at 4 degree C. I prefer TECP because it is a way stronger reducing agent than DTT, but you need to avoid using any phosphate buffer in the solvent.
Make sure you have sufficient amount of reducing agents (20~50-mM DTT or 0.5~1-mM TCEP) and buffer molecules to maintain solvent pH even if most reducing agents work with a wide pH range (for example, TCEP is useful at the range of pH 1.5-8.5). I will suggest to keep your buffer at lower pH, which can prevent disulfide bond formation after the reaction.
Lyophilize the sample solution right after the reaction is done. This step will remove the solvent which is a critical step to prevent from the re-oxidation.
Check the molecular weight using LC/GC mass spectrometry. If you don't want to heat up your molecule, use LC mass spectrometry.