Methylimidazolium N-ethylamine (MIEA) is synthesized successfully with good yield in the high performances and green chemical process, using N-methylimidazole and tert-butyl N-(2-bromoethyl) carbamate as starting materials. Following the mechanism of reductive amination, this ionic liquid was a suitable ligand for reductive amination with the carbonyl group of the carbohydrates, and the activity of an ionic liquid is disclosed by mass spectrometric techniques. This work illustrates that methylimidazolium N-ethylamine as an ionic liquid labelling carbohydrate including GlcNAc and its derivatives, for example bovine lactoferrin (BL), and horseradish peroxidase (HRP) have been selected as examples of glycoproteins. The detection of profiling labels of oligosaccharides and glycoproteins is performed by using UPLC/ESI-QTOF and by MALDI-TOF mass spectrometry. Moreover, the ionic synthesis as a multifunctional oligosaccharide label for analysis carbohydrate was investigated, using as comparable with the others ligands such 2-AB labelled GlcNAc and its derivatives. Labelling glycoproteins by IL-MIEA has improving ESI ionization efficiency, even better than 2-AB derivatives. Relevantly, this ionic liquid is applicable as advancement and development in catalytic methods of modification of small molecules as potential drugs for anti-viruses and microbes’ infections.