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Protein glycosylation is an important post-translational modification of proteins that has profound effects on structure and function. However, the complex and nontemplated nature of glycans has been a barrier to studying many of their basic features, especially on a proteome-wide scale. We introduce a glycoproteomic method, glycoprotein identification and glycan mapping (GIDmap), that tailors the isolation of specific glycoprotein subpopulations based on display of metabolically inserted alkynyl sugar probes that can be selectively manipulated using the bioorthogonal Cu(I)-catalyzed [3 + 2] azide-alkyne cycloaddition. This saccharide-selective glycoprotein immobilization allows for subsequent manipulation and analysis of peptides and glycopeptides by liquid chromatography-tandem mass spectrometry. The power of GIDmap was demonstrated by mapping over 200 N-linked glycosylation sites from glycoproteins isolated from prostate cancer cells treated with an alkynyl sugar derivative of N-acetylmannosamine.