|Protein glycosylation is one of the most important post-translational modifications, and it is involved in many biological processes, including inter-/intra cell signaling, protein recognition, and receptor binding, etc. It is estimated that 50-60% of cell-surface and secreted proteins are glycosylated. Alteration in the glycan structures on these proteins has been implicated in various disease states, such as, cancer, Alzheimer's disease, rheumatoid arthritis, and chronic obstructive pulmonary disease, etc. Thus, characterizing glycans and monitoring the changes of glycan profiles on proteins are essential to elucidate their biological significance and facilitate disease diagnosis. Mass spectrometry is a powerful tool for characterizing glycans on proteins, due to its high sensitivity, selectivity and small sample requirements for analysis. In order to elucidate a variety of glycan profiles (including both neutral and acidic glycans) on glycoproteins, several efficient MS-based approaches have been developed, and they are described herein. These approaches include an ion-pairing strategy in conjunction with ESI-MS/MS to identify the acidic functional groups (sulfate, and phosphate) in carbohydrates and glycopeptides; and a glycopeptide-based MS approach (liquid chromatography followed by MALDI-TOF/TOF) to characterize glycans on different glycoproteins that vary in the number of glycosylation sites and their corresponding glycan profiles. Aside from protein glycosylation, disulfide connectivity is another important modification present in proteins, and it plays a key role in establishing/maintaining protein structures in their biologically active forms. Therefore, determination of disulfide bond arrangement provides chemical structural information about proteins, and it may lead to insights into their functional roles. To achieve this goal of determining disulfide bonding patterns in proteins, a mass spectrometric approach using liquid chromatography followed by electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (LC/ESI-FTICR-MS) has been validated and used to determine the disulfide bond arrangement in an HIV envelope protein. This study contributes to the understanding of this protein's structure, and these findings are essential in understanding and improving the protein's immunogenicity.