Using an oligo(phenylene ethynylene) prototype molecular wire, we study the optimum preparation conditions for acetyl-protected conjugated dithiols to be tested in a break-junction experiment. Even without adding a deprotection agent, molecular junctions are formed in reasonable percentage in all experiments, both under solvent and in air. Under liquid conditions, a higher rate of junction formation is achieved by deprotecting the molecules with a specific agent. A similar rate can be achieved by performing the experiment in air without adding a deprotection agent. No significant variations of the conductance values of the molecule were observed with the change of environment or deprotection conditions.