Flowchart for analysis of crude membrane proteome and N-glycoproteome in BV-2 microglia cell line. (A) Experiments were performed using 2 schemes. Crude membrane fractions, obtained from CM methods 1 and 2, KITs 1 and 2, and 4% SDS, were digested by MED-FASP or single-FASP. Peptides were analyzed by reverse-phase LC-MS/MS and high-resolution mass spectrometry (Orbitrap Velos and Q Exactive). To enrich N-glycopeptides, N-glyco-FASP was performed on whole-cell lysates or crude membrane fractions. (B) Area-proportional Venn diagram for all identified proteins with FDR < 1%. Overlap between the 2 proteomes is shown (light blue: crude membrane proteome; orange: N-glycoproteome). (C) Area-proportional Venn diagram for proteins identified as GO term “membrane” and transmembrane domain-containing proteins. For “GO:membrane,” the overlap between 2 proteomes is shown as a Venn diagram (light blue: crude membrane proteome; red: N-glycoproteome). For “transmembrane domain,” the overlap between the 2 proteomes is shown as a Venn diagram (light blue: crude membrane proteome; green: N-glycoproteome).