The identification of cross ring 0,2A fragments in the MS2 spectra of the [M - H]- ions at m/z 1098 confirmed that this structure contained 4 linked HexNAc (data not shown). Since this structure was not affected by various β- hexosaminidase digestion suggesting that it contained the α1-4 linked GlcNAc to Gal. Having identified that the second terminal HexNAc in the [M - H]- ions at m/z 790 is 4 linked, the investigations were extended further

to uncover the identity of the 4 linked HexNAc. The literature suggests that some of the terminal 4 linked HexNAc have been identified in the gastric mucin previously. These include the GlcNAcβ1-4GlcNAc chitobiose Inhibitors,research,lifescience,medical [23], the antibacterial GlcNAca1-4 motif [24] and the GalNAcβ1-4GlcNAc lacdiNAc motifs [25]. An MS3 approach was adopted, whereby the fragmentation pattern of known standards containing GlcNAc1-4 (chitotriose) and GalNAc1-4 (GalNAcβ1-4Gal) were compared to the fragmentation of the 4 linked Inhibitors,research,lifescience,medical HexNAc structure identified in the dominating m/z 790 isomer in PGM. The cross ring 0,2A fragment with an m/z 304 characteristic for the C-4 extension of the core 1 HexNAc (selleck chem Figure 3b) was selected for MS3 fragmentation for both the sample Inhibitors,research,lifescience,medical and the standards, and the comparison allows assignment

of the terminal epitope, since the mechanism for the generation of this fragment [26] removes the anomeric information as well as the stereospecificity of the cross Inhibitors,research,lifescience,medical ring fragmentation remnant. Figure 3c shows the spectra for the MS3 of PGM with m/z 790 parent and subsequent collision of the daughter ion m/z 304 and the MS3 spectra of the daughter ion m/z 304 after collision of the [M - H]- ions for both the standards. Correlation of the MS3 fragments and their intensities from the PGM sample with the

standards showed that standard oligosaccharide with the GalNAc1-4 had an R2 value of 0.37; whereas the GlcNAc1-4 had an R2 value of 0.86. This data Inhibitors,research,lifescience,medical confirms that the second terminal HexNAc in the [M - H]- ions of m/z 790 in PGM is 4- linked GlcNAc. However, this data does not suggest the β-configuration due to loss of the anomeric configuration in the 0,2A1α – H2O fragment ion [26]. The terminal 4 linked GlcNAc was not affected by hexosaminidases digestion, which removes the β 2, 4 and 6 linked AV-951 GlcNAc and a 3HexNAc, indicating that this terminal GlcNAc is α1-4 linked. Thus, MS3 can be used as an alternative, when the lack of exoglycosidases does not allow the assignment of non-reducing monosaccharide moieties. The inability for digestion of this particular terminal HexNAc with currently available N-acetylhexosaminidases of known specificity in combination with MS3 suggested that the [M - H]- ions at m/z 790 in PGM contains the antibacterial terminal α1,4 linked GlcNAc epitope [24]. 2.3.

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