The HL241 mutant strain of the cellular slime mold Dictyostelium
discoideum is a potential model for human congenital disorder
of glycosylation type IL (ALG9-CDG) and has been previously predicted
to possess a lower degree of modification of its N-glycans with anionic
moieties than the parental wild-type. In this study, we first showed
that this strain has a premature stop codon in its alg9 mannosyltransferase gene compatible with the occurrence of truncated
N-glycans. These were subject to an optimized analytical workflow,
considering that the mass spectrometry of acidic glycans often presents
challenges due to neutral loss and suppression effects. Therefore,
the protein-bound N-glycans were first fractionated, after serial
enzymatic release, by solid phase extraction. Then primarily single
glycan species were isolated by mixed hydrophilic-interaction/anion-exchange
or reversed-phase HPLC and analyzed using chemical and enzymatic treatments
and MS/MS. We show that protein-linked N-glycans of the mutant are
of reduced size as compared to those of wild-type AX3, but still contain
core α1,3-fucose, intersecting N-acetylglucosamine,
bisecting N-acetylglucosamine, methylphosphate, phosphate,
and sulfate residues. We observe that a single N-glycan can carry
up to four of these six possible modifications. Due to the improved
analytical procedures, we reveal fuller details regarding the N-glycomic
potential of this fascinating model organism.