Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PDHE1a (S293) | Calbiochem | Cat#: AP1062; RRID: AB_10616069 |
| Total PDHE1a | Abcam | Cat#: ab110330; RRID: AB_10858459 |
| MKT (Acaa2) | Millipore Sigma | Cat#: WH0010449M1; RRID: AB_2219394 |
| BDH1 | ProteinTech | Cat#: 15417–1-AP; RRID: AB_2274683 |
| SCOT | ProteinTech | Cat#: 12175–1-AP; RRID: AB_2157444 |
| ATP5a | Abcam | Cat#: ab14748 RRID:AB_301447 |
| ACAT1 | BioRad | Cat#: VMA00962 |
| Chemicals, peptides, and recombinant proteins | ||
| Ethyl [U-13C]acetoacetate | Cambridge Isotope Laboratories | Cat#: CLM-3297 CAS#: 84508–55-4 |
| [U-13C]3OHB | Cambridge Isotope Laboratories | Cat#: CLM-3853 CAS#: 2483735–72-2 |
| [U-13C]palmitic acid | Cambridge Isotope Laboratories | Cat#: CLM-6059 CAS#: 2483736–17-8 |
| [U-13C]glucose | Cambridge Isotope Laboratories | Cat#: CLM-1396 CAS#: 110187–42-3 |
| Lithium acetoacetate | Millipore Sigma | Cat#: A8509 CAS#: 3843–11-2 |
| Sodium 3OHB | Millipore Sigma | Cat#: 54965 CAS#: 150–83-4 |
| Sodium palmitate | Millipore Sigma | Cat#: P9767 CAS#: 408–35-5 |
| Sodium oleate | Millipore Sigma | Cat#: O3880 CAS#: 143–19-1 |
| Bovine Serum Albumin (Fatty Acid Free) | Millipore Sigma | Cat# A9205 CAS# 9048–46-8 |
| Porcine Insulin | Millipore Sigma | Cat#: I5523 CAS#: 12584–58-6 |
| L-Carnitine HCl | Millipore Sigma | Cat# C0283 CAS# 6645–46-1 |
| Norvaline | Millipore Sigma | Cat# N7627 CAS# 6600–40-4 |
| [2H9]L-carnitine | Cambridge Isotope Laboratories | Cat# DLM-3555 CAS# 126827–79-0 |
| [2,2,3,3,4,4,5,5,5-2H9]pentanoic acid | Millipore Sigma | Cat# 493201 CAS# 115871–50-6 |
| Methylhydroxylamine (MOX) | Millipore Sigma | Cat# 226904 CAS# 593–56-6 |
| MTBSTFA (with 1% t-BDMCS) | Millipore Sigma | Cat# M-108 CAS# 77377–52-7 |
| Methanol | Millipore Sigma | Cat# 439193 CAS# 67–56-1 |
| Chloroform | Millipore Sigma | Cat# C2432 CAS# 67–66-3 |
| Acetonitrile | Fisher Scientific | Cat# A955 CAS# 75–05-8 |
| Ammonium formate | Millipore Sigma | Cat# 516961 CAS# 540–69-2 |
| Acetic acid | Millipore Sigma | Cat# 695092 CAS# 64–19-7 |
| Acidic methanol (3N in HCl) | Millipore Sigma | Cat# 90964 CAS# 7647–01-0 |
| 2–2(pyridyl)ethyl-functionalized silica gel | Millipore Sigma | Cat# 537985 CAS# N/A |
| Pentobarbital (Nembutal) | Oak Pharmaceuticals | N/A |
| Protease Inhibitor Cocktail | Millipore Sigma | Cat# P8340 |
| Phosphatase Inhibitor Cocktail 2 | Millipore Sigma | Cat# P5726 |
| Phosphatase Inhibitor Cocktail 3 | Millipore Sigma | Cat# P0044 |
| Pierce Reversible Protein Stain Kit for Nitrocellulose Membranes (Memcode) | ThermoFisher Scientific | Cat# 24580 |
| 4–15% Criterion TGX Stain-Free Protein Gel, 18well | BioRad | Cat# 5678084 |
| 10X Tris Glycine SDS Running Buffer | BioRad | Cat# 1610732 |
| 10X Tris Buffered Saline | BioRad | Cat# 1706435 |
| Fish Gelatin | Millipore Sigma | Cat# G7765 |
| Casein | Millipore Sigma | Cat# C0626 |
