Table 1. Putative β-secretase substrates identified by quantitative proteomics.
| Gene | Protein | Topology | Cell Line | PSMs | Unique PSMs | Ratio |
| APP | AMYLOID BETA A4 PROTEIN | Type I | HEK HeLa | 169 | 8 | 0.89 |
| APLP1 | AMYLOID-LIKE PROTEIN 1 | Type I | HEK HeLa | 10 | 4 | 0.89 |
| APLP2 | AMYLOID-LIKE PROTEIN 2 | Type I | HEK HeLa | 165 | 9 | 0.96 |
| IGF2R | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | Type I | HEK HeLa | 135 | 4 | 0.88 |
| IL6ST | INTERLEUKIN-6 RECEPTOR BETA CHAIN | Type I | HEK HeLa | 8 | 3 | 0.98 |
| MET | HEPATOCYTE GROWTH FACTOR RECEPTOR | Type I | HEK HeLa | 13 | 3 | 0.74 |
| CPD | CARBOXYPEPTIDASE D | Type I | HEK | 91 | 3 | 0.87 |
| EPHA2 | EPHRIN TYPE-A RECEPTOR 2 | Type I | HEK | 2 | 1 | 0.94 |
| EPHA4 | EPHRIN TYPE-A RECEPTOR 4 | Type I | HEK | 5 | 1 | 0.93 |
| EPHA7 | EPHRIN TYPE-A RECEPTOR 7 | Type I | HEK | 10 | 2 | 0.93 |
| EPHB4 | RECEPTOR PROTEIN TYROSINE KINASE VARIANT EPHB4V1 | Type I | HEK HeLa | 7 | 3 | 0.95 |
| NCAM1 | NEURONAL CELL ADHESION MOLECULE 1 | Type I | HEK | 11 | 4 | 0.88 |
| L1CAM | NEURAL CELL ADHESION MOLECULE L1 | Type I | HeLa | 7 | 2 | 0.78 |
| SEMA4B | SEMAPHORIN-4B | Type I | HEK HeLa | 7 | 2 | 0.79 |
| SEMA4C | SEMAPHORIN-4C | Type I | HEK | 8 | 2 | 0.92 |
| SEMA6A | SEMAPHORIN-6A | Type I | HEK | 1 | 1 | 0.70 |
| SEMA6D | SEMAPHORIN-6D | Type I | HEK | 1 | 1 | 0.92 |
| LRIG1 | LEUCINE-RICH REPEATS AND IMMUNOGLOBULIN-LIKE DOMAINS PROTEIN 1 | Type I | HEK | 2 | 2 | 0.85 |
| LRIG2 | LEUCINE-RICH REPEATS AND IMMUNOGLOBULIN-LIKE DOMAINS PROTEIN 2 | Type I | HEK | 1 | 1 | 0.92 |
| LRIG3 | LEUCINE-RICH REPEATS AND IMMUNOGLOBULIN-LIKE DOMAINS PROTEIN 3 | Type I | HEK | 2 | 2 | 0.89 |
| ROBO1 | ROUNDABOUT HOMOLOG 1 | Type I | HEK HeLa | 27 | 3 | 0.81 |
| ROBO2 | ROUNDABOUT HOMOLOG 2 | Type I | HEK | 1 | 1 | 1.00 |
| SDK1 | SIDEKICK-1 | Type I | HEK | 14 | 1 | 0.88 |
| SDK2 | SIDEKICK-2 | Type I | HeLa | 8 | 2 | 0.91 |
| PVR | POLIOVIRUS RECEPTOR | Type I | HEK HeLa | 11 | 3 | 0.73 |
| SORL1 | SORTILIN-RELATED RECEPTOR | Type I | HEK | 2 | 1 | 0.71 |
| SORT1 | SORTILIN | Type I | HEK | 8 | 1 | 0.84 |
| PCDH21 | PROTOCADHERIN 21 | Type I | HEK | 10 | 2 | 0.76 |
| PCDH7 | PROTOCADHERIN 7 | Type I | HEK | 14 | 2 | 0.89 |
| PCDHGA11 | PROTOCADHERIN GAMMA A11 | Type I | HEK | 2 | 1 | 0.90 |
| PCDHGA5 | PROTOCADHERIN GAMMA A5 | Type I | HEK | 1 | 1 | 0.99 |
| PCDHGA8 | PROTOCADHERIN GAMMA A8 | Type I | HEK | 1 | 1 | 0.95 |
| PCDHGC3 | PROTOCADHERIN GAMMA C3 | Type I | HEK | 1 | 1 | 0.83 |
| CD276 | CD276 ANTIGEN | Type I | HEK | 3 | 2 | 0.70 |
| LRP11 | LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 11 | Type I | HEK HeLa | 9 | 3 | 0.91 |
| LRP4 | LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 4 | Type I | HEK | 7 | 1 | 0.89 |
