Updated project metadata. Mass spectrometry-based discovery glycoproteomics is highly dependent on the use of chromatography paradigms amenable to analyte retention separation. When compared against established stationary phases such as reversed phase and hydrophilic interaction liquid chromatography, reports utilizing porous graphitic carbon (PGC) have detailed its numerous advantages. Recent efforts have detailed the utility in porous graphitic carbon in high throughput glycoproteomics, principally through enhanced profiling depth and liquid phase resolution at higher column temperatures. However, increasing column temperature was shown to impart disparaging effects in glycopeptide identification. Herein we further elucidate this trend, describing qualitative and quantitative effects of increased column temperature on glycopeptide identification rates, signal intensity, resolution, and spectral count linear response. Through analysis of enriched bovine and human glycopeptides, species with high mannose and sialylated glycans were shown to most significantly benefit and suffer from high column temperatures, respectively. These results provide insight as to how porous graphitic carbon separations may be appropriately leveraged for glycopeptide identification while raising concerns over quantitative and pseudo-quantitative label free comparisons as temperature changes.