Glycosylation is one of the most important post-translational modifications (PTMs) as it is responsible for the homeostasis of cellular immunity and adhesion, and protein translation and degradation. There are two main types of glycosylation; N-linked glycans which are complex sugars attached to asparagine residues and O-linked glycans which are complex sugars attached to serine or threonine residues. Of these two types, it is estimated that 60% of proteins are glycosylated with 90% of glycoproteins being N-glycosylated. One of the most common analytical techniques to analyse N-glycans is liquid chromatography coupled to mass spectrometry (LC-MS), which results in the separation of N-glycans followed by MS acquisition and quantitative analysis. Hydrophilic interaction chromatography (HILIC) is a well-established separation technique whereby polar compounds are separated based on hydrogen bonding, ionic interactions and dipole-dipole interactions. Although HILIC is advantageous for separating N-glycans, an alternative separation technique, such as porous graphitised carbon (PGC), possesses improved resolving capability that cannot be achieved by HILIC. For multiple groups, PGC capillary columns have become the gold standard due to this resolving capability. However, there currently are limited commercial options for such columns. Therefore, our group have successfully developed an in-house packed PGC nano column using Hypercarb material (3um) and a 15cm glass capillary (75µm ID, 360µm OD). To assess these columns, we firstly released N-glycans from an in-house glycoprotein standard and formalin-fixed paraffin-embedded (FFPE) egg white as a quality control. These N-glycans were then separated on an Agilent 1290 Infinity II UHPLC with an Agilent Infinity UHPLC nanodaptor coupled to an Agilent 6550 iFunnel Q-TOF Mass Spectrometer. This optimsied workflow was then applied to N-glycans released from FFPE ovarian and endometrial cancer tissue to (1) further validate this novel PGC nano column and (2) investigate N-glycan alterations between these gynaecological cancers which may lead to the discovery of diagnostic markers or therapeutic targets. It is envisioned that this novel PGC nano column could be packed in-house by other groups, thereby overcoming the caveat of commercial options while maintaining sensitivity and reproducibility.