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tmt16plex isobaric label reagent set  (Thermo Fisher)


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    Thermo Fisher tmt16plex isobaric label reagent set
    Tmt16plex Isobaric Label Reagent Set, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tmt16plex+isobaric+label+reagent+set/tmt+reagent/pmc12046290-117-15-20
    Average 90 stars, based on 1 article reviews
    tmt16plex isobaric label reagent set - by Bioz Stars, 2026-09
    90/100 stars

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    Labeling:

    Article Title: ART26.12, an FABP5 Inhibitor, Shows Efficacy in Preclinical Psoriasis Models.
    Article Snippet: FABP5 is upregulated in psoriasis.. This study assessed the efficacy of the potent, selective, and orally active FABP5 inhibitor ART26.12 in preclinical psoriasis models.. In vitro, reconstructed human epidermis was stimulated with cytokines (IL-17 þ IL-22 þ TNF at 3 ng/ml each) and treated with ART26.12 (1, 3, or 10 mM) or Jak1 inhibitor (10 mM) for 24 hours; after which, 64 psoriasis-related genes were measured.

    Virus:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Recombinant:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Protease Inhibitor:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Protein Extraction:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    SYBR Green Assay:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Cloning:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Reverse Transcription:

    Article Title: Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies iMet-14-3-3 gamma Antibody (HS23) Novus Cat#NB100-407, RRID: AB_10003122 Anti-GST Novus Cat#NB600-326, RRID: AB_10001229 Anti-Rabbit IgG - HRP conjugated Sigma-Aldrich Cat#A0545, RRID: AB_257896 Anti-Mouse IgG - HRP conjugated Sigma-Aldrich Cat#A9044, RRID: AB_258431 Bacterial and virus strains Escherichia coli BL21(DE3) NEB Cat#C2527H Chemicals, peptides, and recombinant proteins Roche cOmpleteTM Mini EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich Cat#4693159001 MicroSpin Columns, C18 Silica The Nest Group Cat#SEM SS18V Chelex 100 sodium form Sigma-Aldrich Cat#C7901 Octapeptide MSSHRWDW (95% purity) Sigma-Aldrich N/A L-methionine p-nitroanilide (L-Met pNA) Sigma-Aldrich Cat#M3529 Ninhydrin Sigma-Aldrich Cat#151173 HisPurTM Ni-NTA Resin ThermoFisher Cat#88222 Biolock IBA Lifesciences Cat#2-0205-050 Strep-Tactin Sepharose resin IBA Lifesciences Cat#2-1201-025 Malachite Green Sigma-Aldrich Cat#229105 ZTP Biorbyt Cat#orb63207 GTP Sigma-Aldrich Cat#G8877 GMP-PNP Sigma-Aldrich Cat#G0635 4-20% Mini PROTEAN TGX Bio-Rad Cat#4561094 SuperSignalTM West Pico PLUS Chemiluminescent Substrate ThermoFisher Cat#34579 B-PER Bacterial Protein Extraction Reagent ThermoFisher Cat#78248 Y-PER Yeast Protein Extraction Reagent ThermoFisher Cat#78991 30-kDa cutoff Amicon centrifugal filter units Millipore Sigma Cat#UFC903024 (15ML) Cat#UFC503024 (0.5ML) Trypsin, TPCK treated Sigma-Aldrich Cat#T1426 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 iTaq Universal SYBR Green Supermix BioRad Cat#1725124 Critical commercial assays Gibson Assembly Cloning Kit NEB Cat#E2611L TMT16plex Isobaric Label Reagent Set ThermoFisher CatA44520 Micro-Organism Lysing Mix glass bead tubes Omni international Cat#SKU 19-621 RNeasy Mini Kit Qiagen Cat#74104 Quick-RNA MiniPrep kit Zymo Research Cat#R1054 RevertAid Reverse Transcriptase kit ThermoFisher Cat#K1691 Deposited data Proteomics: Raw spectrum runs, supporting worked up raw files and metadata this study MassIVE: MSV000088135 Experimental models: Organisms/strains S. cerevisiae: BY4742 (referred to as ‘‘WT’’): MATa his3D1 leu2D0 lys2D0 ura3D0 Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘zng1D’’): BY4742 ynr029cD::KanMX Horizon Discovery Cat#YSC1054 (Continued on next page) Cell Reports 39, 110834, May 17, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER S. cerevisiae: (referred to as ‘‘map2D’’) BY4742 map2D::KanMX Horizon Discovery Cat#YSC1054 S. cerevisiae: (referred to as ‘‘map2D zng1D’’) BY4742 map2D::KanMX ynr029cD::URA3 this study N/A Oligonucleotides See Table S2 this study N/A Recombinant DNA 14-3-3g-GST fusion this study N/A TurboID-Myc fusion this study N/A Plasmid: pET11e (E. coli expression vector) Joint Genome Institute N/A Plasmid: pCH600 (pET11e-ZNG1) this study N/A Plasmid: pCH601 (pET11e-MAP1) this study N/A Plasmid: p413-GPD (S. cerevisiae expression vector) Mumberg et al., 1995 N/A Plasmid: pCH602 (p413-GPD-ZNG1) this study N/A Plasmid: pCH603 (p413-GPD-MAP2) this study N/A Plasmid: pCH604 (p413-GPD-14-3-3g-GST) this study N/A Plasmid: pGBKT7 Takara Cat#630443 Plasmid: pGADT7-AD Takara Cat#630442 Plasmid: pGBKT7-AtAN Xie et al., 2020 N/A Plasmid: pGADT7-AD-AtAN Xie et al., 2020 N/A Plasmid: pNG003 (pGBKT7-ZNG1) this study N/A Plasmid: pNG004 (pGADT7-AD-MAP1) this study N/A Plasmid: pNG005 (pGADT7-AD-MAP2) this study N/A Plasmid: pNG006 (pET11e-ZNG1-5xMycTEV-StrepTagII) this study N/A Plasmid: pNG007 (pET11e-MAP1-TEV-StrepTagII) this study N/A Plasmid: pNG008 (pET11e-trMAP1-TEV-StrepTagII) this study N/A Plasmid: pNG009 (pGBKT7-trZNG1) this study N/A Plasmid: pNG010 (pGBKT7-ZNG1-C139S) this study N/A Plasmid: pNG011 (pGBKT7-ZNG1-C136SC138S-C139S) this study N/A Plasmid: pNG012 (pGADT7-AD-trMAP1) this study N/A Plasmid: pNG013 (pGADT7-AD-MAP1-C201S) this study N/A Plasmid: pNG014 (pGADT7-AD-MAP1-C292S) this study N/A Plasmid: pNG015 (pGADT7-AD-MAP1-C302S) this study N/A Software and algorithms Cobalt Papadopoulos and Agarwala, 2007 https://www.ncbi.nlm.nih.gov/ tools/cobalt/re_cobalt.cgi FastTree 2.1 Price et al., 2010 N/A Cipres Miller et al., 2010 https://www.phylo.org/ iTOL Letunic and Bork, 2019 https://itol.embl.de/ Cytoscape V3.5.0 Shannon et al., 2003 https://cytoscape.org/download.html EFI-EST tool Gerlt et al., 2015 http://efi.igb.illinois.edu/efi-est/ BioGRID V3.5.186 Stark et al., 2006 https://thebiogrid.org/ EdgeR Robinson et al., 2010 https://bioconductor.org/packages/ release/bioc/html/edgeR.html clusterProfiler Yu et al., 2012 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Jalview Waterhouse et al., 2009 https://www.jalview.org/ (Continued on next page) e2 Cell Reports 39, 110834, May 17, 2022

