KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| APP (mAbP2–1) | Thermo Fisher Scientific | Cat# OMA1–031232; RRID:AB_ 325526 |
| Amyloid-Beta (B-4) | Santa Cruz Biotechnology | Cat# sc-28365; RRID:AB_626669 |
| IgG from Rabbit Serum | Sigma-Aldrich | Cat#: I5006, RRID:AB_1163659 |
| IgG from Mouse Serum | Sigma-Aldrich | Cat#: I5381 RRID:AB_1163670 |
| Amyloid-Beta (82E1) | Immuno-Biological Laboratories | Cat# 10323, RRID:AB_10707424 |
| AP180 (Snap91) | Synaptic Systems | Cat# 155 003, RRID:AB_887691 |
| α-Synuclein | Synaptic Systems | Cat# 128 102, RRID:AB_887858 |
| Bassoon | Synaptic Systems | Cat# 141 004, RRID:AB_2290619 |
| Calmodulin (Calm) | Thermo Fisher Scientific | Cat# MA5–32074, RRID:AB_2809368 |
| Pip5k1c | Novus | Cat# NBP1–82986, RRID:AB_11029240 |
| PSD-95 | Thermo Fisher Scientific | Cat# MA1–046, RRID:AB_2092361 |
| Snap25 | Synaptic Systems | Cat# 111 002, RRID:AB_887790 |
| Synaptobrevin 2 (Vamp2) | Synaptic Systems | Cat# 104 202, RRID:AB_887810 |
| Synaptotagmin 1/2 cytoplasmic tail | Synaptic Systems | Cat# 105 003AF, RRID:AB_2744565 |
| Syntaxin 1B | Synaptic Systems | Cat# 110 402, RRID:AB_887901 |
| Vamp1 | Abcam | Cat# ab41324, RRID:AB_1281203 |
| Vesicular Glutamate Transporter 1 (VGLUT1) | Millipore | Cat# AB5905, RRID:AB_2301751 |
| Vgat | Synaptic Systems | Cat# 131 004, RRID:AB_887873 |
| Anti-Rabbit IgG (H+L) Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-11034, RRID:AB_2576217 |
| Anti-Mouse IgG (H+L) Alexa Fluor 568 | Thermo Fisher Scientific | Cat# A-11031, RRID:AB_144696 |
| Anti-Guinea pig IgG (H+L) Alexa Fluor 647 | Abcam | Cat# ab150187 RRID:AB 2827756 |
| Amyloid beta precursor protein (Y188) | Abcam | Cat# ab32136, RRID: AB_2289606 |
| Gapdh | Santa Cruz Biotechnology | Cat# sc-47724, RRID: AB_627678 |
| Synaptophysin | Sigma-Aldrich | Cat# S5768, RRID: AB_477523 |
| Ubiquitin (P4D1) | Santa Cruz Biotechnology | Cat# sc-8017, RRID: AB_628423 |
| VCP | Abcam | Cat# ab11433, RRID: AB_298039 |
| IRDye 800CW Donkey anti Rabbit IgG | LI-COR Biosciences | Cat# 926–32213, RRID: AB_621848 |
| IRDye 680CW Donkey anti Mouse IgG | LI-COR Biosciences | Cat# 925–68072, RRID: AB_2814912 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Mouse Express (15N, 98%) mouse feed prepared with Spirulina (U-15N, 98%+) | Cambridge Isotopes Laboratories | MF-SPIRULINA-A |
| ProteaseMax | Promega | Cat# V2071 |
| Sequencing grade modified Trypsin | Promega | Cat# V5280 |
| Proteasome Inhibitor MG-132 | EMD Millipore | Cat# 474790 |
| Beta-Amyloid Peptide (1–42) (human) Sequence: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA | Abcam | Cat# ab120301 |
| Teplow’s Amyloid β-Protein (1–42) (scrambled II). Sequence: YHAGVDKEVVFDEGAGAEHGLAQKIVRGFGVSDVSMIHINLF | BACHEM | Cat# 4104168 |
| Critical Commercial Assays | ||
| 10% Tris-Glycine Gels | Thermo Fisher Scientific | Cat# XV00100PK20 |
| 16% Tris-Glycine Gelts | Thermo Fisher Scientific | Cat# XP00162BOX |
| SimplyBlue™ SafeStain Kit | Thermo Fisher Scientific | Cat# LC6065 |
| Odyssey Blocking Buffer | LI-COR | Cat# 92740003 |
| Pierce BCA Protein Assay Kit | ThermoFisher Scientific | Cat# 23225 |
| Pierce microBCA Assay Kit | Thermo Fisher Scientific | Cat# 23235 |
| RNeasy Lipid Tissue Mini Kit | Qiagen | Cat# 74804 |
| Tandem Ubiquitin Binding Entities (TUBEs) | LifeSensors | Cat# UM401M |
| Amyloid Beta 42 Human ELISA Kit | Thermo Fisher Scientific | Cat# KHB3441 |
| Amyloid Beta 42 Human ELISA Kit, Ultrasensitive | Thermo Fisher Scientific | Cat# KHB3544 |
| Oligomeric Amyloid-beta ELISA Kit | Biosensis | Cat# BEK-2215–1P |
| Software and Algorithms | ||
| Graphpad | Graphpad | Version 8 |
| PANTHER | PANTHER | Version 15.0 |
| OpenMIMS FIJI Plugin | NIH | Version 3.0 |
| pClamp | Axon Instruments | Version 10 |
| Mini Analysis | Synaptosoft | Version 6 |
| Integrated Proteomics Pipeline(IP2) | Integrated Proteomics Applications, Inc | Version 5.0.1 |
| ProLuCID/SEQUEST algorithm | Yate Laboratory, The Scripps Research Institute | Version 3.1 |
| Census | Yate Laboratory, The Scripps Research Institute | Version 6.0 |
| RawExtract | Yate Laboratory, The Scripps Research Institute | Version 1.9.9 |
| Other | ||
| Gelatin-Subbed Microscope Slides | SouthernBiotech | Cat# SLD01-CS |
| Fluoromount-G | SouthernBiotech | Cat# 0100–01 |
| Jupiter C18 resin capillary | Phenomenex | N/A |
| Fusion Orbitrap mass spectrometer | Thermo Finnigan | N/A |
| Precellys 24 | Bertin Technology | N/A |
| nanoViper™ Analytical Column | Thermo Scientific | Cat# 164570 |
| HyperSep™ SCX Cartridges | ThermoFisher Scientific | Cat# 60108–420 |
| HyperSep™C18 Cartridges | Thermo Fisher Scientific | Cat# 60108–302 |
| Pierce C18 Spin Columns | Thermo Fisher Scientific | Cat# 89873 |
| RP IMCSTIPS® | IMCS | Cat# 04T-H6R05-1-20-96 |
| Dynabeads M-270 Epoxy | Invitrogen | Cat# 14301 |
| Synergy HTX multi-mode microplate reader | Biotek | N/A |
| Raw Proteomic Datasets | Massive | MSV000085004 |