Reagent/Resource	Reference or Source	Identifier or Catalog number
Experimental models
Human: HEK 293 cell line	ATCC	Cat# CRL‐1573
Human: HEK Flp‐In T‐REx 293 cell line	Thermo Fisher Scientific	Cat# R78007
Recombinant DNA
ATF2 reporter vector	Qiagen	Cat# CCA‐901L
Gateway™ pDONR221™	Thermo Fisher Scientific	12536017
MAC‐GFP	Liu et al (2018)	Addgene, plasmid no. 139636
MAC‐tag‐C destination vector	Liu et al (2018)	Addgene, plasmid no. 108077
pOG44 Flp‐Recombinase expression vector	Thermo Fisher Scientific	Cat# V600520
Human ALK gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100061564
Human AXL gateway entry clone	Varjosalo et al (2008)	N/A
Human AXL KD gateway entry clone	Varjosalo et al (2008)	N/A
Human CSF1R gateway entry clone	Varjosalo et al (2008)	N/A
Human DDR1 gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no 23910
Human DDR2 gateway entry clone	Varjosalo et al (2008)	N/A
Human DDR2 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EGFR gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA1 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA10 gateway entry clone	Orfeome collection 5.1	ORF ID 14424
Human EphA2 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA3 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA3 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA4 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA5 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA5 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA6 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100058877
Human EphA7 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA7 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EphA8 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100014738
Human EphB2 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphB2 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EphB4 gateway entry clone	Varjosalo et al (2008)	N/A
Human EphB4 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human EphB6 gateway entry clone	Orfeome collection 5.1	ORF ID 52951
Human ErbB2 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100058794
Human ErbB3 gateway entry clone	Varjosalo et al (2008)	N/A
Human FGFR1 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100009459
Human FGFR2 gateway entry clone	Varjosalo et al (2008)	N/A
Human FGFR2 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human FGFR3 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100066410
Human FGFR4 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100010808
Human FLT1 gateway entry clone	Varjosalo et al (2008)	N/A
Human FLT3 gateway entry clone	Varjosalo et al (2008)	N/A
Human FLT4 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100068206
Human IGF1R gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100009391
Human INSR gateway entry clone	Varjosalo et al (2008)	N/A
Human INSRR gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100062381
Human KDR gateway entry clone	Orfeome collection 5.1	ORF ID 56932
Human LMR1 gateway entry clone	Varjosalo et al (2008)	N/A
Human LMR2 gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23914
Human LMR3 gateway entry clone	GeneScript	Synthesized plasmid
Human LTK gateway entry clone	GeneScript	Synthesized plasmid
Human MER gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23900
Human MER KD gateway entry clone	Varjosalo et al (2008)	N/A
Human MET gateway entry clone	Varjosalo et al (2008)	N/A
Human MUSK gateway entry clone	Orfeome collection 5.1	ORF ID 53052
Human NTRK1 gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23891
Human NTRK2 gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23883
Human NTRK3 gateway entry clone	Varjosalo et al (2008)	N/A
Human NTRK3 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human PDGFRA gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23892
