| Cell lines | | |
| HEK293T/17 cells | ATCC | CRL-11268 |
| Antibodies | | |
| Mouse anti-FLAG (M1) | Sigma | F-3040 |
| Mouse anti-Vimentin | Invitrogen | MA3-745 |
| Rabbit anti-E Cadherin | CST | 3195T |
| Mouse anti-RAB5A | Fisher | 89333555 |
| Mouse anti-RAB9 | Invitrogen | MA3-067 |
| Rabbit anti Golgin-97 | CST | 13192 |
| Chicken anti-GFP | VWR | RL600-901-215 |
| AF488-labeled goat anti-Chicken | Invitrogen | A11039 |
| AF555-labeled goat anti-Mouse | Invitrogen | A21422 |
| AF647-labeled goat anti-Rabbit | Invitrogen | A21244 |
| Rabbit HRP anti-GAPDH | Bio-legend | 607904 |
| HRP anti-Streptavidin | VWR | N100 |
| Recombinant DNA | | |
| NES-APEX2 | This study | N/A |
| 2xFYVE-APEX2 | This study | N/A |
| GalT-APEX2 | This study | N/A |
| LAMP1-APEX2 | This study | N/A |
| LAMTOR1-APEX2 | This study | N/A |
| Lyn11-APEX2 | This study | N/A |
| 5HT2A-APEX2 | This study | N/A |
| Gαq-RLuc8 | Addgene | 140982 |
| Gβ3 | Addgene | 140988 |
| GFP2-Gγ9 | Addgene | 140991 |
| 5HT2A | (Kim et al, 2020) | N/A |
| Chemical, enzymes and other reagents | | |
| Dulbecco’s Modification of Eagle’s Medium (DMEM) | Corning | 10-013-CV |
| Fetal bovine serum (FBS) | Gibco | A31605-01 |
| Dulbecco’s Phosphate-Buffered Saline (DPBS) | Corning | 21-031-CV |
| 0.05% Trypsin-EDTA | Gibco | 25300-054 |
| Penicillin streptomycin solution | Corning | 30-002-CI |
| PolyJet | SignaGen | SL100688 |
| 0.45 µm PVDF filter unit | Millipore | SE1M003M00 |
| Cellstripper | Corning | 25-056-CI |
| Attune performance tracking beads | Thermo Fisher | 4449754 |
| ECL western blotting substrate | Pierce | 32106 |
| Streptavidin magnetic beads | Pierce | 88817 |
| Biotin phenol (Biotin Tyramide) | Iris Biotech | LS-3500 |
| Hydrogen peroxide | Sigma | H1009-100ML |
| Sodium azide | Sigma | S2002 |
| Sodium ascorbate | Spectrum | S1349 |
| Trolox (6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid) | Sigma | 238813 |
| 16% Formaldehyde (w/v) | Pierce | 28908 |
| EverBrite mounting medium with DAPI | Biotium | 23002 |
| cOmplete protease inhibitor cocktail tablets mini, EDTA-free | Roche | 11846170001 |
| 660nm protein assay kit | Pierce | 22662 |
| TCEP | Pierce | 20490 |
| Dithiothreitol (DTT) | Sigma | D0632 |
| Iodoacetamide (IAA) | Sigma | I1149 |
| Sequencing-grade modified trypsin | Promega | V5111 |
| Lysyl endopeptidase | VWR | 100369-822 |
| BioPureSPE 96-well C18 plate | NEST | HNS S18V |
| Ascorbic Acid | Sigma | A5960 |
| BSA, Free Fatty Acid | Akron | AK8909 |
| Coelenterazine 400a | Nanolight | 340-1 |
| Dialyzed FBS | Omega Scientific | FB-03 |
| Hank’s Balanced Salt Solution | Gibco | 14065056 |
| Sodium chloride | Sigma | S7653-250G |
| Tris HCl pH 7.5 | Corning | 46-030-CM |
| Tris HCl pH 8.0 | Corning | 46-031-CM |
| Sodium deoxycholate | Sigma | D6750-500G |
| Triton-x100 | Sigma | T9284-100ML |
| Sodium dodecyl sulfate | Fisher BioReagents | BP166-500 |
| Urea | Promega | V3171 |
| Potassium chloride | Sigma | P9541-1KG |
| Sodium carbonate | Sigma | S2127-500G |
| Pierce 660 nm Protein Assay Reagent | Thermo Scientific | 22660 |
| Software | | |
| Spectronaut (version 16.0) | Biognosys | https://biognosys.com/shop/spectronaut |
| MSstats (version 4.4.0) | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/MSstats.html |
| Attune NxT software | Thermo Fisher Scientific | |
| FlowJo | FlowJo, LLC | https://www.flowjo.com/ |
| Fiji | imageJ | https://imagej.net/software/fiji/ |
| NIS-Elements software (v. 5.30.01 build 1541) | Nikon | |
| Prism (v8.0) | GraphPad Software | |
| Other | | |
| Orbitrap Exploris 480 MS with internal calibration option | Thermo Fisher Scientific | BRE725533 |
| EASY-nLC 1200 system | Thermo Fisher Scientific | |
| Nikon Ti2-E microscope | Nikon | |
| Attune NxT Flow Cytometer | Thermo Fisher Scientific | |
| KingFisher Flex system | Thermo Fisher Scientific | |