Fig. S4.

Ligand proximal photooxidation in vivo with NP41–DBF pyridylhydrazine–biotin (NP41–DBF–HB) conjugate shows enrichment of laminin, collagen, and associated proteins. (A) Structure of NP41–DBF–HB conjugate. (B) Relative quantification of spectral counts in PO sample versus NL control for each protein identified by MS. (Left) In vivo photooxidation of DBF–NP41–HB shows high enrichment of basement membrane proteins, including laminin subunits and nidogens. Collagen VI subunits showed high abundance and low enrichment, and laminin a5 showed high enrichment but low abundance. Two abundant, nerve-specific proteins, neurofilament and myelin protein P0, were not enriched. (Right) By comparison, in vivo photooxidation of a control conjugate with all D-amino acids showed low enrichment and low abundance of the same proteins. (C) Table of values of proteins identified in the graph, showing x and y values of each identified protein. (D) Relative spectral counts of a photooxidized NP41–DBF–HB conjugate compared with a photooxidized d-NP41 control conjugate, showing enrichment and total abundance of identified proteins. Laminin subunits and nidogen showed the highest target-specific enrichment with abundant spectral counts. Laminin-α5 showed high enrichment but low spectral counts, and collagen subunits showed high spectral counts but low enrichment. (E) Relative quantification of other proteins slightly enriched in the NP41–DBF–HB experiment not identified in NP41–MB as enriched and abundant. Proteins showing moderate enrichment (>0.69) upon photooxidaton of NP41–DBF–HB compared with NL control had low enrichment in comparison with the photooxidized D-amino acid control, except for testis-specific ser/thr kinase and lumican. In the MB–NP41 photooxidation experiment, the former was not identified and the latter was unenriched.