Human PDGFRB gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100011461
Human RET gateway entry clone	Johannessen et al (2010)	Addgene, plasmid no. 23906
Human RON gateway entry clone	Varjosalo et al (2008)	N/A
Human ROR1 gateway entry clone	Varjosalo et al (2008)	N/A
Human ROR1 KD gateway entry clone	Varjosalo et al (2008)	N/A
Human ROR2 gateway entry clone	Varjosalo et al (2008)	N/A
Human ROS1 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100066413
Human RYK gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100015603
Human STYK1 gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100001903
Human TEK gateway entry clone	University of Helsinki genome biology unit	Orfeome collection 100011460
Human TYRO3 gateway entry clone	Varjosalo et al (2008)	N/A
Antibodies
Alexa Fluor488‐conjugated secondary antibody	Thermo Fisher Scientific	Cat# A‐11001
Goat anti‐mouse IgG H&L (HRP)	Abcam	97023
Anti‐V5 antibody	Invitrogen	37‐7500
Mouse monoclonal anti‐HA tag	Thermo Fisher Scientific	Cat# 26183
Chemicals, enzymes and other reagents
Amersham™ ECL™ Prime	Cytiva	RPN2232
Ammonium bicarbonate (AMBIC)	Sigma‐Aldrich	1066‐33‐7
Benzonase® Nuclease	Santa Cruz Biotechnology	sc‐202391
Bio‐Spin® Chromatography Columns	Bio‐Rad	732‐6008
Biotin	Thermo Fisher Scientific	29129
Bradford reagent	Bio‐Rad	500‐0006
DAPI	Sigma‐Aldrich	Cat# D9542
DMEM	Life Technologies	41965062
ECL Western Blotting Detection Reagent	GE Healthcare	RPN2209
Fetal bovine serum (FBS)	Gibco	10270‐106
Formic Acid, ≥ 95%	Sigma	64‐18‐6
FSBA	Sigma‐Aldrich	Cat# F9128
FuGENE 6 transfection reagent	Promega	Cat# E2691
Gateway™ LR Clonase™ Enzyme Mix	Life Technologies	11791043
HEPES	Sigma	7365‐45‐9
Hygromycin B	Thermo Fisher Scientific	Cat# 10687‐010
IGEPAL (electrophoresis reagent) CA630	Sigma	9002‐93‐1
Iodoacetamide (IAA)	Sigma‐Aldrich	64‐69‐7
Laemmli sample buffer	Bio‐Rad	1610737
Mouse monoclonal Anti‐HA−Agarose conjugated beads	Sigma‐Aldrich	Cat# A2095
Mowiol 4‐88	Sigma‐Aldrich	Cat# 81381
Penicillin–streptomycin	Life Technologies	15140130
Phenylmethanesulfonylfluoride (PMSF) > 98.5%	Sigma	329‐98‐6
Pierce™ BCA Protein assay	Thermo Fisher Scientific	23225
Protease Inhibitor cocktail	Sigma‐Aldrich	Cat# P8340
Pure nitrocellulose membrane 0.45 µm	Perkin‐Elmer	NBA085C001EA
Restore Plus Stripping buffer	Thermo Fisher	46430
SDS‐PAGE gel	Bio‐Rad	4561096
Sequencing grade trypsin	Promega	Cat# V5113
Skimmed milk powder	Valio	D1‐5824
Sodium chloride	Merck	7647‐14‐5
Sodium dodecyl sulfate	Sigma	151‐21‐3
Sodium fluoride	Sigma	7681‐49‐4
Strep‐Tactin® Sepharose® 50% (vol/vol) suspension	IBA life sciences	2‐1201‐010
Tetracycline hydrochloride	Sigma‐Aldrich	Cat# T‐3383
Tris(2‐carboxyethyl)phosphine (TCEP)	Sigma‐Aldrich	51805‐45‐9
Triton X‐100	Sigma	X100‐500
Trypsin‐EDTA	Gibco	25200‐56
TWEEN®20	Sigma‐Aldrich	P1379‐250ML
Water MS‐grade	Merck	7732‐18‐5
γ[18O4]‐ATP	Cambridge Isotope Laboratory	Cat# OLM‐7858‐PK
Recombinant human ALK	Thermo Fisher Scientific	Cat# PV3867
Recombinant human AXL	Thermo Fisher Scientific	Cat# PV3971
Recombinant human CSF1R	Thermo Fisher Scientific	Cat# PV3249
Recombinant human DDR1	Thermo Fisher Scientific	Cat# PV6047
Recombinant human DDR2	Thermo Fisher Scientific	Cat# PV4188
Recombinant human EGFR	Thermo Fisher Scientific	Cat# PV3872
Recombinant human EPHA1	Thermo Fisher Scientific	Cat# PV3841
Recombinant human EPHA2	Thermo Fisher Scientific	Cat# PV3688
Recombinant human EPHA3	Thermo Fisher Scientific	Cat# PV3359
Recombinant human EPHA4	Thermo Fisher Scientific	Cat# PV3651
Recombinant human EPHA6	Thermo Fisher Scientific	Cat# PV6339
Recombinant human EPHA7	Thermo Fisher Scientific	Cat# PV3689
Recombinant human EPHA8	Thermo Fisher Scientific	Cat# PV3844
Recombinant human EPHB1	Thermo Fisher Scientific	Cat# PV3786
Recombinant human EPHB2	Thermo Fisher Scientific	Cat# PV3625
