Fig 1: Proteome-wide discovery of antibody binding targets and surfaceome nanoscale organization.a Schematic of decorating an antibody (Ab) with the singlet oxygen generator (SOG) thiorhodamine. b Flow cytometric analysis of human peripheral blood mononuclear cells (PBMC) stained for cell surface biotin and immunoglobulin before and after LUX-labeling with anti-CD20 antibody-SOG conjugate (anti-CD20-SOG) (>60,000 cells per condition). c Histogram plot showing light-dependent cell surface biotinylation of LUX-labeled B-lymphoma SUDHL6 cells (>50,000 cells per condition). d Scatter plot showing light-dependent enrichment of LUX-MS quantified proteins from anti-CD20-SOG treated B-lymphoma SUDHL6 cells. e Fraction of surface proteins of LUX-MS quantified proteins found to be 5-fold enriched or not enriched after illumination of anti-CD20-SOG-treated B-lymphoma SUDHL6 cells. f Left, Volcano plot showing relative abundance changes of LUX-MS quantified proteins from anti-CD20-SOG treated B-lymphoma SUDHL6 cells with and without illumination for 5 min, tested using a two-sided Student’s t test. Green and blue dots represent known and previously unknown CD20 associated proteins, respectively. Orange and red dots represent chains of the used antibody and the primary binding target CD20. Right, literature and LUX-MS-based cell surface interaction network of CD20. g Venn diagram showing overlap of CD20 proximal candidates identified on resting human B cells (Ramos) using horseradish peroxidase (HRP) conjugated antibodies or LUX-MS performed once in water (H2O) or heavy water (D2O) based buffer. h PCA analysis of CD38, CD54, CD166, and CD220 receptor microenvironments identified by antibody-guided LUX-MS on living B-lymphoma SUDHL6 cells. Source data are provided as a Source Data file and interactive volcano plots (Supplementary Data 1).