REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti-Mouse IgG (H + L)-HRP	Biorad	Cat#1706516
Goat anti-Rabbit IgG (H + L)-HRP	Biorad	Cat#1706515
Mouse monoclonal anti-FLAG M2 antibody	Sigma	F1804
Rabbit polyclonal anti-Atg8 antibody	Papinski et al., 2014	N/A
Rabbit polyclonal anti-Ape1 antibody	Kraft et al., 2012	N/A
Bacterial and virus strains
Subcloning Efficiency DH5α Compentent Cells	Thermo Fisher	Cat#18265-017
Rosetta 2 Competent Cells	Novagen	Cat#71402
DH10Multibac Cells	Schreiber et al., 2011	N/A
BL21-CodonPlus (DE3)-RIL Competent Cells	Agilent Technologies	Cat#230245
Chemicals, peptides, and recombinant proteins
NaCl	Sigma	Cat#S9888
1,4-Dithiothreitol (DTT)	Melford	Cat#D11000
HEPES	Sigma	Cat#H3375
MES	Sigma	Cat#M8250
UREA	Invitrogen	Cat#AM9902
EDTA	Sigma	Cat#E5134
Ammonium bicarbonate	Sigma	Cat#A6141
Glucose	Sigma	Cat#7021
Glycerol	Sigma	Cat#G5516
Acetic acid	Sigma	Cat#695092
Chloroform	Alfa Aesar	Cat#11398187
Acetone	Sigma	Cat#179124
Acetonitrile	Thermo Fisher Scientific	Cat#51101
Iodoacetamide	Thermo Fisher Scientific	Cat#39271
Diethyl ether	Sigma	Cat#179272
Isopropanol	Sigma	Cat#I9516
G418 solution	Sigma	Cat#G8168
clonNAT	Jena Bioscience	AB-102XL
Zeocin	VWR	Cat#67140
Ampicillin	Sigma	Cat#A9393
Gentamicin sulfate	Sigma	Cat#G1914
Kanamycin sulfate	Thermo Fisher Scientific	Cat#11815032
Tetracycline	Alfa Aesar	Cat#J61714
Chloramphenicol	Sigma	Cat#C0378
Bluo-gal	Invitrogen	Cat#15519028
IPTG	Invitrogen	Cat#15529019
Penicillin-Streptomycin-Glutamine	GIBCO	Cat#10378016
G418 solution	Sigma	Cat#G8168
clonNAT	Jena Bioscience	AB-102XL
Zeocin	VWR	Cat#67140
DMSO	Sigma	Cat#D8418
Trichloroacetic acid	Sigma	Cat#T6399
Formic acid	Fisher Scientific	Cat#10596814
TCEP	Thermo Fisher Scientific	Cat#77720
DDM	Anatrace	Cat#D310HA
LDAO	Avanti	Cat#850545P
BODIPY TMR C5-Maleimide	Thermo	Cat#B30466
ATP	Sigma	Cat#A2383
[γ-32P]-ATP	Hartmann Analytics	SRP301
d-Desthiobiotin	Sigma	Cat#D1411
dNTPs	Thermo Fisher Scientific	Cat#R0193
L-Glutathione reduced	Sigma	Cat#G4251
p-Nitrophenyl Phosphate	NEB	P0757
L-a-Phosphatidylethanolamine	Avanti	Cat#840026
L-a-Phosphatidylinositol	Avanti	Cat#840042
L-a-Phosphatidylcholine	Avanti	Cat#840055
L-a-Phosphatidylserine	Avanti	Cat#840032
PageRuler Plus Prestained Protein ladder	Thermo Fisher Scientific	Cat#26620
cOmplete EDTA-free Protease Inhibitor Cocktail	Roche	5056489001
PhosSTOP phosphatase inhibitors	Roche	4906837001
Yeast nitrogen base without amino acids and ammonium sulfate	Millipore	Cat#Y1251
PMSF	Thermo Fisher Scientific	Cat#36978
Leupeptin	Thermo Fisher Scientific	Cat#78435
Pepstatin A	Thermo Fisher Scientific	Cat#78436
Benzamidine hydrochloride hydrate	Sigma	Cat#6506
c-Myc-peptide	Thermo Fisher Scientific	Cat#20170
3xFLAG peptide	Generon	Cat#A6001
GeneJuice	Sigma	Cat#70967
Lambda protein phosphatase	NEB	Cat#P0753
Apyrase	NEB	Cat#M0398
Pierce Universal nuclease	Thermo Fisher Scientific	Cat#88701
cAMP-dependent Protein Kinase (PKA) catalytic subunit	NEB	Cat#P6000
Polo-like kinase 1 (Plk1)	SignalChem	Cat#P41-10H
Trypsin	Thermo Fisher Scientific	Cat#90058
Ubiquitin	R&D Systems	Cat#U-100H-10M
Lysyl-endopeptidase (LysC)	Wako	Cat#125-05061
Phusion High-Fidelity DNA polymerase	NEB	Cat#M0530
USER enzyme	NEB	Cat#M5505
