Multistage mass spectrometry, as implemented using low-energy collision-induced dissociation (CID) analysis in three-dimensional (3D) quadrupole ion traps (QITs), has become a powerful tool for the investigation of protein glycosylation. In addition to the well-known combination of QITs with electrospray ionization (ESI), also a matrix-assisted laser desorption/ionization--quadrupole ion trap--reflectron time-of-flight (MALDI-QIT-rTOF) mass spectrometer has recently become available. This study systematically investigates the differences between these types of instrument, as applied to characterization of glycopeptides from human antithrombin. The glycopeptides were obtained by tryptic digestion followed by lectin-affinity purification. Some significant differences between the ESI-QIT and MALDI-QIT-rTOF approaches appeared, most of them are causally related to the desorption/ionization process. The combination of a vacuum MALDI source with an ion-trap analyzer accentuates some characteristic differences between MALDI and ESI due the longer time frame needed for the trapping process. In contrast to ESI, MALDI generated ions that exhibited considerable metastable fragmentation during trapping. The long time span of the QIT process (ms range) compared with that for conventional rTOF experiments (micros range) significantly magnified the extent of this metastable fragmentation. With the investigated glycopeptides, a complete depletion of the terminal sialic acids of the glycopeptides as well as a variety of other fragment ions was already found in the MS1 spectra from the MALDI-QIT-rTOF instrument. The positive ion low-energy CID spectra (MS2) of the selected glycopeptides obtained using the two different QIT equipped instruments were found to be quite similar. In both approaches, fragmentation of the glycan and peptide structures occurred sequentially, allowing unambiguous sequence determination. In the case of ESI-QIT-MS, fragmentation of the glycan structure occurred at the MS2 stage and fragmentation of the peptide structure was obtained only at the MS3 stage, which indicates the necessity of multistage CID experiments for complete structure elucidation. The MALDI-QIT-rTOF instrument yielded both kinds of fragments at the MS2 stage but without mutual interference.

The carbohydrate structures of five isoforms of alpha-AT and two isoforms of beta-AT were determined by applying capillary zone electrophoresis (CZE) on-line coupled to electrospray ionization-mass spectrometry (ESI-MS) using an ion-trap analyzer. For the AT preparations gained from a plasma pool at least semiquantitative information on the isoform-distributions could be gained. Unlike to the commonly used approaches starting from enzymatically treated glycoproteins, this approach deals with intact proteins. The high accuracy of the molecular mass determination obtained by the ion-trap analyzer allows one to calculate and ascertain the carbohydrate composition assuming no variations in the protein moiety of AT and to exclude or confirm the presence of the potential post-translational or other modifications. Therefore, the direct coupling of CZE with ESI-MS does not only represent a fast alternative technique to two-dimensional electrophoresis (2-DE) but serves as a method which provides structural information complementary to that gained from peptide mapping methods.

Defined conditions of EOF along with different pH values of the BGE were compared for the purpose of analyzing glycopetides by CZE coupled to MS (CZE-MS). Hyphenation to MS involved ESI as well as MALDI, and single-stage and multistage MS were applied. Variation of the EOF was accomplished by selecting appropriate coatings for the capillary, namely hexadimethrine bromide (HDMB) and HDMB/dextran sulfate. A high and reproducible anodic and cathodic EOF, respectively, was obtained in both approaches, allowing the detection of analytes with net positive as well as negative charge in one single run. Thus, a fast and sensitive determination of the glycopeptides in a tryptic digest of antithrombin, chosen as a test sample, was achieved. Ionization suppression effects, a phenomenon typically observed with glycopeptides in MS analysis, were minimized thanks to separation from other peptides present. The high stability of the coatings permitted the generation of mass spectra without interfering peaks originating from the coating polymers. The high EOF generated by the coatings facilitated the maintenance of a stable spray when coupling to ESI-MS, and a stable CZE current when working with a sheath flow-assisted analyte deposition onto MALDI targets, respectively. In conclusion, CZE-MS could be demonstrated as a robust complementary method to capillary RP-HPLC-MS in combination with both soft-ionization techniques, ESI and MALDI, generally, and particularly in the context of glycopeptide analysis.

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