Jan 17, 2024
A proximity proteomics pipeline for subcellular proteome and protein interaction mapping
- Xiaofang Zhong1,
- Qiongyu Li1,
- Ruth Hüttenhain1
- 1Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
- Metabolomics Protocols & WorkflowsTech. support email: [email protected]
Protocol Citation: Xiaofang Zhong, Qiongyu Li, Ruth Hüttenhain 2024. A proximity proteomics pipeline for subcellular proteome and protein interaction mapping. protocols.io https://dx.doi.org/10.17504/protocols.io.yxmvm3jbbl3p/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 17, 2024
Last Modified: January 17, 2024
Protocol Integer ID: 93712
Keywords: proximity proteomics pipeline for subcellular proteome, scale sample processing for proximity proteomic, proximity proteomics pipeline, proximity proteomic, subcellular proteomes for endosome, applicable for pl proteomic, protein interaction mapping proximity labeling, subcellular proteome, proximal protein interactions in living cell, pl proteomic, proximal protein interaction, optimization of the quantitative mass spectrometry, enrichment of biotinylated protein, quantitative mass spectrometry, mass spectrometry, protein identification, reproducibility of protein identification, protein, biotinylated protein, protein interaction, late endosome, endosome, dynamics in protein, lysosome, based pl enzyme, pl enzyme, automated enrichment, biotinylation
Abstract
Proximity labeling (PL) coupled with mass spectrometry has emerged as a powerful technique to map proximal protein interactions in living cells. Large-scale sample processing for proximity proteomics necessitates a high-throughput workflow to reduce hands-on time and increase quantitative reproducibility. To address this issue, we developed a scalable and automated PL pipeline, including generation and characterization of monoclonal cell lines, automated enrichment of biotinylated proteins in a 96-well format, and optimization of the quantitative mass spectrometry (MS) acquisition method. Combined with data-independent acquisition (DIA) MS, our pipeline outperforms manual enrichment and data-dependent acquisition (DDA) MS regarding reproducibility of protein identification and quantification. We apply the pipeline to map subcellular proteomes for endosomes, late endosomes/lysosomes, the Golgi apparatus, and the plasma membrane. Moreover, using serotonin receptor (5HT2A) as a model, we investigated agonist-induced dynamics in protein-protein interactions. Importantly, the approach presented here is universally applicable for PL proteomics using all biotinylation-based PL enzymes, increasing both throughput and reproducibility of standard protocols.
Materials
Reagents and Tools
| Reagent/resource | Reference or source | Identifier or catalog number | |
| 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 |
Troubleshooting
Cell culture
Seeding 3-4 million cells in a 10-cm dish or 500K cells in a 6-well plate on Day One. The cells will be ~70% confluent after 48 hours.
Add doxycycline (final concentration of 1ug/mL) to induce cells for 24 hours on Day Two.
APEX proximity labeling
Perform APEX proximity labeling on Day Three.
Incubate cells with 500uM BP in complete medium pre-warmed to 37 oC for 30min.
Add 2mM H2O2-containing medium (DMEM+10% FBS) to the 10-cm dish or 6-well plate to have a final concentration of 1mM H2O2.
Allow the reaction to go for 45sec at room temperature.
Invert the dish/plate and pour out the medium.
Immediately wash the cells 3x with ice-cold quencher solution (PBS+ 5mM Trolox, 10 mM sodium azide, 10 mM sodium ascorbate) for 1min (8mL for 10cm dish or 1mL for 6-well plate). Aspirate or invert to remove.
Collect the cells in fresh quencher solution (8ml for 10cm plate or 1mL for 6-well plate) and pellet the cells by centrifugation at 3000g for 10min at 4 oC, remove supernatant and continue to cell lysis or freeze cell pellets in dry-ice for storage
Cell lysis
Lyse cells in 1ml RIPA buffer supplement with protease inhibitors, antioxidants, and DTT
Perform a freeze-thaw cycle on dry ice and thaw in a 37 °C water bath
Sonicate samples (5 seconds, 15% Duty Cycle x 2)
Transfer samples to 1.5ml Eppendorf tubes
Centrifuge samples at 13,000xg for 10min at 4 °C and save the supernatant.