| PAM | PEPTIDYL-GLYCINE ALPHA-AMIDATING MONOOXYGENASE | Type I | HEK | 19 | 3 | 0.74 |
| PODXL | PODOCALYXIN-LIKE PROTEIN 1 | Type I | HEK | 2 | 2 | 0.95 |
| SDC4 | SYNDECAN-4 | Type I | HEK | 10 | 4 | 0.96 |
| BACE1 | BETA-SECRETASE 1 | Type I | HEK | 10 | 4 | 0.90 |
| HLA | HLA CLASS I HISTOCOMPATIBILITY ANTIGEN (Combined) | Type I | HEK HeLa | 15 | 12 | 0.92 |
| PLXDC2 | PLEXIN DOMAIN-CONTAINING PROTEIN 2 | Type I | HEK HeLa | 10 | 3 | 0.81 |
| BSG | BASIGIN | Type I | HEK HeLa | 3 | 3 | 0.81 |
| PTPRS | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S | Type I | HEK | 2 | 2 | 0.88 |
| ALCAM | CD166 ANTIGEN | Type I | HEK HeLa | 2 | 2 | 0.92 |
| LMAN2 | VESICULAR INTEGRAL-MEMBRANE PROTEIN VIP36 | Type I | HEK | 2 | 1 | 0.75 |
| CACHD1 | CACHE DOMAIN CONTAINING 1 | Type I | HEK | 45 | 1 | 0.84 |
| SEZ6L2 | SEIZURE 6-LIKE PROTEIN 2 | Type I | HEK | 19 | 1 | 0.92 |
| NEO1 | NEOGENIN | Type I | HEK | 10 | 1 | 0.75 |
| PRTG | PROTOGENIN | Type I | HEK | 9 | 1 | 0.97 |
| UNC5C | NETRIN RECEPTOR UNC5C | Type I | HEK | 8 | 1 | 0.92 |
| ITFG1 | T-CELL IMMUNOMODULATORY PROTEIN | Type I | HEK | 5 | 1 | 0.97 |
| CSPG4 | CHONDROITIN SULFATE PROTEOGLYCAN 4 | Type I | HEK | 4 | 1 | 0.68 |
| TMEM132A | TRANSMEMBRANE PROTEIN 132A | Type I | HEK | 3 | 1 | 0.72 |
| ADAM10 | DISINTEGRIN AND METALLOPROTEINASE DOMAIN-CONTAINING PROTEIN 10 | Type I | HEK | 2 | 1 | 0.68 |
| BAMBI | BMP AND ACTIVIN MEMBRANE-BOUND INHIBITOR HOMOLOG | Type I | HEK | 2 | 1 | 0.98 |
| SPINT2 | KUNITZ-TYPE PROTEASE INHIBITOR 2 | Type I | HEK | 2 | 1 | 0.96 |
| DSG2 | DESMOGLEIN 2 | Type I | HEK | 1 | 1 | 0.95 |
| CRIM1 | CYSTEINE-RICH MOTOR NEURON 1 PROTEIN | Type I | HEK | 1 | 1 | 0.90 |
| GLG1 | GOLGI APPARATUS PROTEIN 1 | Type I | HeLa | 1 | 1 | 0.89 |
| JAG1 | JAGGED-1 | Type I | HEK | 1 | 1 | 0.97 |
| LRRC33 | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 33 | Type I | HeLa | 1 | 1 | 1.00 |
| TGOLN2 | TRANS-GOLGI NETWORK INTEGRAL MEMBRANE PROTEIN 2 | Type I | HEK | 1 | 1 | 0.90 |
| TLR9 | TOLL-LIKE RECEPTOR 9 | Type I | HeLa | 1 | 1 | 0.66 |
| TNFRSF21 | TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 21 | Type I | HEK | 1 | 1 | 1.00 |
| CNTN1 | CONTACTIN-1 | GPI | HEK | 4 | 2 | 0.87 |
| EFNA5 | EPHRIN-A5 | GPI | HEK HeLa | 2 | 2 | 0.71 |
| GPC3 | GLYPICAN-3 | GPI | HEK | 2 | 2 | 0.75 |
| GOLIM4 | GOLGI PHOSPHOPROTEIN 4 | Type II | HEK | 5 | 2 | 0.92 |
Columns indicate the gene and protein names, membrane topology, the cell line in which the protein was identified, the number of peptide spectral matches (PSMs) for the indicated protein, unique PSMs (indicating how many unique peptides were identified), and the average ratio of BACE1 peptides to total peptides identified. Data are sorted according to protein families.