Plasma membrane profiling (PMP) of primary samples and cell lines leads to quantification of the cell surface proteome in myeloma at high coverage. (A) PMP overview. Ten human myeloma cell lines (HMCL) were profiled in a 10-plex and 8 primary myeloma samples plus 2 repeat HMCL were profiled in a second 10-plex. Sugar residues were oxidized with sodium periodate (NaIO4) to form aldehydes, which were then treated with aminooxy-biotin resulting in biotinylation via stable oxime bonds. This was followed by streptavidin pull-down, tandem mass tag (TMT) labeling, and mass spectrometry (MS3). (B) Identified proteins were annotated as plasma membrane proteins, as endogenously biotinylated contaminants, or unrecognized as plasma membrane proteins. Proportions within the pie charts refer to protein abundance. (C) Comparison of protein quantification by flow cytometry and PMP. Relative protein abundance by TMT labeling and mass spectrometry in arbitrary units (AU; x-axis) is compared with protein abundance by median fluorescence intensity (MFI) as determined by flow cytometry with validated antibodies relative to isotype control (y-axis). Error bars are ±SD of biological replicates; n = 3. *P < .05; **P < .01; ***P < .001; ****P < .0001.
