Selective identification and differentiation of N‐and O‐linked oligosaccharides in glycoproteins by liquid chromatography‐mass spectrometry

A mass spectrometry method has been developed for selective detection of glycopeptides at the low (≤25) picomole level during chromatography of glycoprotein digests and for differentiation of O‐linked from N‐linked oligosaccharides. The technique involves observation of diagnostic sugar oxonium‐ion fragments, particularly the HexNAc+ fragment at m/z 204, from collisionally excited glycopeptides. Collision‐induced fragmentation can be accomplished in either of two regions of a triple quadrupole mass spectrometer equipped with an atmospheric pressure, electrospray (ES) ionization source. If collisions before the first quadrupole are chosen, it is possible to enhance formation of carbohydrate‐related fragment ions without distorting the distribution of peptide and glycopeptide signals by increasing the collisional excitation potential only during that portion of each scan in which the low mass carbohydrate‐related ions are being detected. This procedure, requiring only a single quadrupole instrument, identifies putative glycopeptide‐containing fractions in the chromatogram but suffers from a lack of specificity in the case of co‐eluting peptides. Increased specificity is obtained by selectively detecting only those parent ions that fragment in Q2, the second collision region of the triple quadrupole, to produce an ion at m/z 204 (HexNAc+). Only (M + H)+ ions of glycopeptides are observed in these liquid chromatography‐electrospray tandem mass spectrometry (LC‐ESMS/MS) “parent‐scan” spectra. N‐linked carbohydrates are differentiated from O‐linked by LC‐ESMS/MS analysis of the digested glycoprotein prior to and after selective removal of N‐linked carbohydrates by peptide N:glycosidase F. These methods, which constitute the first liquid chromatography‐mass spectrometry (LC‐MS)‐based strategies for selective identification of glycopeptides in complex mixtures, facilitate location and preparative fractionation of glycopeptides for further structural characterization. In addition, these techniques may be used to assess the compositional heterogeneity at specific attachment sites, and to define the sequence context of the attachment site in proteins of known sequence. The strategy is demonstrated for bovine fetuin, a 42‐kDa glycoprotein containing three N‐linked, and at least three O‐linked carbohydrates. Over 90% of the fetuin protein sequence was also corroborated by these LC‐ESMS studies.