Take a small amount (25 uL) of the lysate for WB analysis
Quantify protein concentration (supernatant) using 600nM Pierce Assay Kit with Detergent Compatibility Reagent (optional)
Automated enrichment protocol for biotinylated proteins in Kingfisher
For the automated biotinylation enrichment protocol, the Kingfisher Flex system (Thermo Fisher) is programmed to simultaneously process a maximum of 96 samples. This protocol below includes two parts, where part 1 (Plate 1-3) is for washing magnetic streptavidin beads and binding of the biotinylated proteins to beads, and part 2 (Plate 4-12) is for washing and collecting beads prior to Lys-C/trypsin digestion. The enrichment protocol is conducted in the cold room using deep-well plates.
1st day, protocol: Biotinylation APEX-MS part 1
Plate 1 (1 mL, stock)
a. RIPA buffer plate 1
b. Add 80 uL of streptavidin beads to each well of 1 mL of RIPA buffer
Plate 2 (1 mL, stock)
a. RIPA buffer plate 2
b. 1 mL of RIPA buffer
Plate 3 (1 mL, fresh lysis)
a. Sample binding plate
b. All samples from lysis are added to the plate
c. Beads are transferred to this plate after 2x RIPA wash and left in this plate for overnight binding
d. Tip comb is left in this plate at the end of the protocol
2nd day, protocol: Biotinylation APEX-MS part 2
Plate 4-6 (1 mL, stock)
a. RIPA buffer plates 4-6
b. Continued from Plate 3
c. Beads with bond samples are collected from Plate 3 and transferred to these plates for 3x RIPA wash
Plate 7 (1 mL, stock)
a. KCl solution wash plate (1M KCl)
b. Stock solution prepared and can be stored for a long time
Plate 8 (1 mL, stock)
a. Na2CO3 solution wash plate (0.1M Na2CO3)
b. Stock solution prepared and can be stored for a long time
Plate 9 (1 mL, fresh)
a. 2M urea in 50mM Tris-HCl [pH=8.0] wash plate
b. 1 M Tris-HCl is ready
c. Urea prepared freshly each time
Plate 10-11 (1 mL, fresh)
a. 50mM Tris-HCl [pH=8.0] wash plates 10-11
b. Prepared from 1M Tris-HCl solution
Plate 12 (200 uL, fresh)
a. Digestion plate with 2M urea in 50mM Tris-HCl [pH=8.0] buffer
b. Beads and tip comb are left in this plate
Protein digestion
Reduce proteins by adding 5mM TCEP (final concentration, add 2ul of a 500mM TCEP solution) and incubate by shaking at 1000rpm @37 degrees for 30min.
Protein alkylation by adding iodoacetamide to 5mM (final concentration, add 2ul of a 500mM iodoacetamide solution) and incubate by shaking at 1000rpm @RT for 30min.
Quench IAA with 5mM DTT (final concentration, add 2ul of a 500mM iodoacetamide solution).
Add 2ul of trypsin (~1ug), and 1 ul of Lys-C (2ug/ul) and incubate O/N at 37 degrees under shaking at 1000 rpm. The on-bead digestion is set to 37 oC for 6h and RT for 12h.
Following morning add additional 0.5 ug of trypsin and incubate an additional 2h at 37 °C .
Transfer supernatant to a new 96-well plate using magnetic rack, and acidify sample with 10% trifluoroacetic acid (TFA) to ~pH2 (~0.5% TFA final).
C18 desalting
The peptide samples are desalted using C18 96-well plate (BioPureSPE, HNS S18V-20mg, the Nest group)
Wash the plate three times with 100 µL 80% acetonitrile (ACN)/0.1% TFA by centrifugation at 800 rpm for 1 min
Equilibrate the plate three times with 100 µL 2% ACN/0.1% TFA by centrifugation at 1200 rpm for 2 min
Load samples by centrifugation at 1600 rpm for 2 min
Re-load samples by centrifugation at 1600 rpm for 2 min
Wash the plate 3 times with 100 µL 2% ACN/0.1% TFA by centrifugation at 1600 rpm for 2 min
Elute twice with 55 µL 50% ACN/0.25% formic acid (FA) by centrifugation at 1600 rpm for 2 min
Dry the samples by vacuum centrifugation (~2h).
Store the dried samples at -20 °C or resuspend them in 20 uL 0.1% formic acid for mass spec analysis.