Restriction enzymes (various)	NEB	N/A
Critical commercial assays
High-Select Fe-NTA Phosphopeptide Enrichment Kit	Thermo Fisher Scientific	Cat# A32992
BCA Protein Assay Kit	Thermo Fisher Scientific	Cat#23225
Zero Blunt TOPO PCR Cloning kit	Invitrogen	Cat#450245
Plasmid Miniprep Kit	Thermo Fisher Scientific	Cat#K0503
Gel Extraction Kit	Thermo Fisher Scientific	Cat#K0691
Deposited data
The mass spectrometry data were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD029047.	Perez-Riverol et al., 2019	PXD029047
Experimental models: Cell lines
Sf9 insect cells	Invitrogen	Cat#10503433
High Five insect cells	Invitrogen	Cat#10747474
Experimental models: Organisms/strains
All Saccharomyces cerevisiae strains used in this study are listed in Table S2	N/A	N/A
Oligonucleotides
All DNA oligonucleotides were purchased from Sigma and are listed in Table S4	N/A	N/A
Recombinant DNA
All plasmids used in this study are listed in Table S3	N/A	N/A
Software and algorithms
Fiji	Schindelin et al., 2012	https://imagej.net/software/fiji/
Micromanager	Edelstein et al., 2014	https://micro-manager.org/
SeqMan Pro	DNASTAR	https://www.dnastar.com/
Chimera	UCSF	https://www.cgl.ucsf.edu/chimera/
NEBcutter V2	NEB	http://nc2.neb.com/NEBcutter2/
MaxQuant 1.6.12.0	Cox and Mann, 2008	https://www.maxquant.org/
Skyline-daily (64-bit) 20.2.1.404	MacLean et al., 2010	https://skyline.ms/
scikit-image 0.18.1	van der Walt et al., 2014	https://scikit-image.org
Other
96-well glass bottom microplates	Greiner Bio-One	Cat#655891
TimsTOF Pro	Bruker Daltonics	N/A
NanoElute	Bruker Daltonics	N/A
5600 TripleTOF	Sciex	N/A
NanoLC Ultra	Sciex/Eksigent	N/A
LTQ-Orbitrap XL	Thermo Fisher Scientific	N/A
EASY-nLC	Thermo Fisher Scientific/Proxeon	N/A
Nikon Eclipse Ti2 Inverted Microscope	Nikon Instruments Inc., (2017)	N/A
Nikon Plan Apo 100X/1.45 Oil	Nikon Instruments Inc., (2017)	N/A
Photometrics Prime 95B sCMOS camera	Teledyne Photometrics	https://www.photometrics.com/
ÄKTA Pure Protein Purification System	Cytiva	N/A
EnSight Multimode Plate reader	Perkin Elmer	HH34000000
Typhoon FLA 9500	GE Healthcare	N/A
Freezer Mill 6875D	Spex SamplePrep	WZ-04577-94
Fermenter New Brunswick BioFlow 510	Eppendorf	N/A
Fermenter New Brunswick BioFlow 610	Eppendorf	N/A
C18 Sep-Pak columns	Waters	WAT023590
Superose 6 Increase 10/300 GL	Cytiva	Cat#29091596
HiLoad 16/600 Superdex 75	Cytiva	Cat#28989333
HiLoad 16/600 Superdex 200	Cytiva	Cat#28989335
Resource Q anion exchange column	Cytiva	Cat#17117901
Resource S cation exchange column	Cytiva	Cat#17118001
GST trap	Cytiva	Cat#17528201
Strep-Tactin Superflow Plus Resin	QIAGEN	Cat#30060
Strep-Tactin Superflow Plus cartridge	QIAGEN	Cat#30004
Anti-FLAG M2 Affinity gel	Sigma	Cat#A2220
Anti-c-Myc Agarose	Thermo Fisher Scientific	Cat#20168
MOPS SDS Running Buffer	Thermo Fisher Scientific	Cat#NP0001
MES SDS Running Buffer	Thermo Fisher Scientific	Cat#NP0002
Quick Coomassie Stain	Neo Biotech	Cat#NB-45-00078
Sypro Ruby Protein Gel Stain	Thermo Fisher Scientific	Cat#12000
Clarity Western ECL Substrate	Biorad	Cat#1705060
PVDF transfer membrane	Millipore	Cat#IPFL85
Nitrocellulose membrane	Thermo Scientific	Cat#88018
SF900 II Medium	GIBCO	Cat#10902104 Cat#10902104