    Produced:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Synthesized:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Western Blot:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Membrane:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Sequencing:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Modification:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Mass Spectrometry:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Transfection:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    Cell Viability Assay:

    Article Title: Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich Cat#: F1804-1MG; RRID:AB_262044 His-Tag (27E8) Mouse mAb Cell Signaling Cat#: 2366; RRID:AB_2115719 Anti-NanoLuc Monoclonal Antibody Promega Cat#: N7000; RRID: AB_3095534 IRDye 800CW Goat anti-Mouse IgG Secondary Antibody VWR Cat#: 926-32210; RRID:AB_621842 LC3B (D11) XP Rabbit mAb Cell Signaling Cat#: 3868; RRID: AB_2137707 Vinculin (E1E9V) XP Cell Signaling Cat#: 13901; RRID: AB_2728768 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#: C2987H Chemicals, peptides, and recombinant proteins Tetramethylrhodamine (TAMRA)-PEG3-azide Synthesized in-house N/A Biotin-PEG4-azide BroadPharm Cat#: BP-22119 Pierce ECL Western Blotting Substrate Thermo Scientific Cat#: 32106 Novex 4-20% Tris-Glycine Mini Gels Invitrogen Cat#: XP04205BOX Nitrocellulose western blotting membrane, 0.45 mM GE Healthcare Amersham Cat#: 10600002 DMSO Corning Cat#: 25-950-CQC Urea Fisher Scientific Cat#: M1084871000 Iodoacetamide Sigma-Aldrich Cat#: I1149-25G Tris(benzyltriazolylmethyl)amine (TBTA) TCI Cat#: T2993 Copper(II) sulfate, anhydrous Sigma-Aldrich Cat#: 451657-10G Tris(2-carboxyethyl)phosphine HCl (TCEP) Sigma-Aldrich Cat#: 75259 Sequencing grade modified trypsin Promega Cat#: V5111 Streptavidin agarose resin Fisher Scientific Cat#: 20349 Micro bio-spin column Bio-rad Cat#: 7326204 Triethylammonium bicarbonate (TEAB) buffer Sigma-Aldrich Cat#: T7408-500ML TMT10plex Isobaric Label Reagent Set Thermo Scientific Cat#: 90406 TMT16plex Isobaric Label Reagent Set Thermo Scientific Cat#: 467804-10ML Formic acid, 98%, for mass spectrometry Honeywell Fluka Cat#: 94318-250ML-F Lipofectamine 3000 Transfection Reagent Thermo Scientific Cat#: L3000001 Polybrene Sigma Aldrich Cat#: TR-1003-G puromycin InvivoGen Cat#: ant-pr-1 PI-103 Sigma Aldrich Cat#: 528101 Critical commercial assays CellTiter-Glo Luminescent Cell Viability Assay Promega Cat#: G7573 NanoBRET Nano-Glo Substrate Promega Cat#: N1571 (Continued on next page) Cell Chemical Biology 32, 1–18.e1–e32, March 20, 2025 e1 ..

    other:

    Article Title: Transcriptome and Proteome Analysis Identify Decorin as a Principal Antifibrotic Component Trapping TGF- β 1 Within Adipose-Derived Stem Cell Secretome
    Article Snippet: TMT16plex Isobaric Label Reagent Set was purchased from Thermofisher Scientific.



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