| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| mouse anti-puromycin antibody (clone 12D10) (IP) | Merck | Cat# MABE343, RRID:AB_2566826 |
| mouse anti-puromycin antibody (clone 3RH11) (1:5,000) | Cosmo Bio | Cat# CAC-PEN-MA001, RRID:AB_2620162 |
| rabbit anti-ubiquitin antibody (1:2,000) | Cell Signaling Technology | Cat# 3933, RRID:AB_2180538 |
| Chemicals, peptides, and recombinant proteins | ||
| puromycin dihydrochloride | FUJIFILM Wako | Cat# 160-23,151 |
| L-(13C6,15N4)-arginine (Arg”10”) | Cambridge Isotope Laboratories | Cat# CNLM-539-H |
| L-(13C6,15N2)-lysine (Lys”8”) | Cambridge Isotope Laboratories | Cat# CNLM-291-H |
| L-(15N4)-arginine (Arg”4”) | Cambridge Isotope Laboratories | Cat# LM-396 |
| L-(D4)-lysine (Lys”4”) | Cambridge Isotope Laboratories | Cat# DLM-2640 |
| MG-132 | Chemscene | Cat# CS-0471 |
| Bortezomib | FUJIFILM Wako | Cat# 021-18901 |
| Silmitasertib | MedChemExpress | Cat# HY-50855 |
| cycloheximide (CHX) | FUJIFILM Wako | Cat# 037-20991 |
| fetal bovine serum (FBS) | Thermo Fisher Scientific | Cat#10270106 |
| DMEM(High Glucose) with L-Glutamine, Phenol Red and Sodium Pyruvate | FUJIFILM Wako | Cat# 043-30085 |
| arginine- and lysine-free Neurobasal-A medium | Research Institute for the Functional Peptides | N/A |
| DMEM for SILAC | Thermo Fisher Scientific | Cat# 88364 |
| neuron dissociation solutions | FUJIFILM Wako | Cat#291-78001 |
| poly-L-lysine | Merck | Cat#A-005-C |
| MEM | Thermo Fisher Scientific | Cat#11095080 |
| D-glucose | Merck | Cat#108337 |
| sodium pyruvate | Nacalai Tesque | Cat#06977-34 |
| penicillin-streptomycin | Thermo Fisher Scientific | Cat#15140122 |
| Neurobasal-A medium | Thermo Fisher Scientific | Cat#10888022 |
| B-27 supplement | Thermo Fisher Scientific | Cat#17504044 |
| GlutaMAX | Thermo Fisher Scientific | Cat#35050061 |
| LPS Salmonella minnesota R595 - TLR4 ligand | InvioGen | Cat#15C10-MM |
| bis(sulfosuccinimidyl)suberate, disodium salt (BS3) | FUJIFILM Wako | Cat# B574 |
| Sodium deoxycholate (SDC) | FUJIFILM Wako | Cat#194-08311 |
| Sodium N-lauroylsarcosinate (SLS) | FUJIFILM Wako | Cat#192-10382 |
| Trifluoroacetic acid (TFA) | FUJIFILM Wako | Cat#204-02743 |
| Ammonium acetate | FUJIFILM Wako | Cat#015-02837 |
| Dimethyl sulfoxide (DMSO) | FUJIFILM Wako | Cat#041-29351 |
| Ponceau-S Staining Solution | Beacle | Cat#BCL-PSS-01 |
| 100 x protease inhibitor cocktail | Merck | Cat#P8340 |
| Lysyl endopeptidase (LysC) | FUJIFILM Wako | Cat#129-02541 |
| Trypsin | Promega | Cat#V5111 |
| SETAPAETATPAPVEKSPAKK-K(biotin), Ac-SETAPAETATPAPVEKSPAKK-K(biotin), Ac-SETAPAETATPAPVEKpSPAKK-K(biotin) | Synpeptide | N/A |
| Nuclease-Free Water (not DEPC-Treated) | Thermo Fisher Scientific | Cat# AM9937 |
| TurboDNase (2U/uL) | Thermo Fisher Scientific | Cat# AM2238 |
| SUPERaseIn | Thermo Fisher Scientific | Cat# AM2694 |
| cOmplete Mini, EDTA-free Protease Inhibitor Cocktail | Sigma-Aldrich | Cat# 11836170001 |
| QIAzol lysis reagent | QIAGEN | Cat# 79306 |
| Trizol LS reagent | Thermo Fisher Scientific | Cat# 10296028 |
| Critical commercial assays | ||
| SuperScript III First-Strand Synthesis SuperMix for qRT-PCR | Thermo Fisher Scientific | Cat# 11752050 |
| TaqMan Gene Expression Master Mix | Thermo Fisher Scientific | Cat# 4369016 |
| Empore SDB-XC membrane | GL Sciences | Cat#5010-30016 |
| Empore cation-SR membrane | GL Sciences | Cat#5010-30031 |
| Dynabeads Protein G Magnetic Beads | Thermo Fisher Scientific | Cat#10003D |
| Pierce™ High Capacity Streptavidin Agarose | Thermo Fisher Scientific | Cat#20357 |
| ReproSil-Pur C18-AQ materials 120 (3 μm) | Dr. Maisch GmbH, Ammerbuch | Cat#r13.aq. |
| ECL reagent | Cytiva | Cat#RPN2124 |
| Deposited data | ||
| Proteomic raw data | this paper | jPOST: PXD024078 |
| Proteomic raw data | this paper | jPOST: PXD031475 |
| Proteomic raw data | this paper | jPOST: PXD024080 |
| Proteomic raw data | this paper | jPOST: PXD024081 |
| Proteomic raw data | this paper | jPOST: PXD024104 |
| Proteomic raw data | this paper | jPOST: PXD026349 |
| Experimental models: Cell lines | ||
| Human: HeLa | ATCC | Cat# CCL-2, RRID: CVCL_0030 |
| Mouse: RAW264.7 | ATCC | Cat#TIB-71, RRID:CVCL_0493 |
| Oligonucleotides | ||
| RPS27 (Hs01378332_g1) TaqMan Assay | Thermo Fisher Scientific | Cat# 4331182 |
| RPL12 (Hs02385039_g1) TaqMan Assay | Thermo Fisher Scientific | Cat# 4331182 |
| RPL5 (Hs00851991_u1) TaqMan Assay | Thermo Fisher Scientific | Cat# 4331182 |
| RPS17 (Hs00734303_g1) TaqMan Assay | Thermo Fisher Scientific | Cat# 4331182 |
| GammaTub23C (Dm01841764_g1) TaqMan Assay | Thermo Fisher Scientific | Cat# 4331182 |
| Software and algorithms | ||
| MaxQuant (v1.6.17.0 or v.1.6.2.10) | Cox and Mann, 2008 | https://www.maxquant.org/ |
| Perseus (v.1.6.5.0) | Tyanova et al., 2016 | https://maxquant.net/perseus/ |
| Metascape | Zhou et al., 2019 | https://metascape.org/gp/index.html#/main/step1 |
| FAIMS MzXML Generator | Hebert et al., 2018 | https://github.com/coongroup/FAIMS-MzXML-Generator |
| R Studio (v 1.2.5001) | Rstudio team | https://www.rstudio.com/ |
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