Phosphorylation and sulfation are important modifications affecting the biological properties of carbohydrates, proteins, and glycoproteins. Identification of these two functional groups facilitates the understanding of the structure/function relationship in various species. Mass spectrometry is one of the methods used to detect the presence of these two modifications in complex biological mixtures. However, phosphorylated and sulfated structures are isobaric; thus, differentiation between them in routinely used mass spectrometers is problematic. Herein, we demonstrate that these two groups can be discriminated by using ion-pairing in conjunction with MS/MS experiments. The characteristic product ions are used to successfully identify the phosphorylation and sulfation present in mono-, disaccharides, and the highly sulfated glycoprotein, ovine luteinizing hormone. This method is a robust approach to differentiate the two isobaric functional groups.