Recombinant human EPHB3	Thermo Fisher Scientific	Cat# PV3658
Recombinant human EPHB4	Thermo Fisher Scientific	Cat# PV3251
Recombinant human ERBB2	Thermo Fisher Scientific	Cat# PV3366
Recombinant human ERBB4	Thermo Fisher Scientific	Cat# PV3626
Recombinant human FGFR1	Thermo Fisher Scientific	Cat# PV3146
Recombinant human FGFR2	Thermo Fisher Scientific	Cat# PV3368
Recombinant human FGFR3	Thermo Fisher Scientific	Cat# PV3145
Recombinant human FGFR4	Thermo Fisher Scientific	Cat# P3054
Recombinant human FLT1	Thermo Fisher Scientific	Cat# PV3666
Recombinant human FLT3	Thermo Fisher Scientific	Cat# PV3182
Recombinant human FLT4	Thermo Fisher Scientific	Cat# PV4129
Recombinant human IGF1R	Thermo Fisher Scientific	Cat# PV3250
Recombinant human INSR	Thermo Fisher Scientific	Cat# PV3781
Recombinant human INSRR	Thermo Fisher Scientific	Cat# PV4111
Recombinant human KDR	Thermo Fisher Scientific	Cat# PV3660
Recombinant human KIT	Thermo Fisher Scientific	Cat# PV3589
Recombinant human LTK	Thermo Fisher Scientific	Cat# PV4651
Recombinant human MERTK	Thermo Fisher Scientific	Cat# PV3627
Recombinant human MET	Thermo Fisher Scientific	Cat# PV3143
Recombinant human MUSK	Thermo Fisher Scientific	Cat# PV3834
Recombinant human NTRK1	Thermo Fisher Scientific	Cat# PV3144
Recombinant human NTRK2	Thermo Fisher Scientific	Cat# PV3616
Recombinant human NTRK3	Thermo Fisher Scientific	Cat# PV3617
Recombinant human PDGFRA	Thermo Fisher Scientific	Cat# PV3811
Recombinant human PDGFRB	Thermo Fisher Scientific	Cat# P3082
Recombinant human RON	Thermo Fisher Scientific	Cat# PV4314
Recombinant human ROR2	Thermo Fisher Scientific	Cat# PV3861
Recombinant human ROS1	Thermo Fisher Scientific	Cat# PV3814
Recombinant human TIE2	Thermo Fisher Scientific	Cat# PV3628
Recombinant human TYRO3	Thermo Fisher Scientific	Cat# PV3828
Recombinant Human EGF	R&D systems	Cat# 236‐EG‐200
Recombinant Human FGF basic	R&D systems	Cat# 3718‐FB‐025
Recombinant Human GDNF	R&D systems	Cat# 212‐GD‐010/CF
Recombinant Human HGF	R&D systems	Cat# 294‐HG‐005/CF
Recombinant Human IGF‐I	R&D systems	Cat# 291‐G1‐200
Recombinant Human NT‐3	R&D systems	Cat# 267‐N3‐005/CF
Recombinant Human PDGF‐BB	R&D systems	Cat# 220‐BB‐010
Recombinant Human VEGF	R&D systems	Cat# 293‐VE‐010/CF
Software
CRAPome v1	Mellacheruvu et al (2013)	http://www.crapome.org/
Cytoscape version 3.7	Shannon et al (2003)	http://www.cytoscape.org/
ImageJ	MacBiophotonics	https://imagej.nih.gov/ij/
MaxQuant version 1.6.4.3	Cox and Mann (2008)	http://www.biochem.mpg.de/5111795/maxquant
Progenesis LC‐MS version 4.0	Nonlinear Dynamics	http://www.nonlinear.com/progenesis/qi/
Proteome Discoverer version 1.4	Thermo Fisher Scientific	https://www.Thermo Fisher.com/fi/en/home.html
SAINTexpress version 3.6	Choi et al (2011)	http://saint‐apms.sourceforge.net/Main.html
Xcalibur version 2.7.0	Thermo Fisher Scientific	https://www.Thermo Fisher.com/fi/en/home.html
Fragpipe version 17	Nesvizhskii Lab	https://fragpipe.nesvilab.org/
Other
Amersham ECL prime western blotting detection reagent kit	GE Healthcare	Cat# RPN2232
BCA protein assay kit	Thermo Fisher Scientific	Cat# 23225
Cignal 45‐Pathway Reporter Array	Qiagen	Cat# 336841
Dual‐Luciferase reporter assay system	Promega	Cat# E1960
Gateway LR Clonase Enzyme Mix	Life Technologies	Cat # 11791043
Bio‐Spin Chromatography Columns	Bio‐Rad	Cat# 732‐6008
C18 reversed‐phase spin columns	Nest Group	Cat# SEM SS18V
C18 macrospin columns	Nest Group	Cat# SMM SS18V
Q Exactive™ Hybrid Quadrupole‐Orbitrap™ Mass Spectrometer	Thermo Fisher Scientific
EASY‐nLC 1000	Thermo Fisher Scientific
Bio‐Dot® Microfiltration System	Bio‐Rad	1703938
Evosep One	Evosep	EV‐1000
Hybrid trapped ion mobility quadrupole TOF mass spectrometer	Bruker	TimsTOF Pro
Electrospray ionization sprayer	Thermo Fisher
Fluorescence microscope	Leica	Leica TCS SP8 STED