Trifluoroacetic acid-based Ion-pairing zwitterionic hydrophilic interaction liquid chromatography solid phase extraction (TFA-IP-ZIC-HILIC-SPE) is a key sample processing step in quantitative glycoproteomics that provides unbiased enrichment of common N-glycopeptides from complex peptide mixtures1. With the discovery of truncated and lowly-hydrophilic N-glycans in the mammalian glycoproteome spanning the paucimannosidic (Man1-3GlcNAc2Fuc0-1)2 and chitobiose core (GlcNAc1-2Fuc0-1)3,4 type structures, it becomes important to investigate if such N-glycopeptides and O-glycopeptides are efficiently enriched using TFA-IP-ZIC-HILIC-SPE. We here investigate this by performing quantitative LC-MS/MS profiling of various tryptic and non-tryptic peptide mixtures containing human N- and O-glycopeptides carrying paucimannosidic, chitobiose and O-GlcNAc moieties using ZIC-HILIC-SPE enrichment with formic acid (FA) and TFA as mobile phase additives. The paucimannosidic peptides including the lowly hydrophilic Man1GlcNAc2-peptides were quantitatively retained using TFA, but the even less hydrophilic chitobiose core peptides, in particular the GlcNAc1-peptides, were often under-represented. Interestingly, using the less hydrophobic ion-pairing reagent FA, both paucimannosidic and chitobiose core peptides were more often quantitatively retained. The O-GlcNAc peptide profiling recapitulated these trends by demonstrating dramatically better retention using FA-IP-ZIC-HILIC-SPE than under TFA condition. The comparatively better retention of lowly hydrophilic glycopeptides with FA-IP-ZIC-HILIC-SPE was rationalised using in silico calculations of the peptide hydropathy (ΔGoct-water) identified relative to published and putative glycopeptides in the human and mouse glycoproteomes, which suggest a significant peptide carrier influence on their retention propensity. In conclusion, we here show that paucimannosidic peptides, but not necessarily chitobiose core peptides, generally are well-retained when using the conventional TFA-IP-ZIC-HILIC-SPE enrichment whereas the less used FA-IP-ZIC-HILIC-SPE appears to be a universally better strategy for quantitative glycoproteomics of mixtures containing lowly-hydrophilic glycopeptides.