| Sodium Nitrate | Millipore Sigma | Cat# S8032 |
| Roche cOmplete ULTRA EDTA-free Protease Inhibitor Mini Tablet | Millipore Sigma | Cat# 05892791001 |
| Roche 1x PhosSTOP Phosphatase Inhibitor Cocktail Tablets | Millipore Sigma | Cat# 04906837001 |
| Lysyl Endopeptidase, Mass Spectrometry Grade | Wako Chemicals | Cat# 125–05061 |
| Sequencing Grade Modified Trypsin | Promega | Cat# V5113 |
| tC18 SEP-PAK Solid Phase Extraction Columns (50 mg) | Waters | Cat# WAT054960 |
| tC18 SEP-PAK Solid Phase Extraction Columns (100 mg) | Waters | Cat# WAT036820 |
| Triethylammonium bicarbonate (TEAB) | ThermoFisher | Cat# 90114 |
| TMT10plex™ Isobaric Label Reagent Set (0.8 mg per tag) | ThermoFisher | Cat# 90110 |
| MyTaq Red 2x Mix | Bioline | Cat# BIO-25044 |
| MOPS Free Acid | Millipore Sigma | Cat# M1254 CAS# 1132–61-2 |
| MES Potassium Salt | Millipore Sigma | Cat# M0895 CAS# 39946–25-3 |
| Bovine Serum Albumin (Fatty Acid Free) | Millipore Sigma | Cat# A3803 CAS# 9048–46-6 |
| EDTA | Millipore Sigma | Cat# E0270 CAS# 65501–24-8 |
| Trypsin from Porcine Pancreas (Mitochondrial Isolation) | Millipore Sigma | Cat# T4799 CAS# 9001–51-8 |
| Potassium Chloride | Millipore Sigma | Cat# P5405 CAS# 7447–40-7 |
| Magnesium Chloride Hexahydrate | Millipore Sigma | Cat# M2670 CAS# 7791–18-6 |
| EGTA | Millipore Sigma | Cat# E4378 CAS# 67–42-5 |
| Potassium Dihydrogen Phosphate | Millipore Sigma | Cat# P9791 CAS# 7778–77-0 |
| Creatine Monohydrate | Millipore Sigma | Cat# C3630 CAS# 6020–87-7 |
| Potassium Salt of Phosphocreatine | Millipore Sigma | |
| Palmitoyl-L-carnitine | Millipore Sigma | Cat# P1645 CAS# 18877–64-0 |
| Octanoyl-L-carnitine | Millipore Sigma | Cat# 50892 CAS# 25243–95-2 |
| Malic Acid (Malate) | Millipore Sigma | Cat# M1000 CAS# 97–67-6 |
| Potassium Pyruvate | Combi-Blocks | Cat# QA-1116 CAS# 4151–33-1 |
| Creatine Kinase from Rabbit Muscle | Roche | Cat# 10127566001 |
| Tetramethylrhodamine Methyl Ester (TMRM) | ThermoFisher | Cat# T668 |
| Rotenone | Millipore Sigma | Cat# R8875 CAS# 83–79-4 |
| Potassium Cyanide | Millipore Sigma | Cat# 60178 CAS# 151–50-8 |
| Alamethicin | AG Scientific | A-1286 CAS#27061–78-5 |
| CDNB | Millipore Sigma | Cat# 237329 CAS# 97–00-7 |
| Critical commercial assays | ||
| Pierce Quantitative Colorimetric Peptide Assay | ThermoFisher | Cat# 23275 |
| Pierce BCA Protein Assay | ThermoFisher | Cat# 23225 |
| ALPCO STELLUX Chemi Rodent ELISA Kit | ALPCO | Cat# 80-INSMR-CH01 |
| FUJIFILM Wako HR Series NEFA-HR Reagent Assay – Color Reagent A | FUJIFILM Medical Systems | Cat# 999–34691 |
| FUJIFILM Wako HR Series NEFA-HR Reagent Assay – Color Reagent B | FUJIFILM Medical Systems | Cat# 991–34891 |
| FUJIFILM Wako HR Series NEFA-HR Reagent Assay – Solvent A | FUJIFILM Medical Systems | Cat# 995–34791 |
| FUJIFILM Wako HR Series NEFA-HR Reagent Assay – Solvent B | FUJIFILM Medical Systems | Cat# 993–35191 |
| Deposited data | ||
