Boronate affinity functionalized materials have recently drawn increasing attention due to their capability to selectively isolate and enrich glycoproteins and glycopeptides. As cheaper and more stable competitors to lectins, boronic acids are generally believed to yield a relatively wider spectrum specificity to glycoproteins. For better understanding and effective utilization of boronate affinity, it is necessary to establish if boronic acids exhibit lectin-like narrow specificity towards individual or a sub-class of glycoproteins. Here we report a pH manipulation strategy for fine-tuning the specificity of boronate affinity monoliths towards two sub-classes of glycoproteins, sialylated and nonsialylated glycoproteins. When the binding pH > the pK(a) of the boronic acid by one pH unit or more, the boronate affinity monolith preferentially binds to glycoproteins containing neutral sugars and excludes sialic acid containing glycoproteins due to electrostatic repulsion. When the binding pH < the pK(a) by one pH unit or more, the boronate affinity monolith binds to sialylated glycoproteins due to the exceptional binding affinity of the boronic acid towards sialic acid residues. The alternative specificity towards sialic acid and neutral sugar was first verified using an off-line combination of boronate affinity extraction with nano-ESI-Orbitrap MS/MS detection. The alternative specificity towards sialylated and nonsialylated glycoproteins was then demonstrated by means of off-line combination of boronate affinity extraction with MALDI-TOF MS. Finally, the developed approach was applied to the alternative extraction of intact sialylated and nonsialylated glycoproteins spiked in human serum.