KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Anti-ATP6V1E1 | Abcam | Cat# ab111733; RRID: AB_10861729 |
| Rabbit Anti-BCAT1 | Abcam | Cat# ab197941; RRID: AB_2858260 |
| Rabbit Anti-BCAT2 | Abcam | Cat# ab111733; RRID: AB_10677595 |
| Rabbit Recombinant Anti-ABAT/GABA-T | Abcam | Cat# ab216465; RRID: AB_2801302 |
| Rabbit Anti-BCKDHB | Abcam | Cat# ab201225; RRID: AB_2858261 |
| Rabbit Anti-PURA | Abcam | Cat# ab79936; RRID: AB_2253242 |
| Rabbit Anti-VPS52 | Aviva Systems Biology | Cat# ARP57644_P050; RRID: AB_10714467 |
| Mouse Anti-β-Actin monoclonal | Cell Signaling Technology | Cat# 3700; RRID: AB_2242334 |
| Rabbit Anti-β-Actin monoclonal | Cell Signaling Technology | Cat# 4970; RRID: AB_222317 |
| IRDye 680RD Donkey anti-Mouse IgG | LI-COR Biosciences | Cat# 926-68072; RRID: AB_10953628 |
| IRDye 800CW Goat anti-Rabbit IgG | LI-COR Biosciences | Cat# 926-32211; RRID: AB_621843 |
| Mouse Anti-GAPDH | Millipore | Cat# CB1001; RRID: AB_2107426 |
| Rabbit Anti-FHOD1 | Novus Biologicals | Cat# NBP1-83900; RRID: AB_11043001 |
| Mouse Anti-MYL7 | Novus Biologicals | Cat# NBP2-03891; RRID: AB_2858262 |
| Rabbit Anti-UNC13C | Sigma-Aldrich | Cat# HPA041516; RRID: AB_10795124 |
| Rabbit Anti-GAPDH | Sigma-Aldrich | Cat# G9545; RRID: AB_796208 |
| Biological Samples | ||
| Table S1A | GTEx (Genotype-Tissue Expression) Consortium | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Acetonitrile, Optima LC/MS Grade, Fisher Chemical | Fisher Scientific | Cat# A955 |
| Water, Optima LC/MS Grade, Fisher Chemical | Fisher Scientific | Cat# W6500 |
| Lysyl Endopeptidase Mass Spectrometry Grade (Lys-C) | Fujifilm Wako Pure Chemical | Cat# 12505061 |
| 2-Chloroacetamide (CAA) | Sigma Aldrich | Cat# 22790 |
| Acetone | Sigma Aldrich | Cat# 179124 |
| Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) | Sigma Aldrich | Cat# C4706 |
| Trizma® base | Sigma Aldrich | Cat# 93350 |
| Guanidine-HCl | Thermo Fisher Scientific | Cat# 24110 |
| Pierce Trypsin Protease, MS Grade | Thermo Fisher Scientific | Cat# 90059 |
| TMT10plex Isobaric Label Reagent Set, 1 × 0.8 mg | Thermo Fisher Scientific | Cat# 90110 |
| Critical Commercial Assays | ||
| TBS W TWEEN (TBST) 20X SOL 1L | Alfa Aesar | Cat# J77500K2 |
| Nitrocellulose Membrane, Precut, 0.2 μm, 7 × 8.4 cm | Bio-Rad | Cat# 1620146 |
| Extra thick blot filter paper 30x15x15 cm sheets | Bio-Rad | Cat# 1703959 |
| Amersham ECL Plex Fluorescent Rainbow Markers | Cytiva | Cat# RPN851E |
| Lysing matrix D tubes | MP Biomedicals | Cat# 6913100 |
| Bovine Serum Albumin | Sigma Aldrich | Cat# A5611 |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23225 |
| MOPS SDS Running Buffer (20X) | Thermo Fisher Scientific | Cat# NP0001 |
| NuPAGE 4-12% Bis-Tris Protein Gels, 1.0 mm, 15 well |
Thermo Fisher Scientific | Cat# NP0323BOX |
| NuPAGE 4x LDS Buffer | Thermo Fisher Scientific | Cat# NP0008 |
| NuPAGE Transfer Buffer (20X) | Thermo Fisher Scientific | Cat# NP00061 |
| Oasis HLB 1 cc Vac Cartridge 10 mg Sorbent per Cartridge 30 μm 100/pk | Waters | Cat# 186000383 |
| Deposited Data | ||
| GENCODE v26 | GENCODE | https://www.gencodegenes.org/human/release_26.html |
| Proteome Data | This study | ProteomeXchange Consortium: PXD016999 |
| OMIM | Amberger et al., 2015 | https://omim.org/ |
| RNA-seq TPM data v8 | GTEx portal | https://www.gtexportal.org/home/ |
| TSomics | This study | http://snyderome.stanford.edu/TSomics.html |
| RNA isoform data v8 | GTEx portal | https://www.gtexportal.org/home/ |
| Software and Algorithms | ||
| Proteome Discoverer (Version 2.1) | Thermo Fisher Scientific | https://www.thermofisher.com/order/catalog/product/OPTON-30945?SID=srch-hj-OPTON-30945#/OPTON-30945?SID=srch-hj-OPTON-30945 |
| Xcalibur (Version 4.0.27.42) | Thermo Fisher Scientific | https://www.thermofisher.com/order/catalog/product/OPTON-30965#/OPTON-30965 |
| Orbitrap Fusion Tune (Version 2.1.1565.24) | Thermo Fisher Scientific | https://www.thermofisher.com/ |
| MassLynx (Version 4.1) | Waters | https://www.waters.com/waters/en_US/MassLynx-Mass-Spectrometry-Software-/nav.htm?cid=513164&locale=en_US |
| BlibSearch | BiblioSpec 2.0 | https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=default |
| Gephi (Version 0.9.2) | Gephi | https://gephi.org/ |
| AdaReg | Wang et al., 2019c | https://github.com/mwgrassgreen/AdaReg |
| AdaTiSS | Wang et al., 2019d | N/A |
| ggplot2 R package v | Wickham H, 2016 | https://ggplot2.tidyverse.org |
| R(v3.6.1) | R core team | https://www.r-project.org/ |
| RobNorm | Wang et al., 2019b | https://github.com/mwgrassgreen/RobNorm |
| Rtsne R package (v0.15) | van der Hinton Geoffrey, 2008 | https://cran.r-project.org/web/packages/Rtsne/Rtsne.pdf |
| STRINGdb R package (v10) | Franceschini et al., 2013 | https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html |