| Proteomics Raw Data Files | This Publication | ProteomeXchange: PXD047114 |
| Data S1 (Excel File) | This Publication | N/A |
| Experimental models: Organisms/strains | ||
| C57BL/6NJ mice | The Jackson Laboratory | Stock# 005304 |
| BDH1 Skeletal Muscle and Heart Specific Knock-Out Mice | •The Jackson Laboratory: Ckmm-cre transgene •Dr. Dan Kelly: BDH1 floxed allele |
•Tg(Ckmm-cre)5Khn/0 [MGI:2182095] •Bdh1tm1a(EUCOMM)Wtsi [MGI:4432883] |
| Oligonucleotides | ||
| BDH1 Genotyping Primers (Bdh1-Fwd): 5’-TGC AGG AAT CAG TGC TCT CTC CTA G-3’ | IDT | N/A |
| BDH1 Genotyping Primers (Bdh1-Rev): 5’-GGT GTC AGG GCT GAA GGA TG-3’ | IDT | N/A |
| Cre Genotyping Primers (Cre26-Fwd): 5’-CCT GGA AAA TGC TTC TGT CCG-3’ | IDT | N/A |
| Cre Genotyping Primers (Cre36-Rev): 5’-CAG GGT GTT ATA AGC AAT CCC-3’ | IDT | N/A |
| Cre Genotyping Primers (Spect a2 8514 P3-Fwd): 5’-TAC ATA GAG AAT GGC CAG TCT TTT GAC-3’ | IDT | N/A |
| Cre Genotyping Primers (Spect a2 8514 P4-Rev): 5’-GCA CAA CTG GGT AAG GTT CCT ATT CC-3’ | IDT | N/A |
| Software and algorithms | ||
| Mass Hunter B.07.00 | Agilent Technologies | N/A |
| Analyst v. 1.6.3 | Sciex | N/A |
| Matlab R2018b | Mathworks | N/A |
| Proteome Discoverer 2.5 | ThermoFisher | N/A |
| Proteomics Statistical Analysis | This publication | https://github.com/dmpio/Williams_et_al_2023_TRF_PRX |
| DatLab 7 | Oroboros Instruments | Product# 20700 |
| CalR | Mina et al., 2018 | https://calrapp.org |
| Other | ||
| 80x MULTIVAP Nitrogen Evaporator | Organomation | Cat# 11880 |
| Agilent Gas Chromatographer | Agilent Technologies | Cat# 7890B GC |
| Agilent Mass Spectrometer | Agilent Technologies | Cat# 5977A MSD |
| Agilent HP-5ms Column | Agilent Technologies | Cat# 19091S-433UI |
| Sciex LC-MS | Sciex | Cat# Exion AD LC System with QTRAP 6500+ MS/MS |
| Pursuit XRs C18 Column | Agilent Technologies | Cat# A6000150X020 |
| Zorbax 300StableBond C8 Column | Agilent Technologies | Cat# 861775–906 |
| Tissue Lyser II | Qiagen | Cat# 85300 |
| Heart perfusion system (Langendorff) | Radnoti | Cat# 130102EZ |
| Mouse diet (10% kcal as fat and 17% kcal as sucrose) | Research Diets | Cat# D12450Hi |
| EDTA-coated capillary tubes MICROVETTE CB300 | Sarstedt Inc. | Cat# 16.444.100 |
| Exer-3/6 treadmill | Columbus Instruments | Cat# 1050-RM |
| Oxygraph-2k | Oroboros Instruments | Cat# O2k-Core |
| QuantaMaster Spectrofluorometer | Horiba Scientific | Cat# QM-400 |
| Spectrosil Quartz Cuvettes | Starna | 23–5.45-Q-5 |
| Spectromax M2E Spectrophotometer | Molecular Devices | Part#: M2E |
| Thermo Scientific LTQ Orbitrap XLTM Mass Spectrometer | ThermoScientific | Cat#: 0726030 |
| Thermo Fisher Scientific nanoEASY nLC | ThermoScientific | Cat #: LC140 |
| Waters Xevo TQ-S triple quadrupole mass spectrometer coupled to a Waters Acquity UPLC system | Waters | Part#: Xevo TQ-S |
| Bio-Rad Turboblot Transfer System | Biorad | Cat# 1704150EDU |