Structural assignment of isomeric 2‐aminopyridine‐derivatized oligosaccharides using negative‐ion MS n spectral matching

To investigate the possibility of structural assignment based on negative‐ion MS 2 spectral matching, three isomeric pairs of 2‐aminopyridine (PA)‐derivatized non‐fucosylated, fucosylated, and sialylated oligosaccharides (complex type N‐glycans) were analyzed using high‐performance liquid chromatography/ion trap mass spectrometry (HPLC/ITMS) with a sonic‐spray ionization (SSI) source. In the SSI negative‐ion mode the deprotonated molecule [M–2H] 2− becomes prominent. Negative‐ion MS 2 spectra derived from such ions contain many fragment types (B and Y, C and Z, A, and D) and therefore are more informative than the positive‐ion MS 2 spectra derived from [M+H+Na] 2+ ions, which usually consist mainly of B and Y fragment ions. In particular the internal ions (D‐ and E‐type ions) provided useful information about the α 1‐6 branching patterns and the bisecting GlcNAc residue. Spectral matching based on the correlation coefficients between negative‐ion MS 2 spectra was performed in a manner similar to the positive‐ion MS 2 spectral matching previously reported. It was demonstrated that negative‐ion MS 2 spectral matching is as useful and applicable to the structural assignment of relatively large non‐fucosylated, fucosylated, and sialylated PA‐oligosaccharide isomers as its positive‐ion counterpart. Copyright © 2005 John Wiley & Sons, Ltd.