Cedars-Sinai Parker Lab - Mitoplex-Mouse

Cedars-Sinai Parker Lab - Mitoplex-Mouse
MitoPlex: A Targeted Multiple Reaction Monitoring Assay for Quantification of a Curated Set of Mitochondrial Proteins
Data License: CC BY 4.0 | ProteomeXchange: PXD017884
  • Organism: Mus musculus
  • Instrument: QTRAP 6500+,TripleTOF 5600+
  • SpikeIn: Yes
  • Keywords: Mitoplex, MRM, metabolomics, statin myopathy, striated muscle, mitochondrial function
  • Lab head: Sarah Parker Submitter: Sarah Parker
Abstract
Mitochondria are the major source of cellular energy (ATP), as well as critical mediators of widespread functions such as cellular redox balance, apoptosis, and metabolic flux. Methods to quantify mitochondrial content are limited to low throughput immunoassays, measurement of mitochondrial DNA, or relative quantification by untargeted mass spectrometry. Here, we present a high throughput, focused multiple reaction monitoring based assay of 32 proteins critical to central carbon chain metabolism and overall mitochondrial function termed ‘MitoPlex’. We coupled this protein multiplex with a parallel analysis of 218 metabolites extracted in tandem from the same sample. In tests of its biological applicability, “MitoPlex plus metabolites” indicated profound effects of HMG-CoA Reductase inhibition (e.g., statin treatment) on mitochondria of differentiating C2C12 skeletal myoblasts, as well as a clear opposite trend of statins to promote mitochondrial protein expression and metabolism in heart and liver, while suppressing mitochondrial protein and aspects of metabolism in the skeletal muscle of C57Bl6 mice. Our results not only reveal new insights into the metabolic effect of statins in skeletal muscle, but present a new high throughput, reliable MS-based tool to study mitochondrial dynamics in both cell culture and in vivo models.
Experiment Description
Targeted MRM Assays (Tier 2) were created to quantify up to 32 mitochondrial proteins selected to be informative of major functional pathways (TCA cycle, ETC, mitochondrial remodeling, etc). A concurrent protein and metabolite extraction protocol was developed to enable analysis of both analyte types from the same cell or tissue sample. A targeted metabolomic panel was measured concomitantly with mitochondrial proteins for comparison. The performance and biological informativeness of the assay was assessed in a series of experiments interrogating metabolic differences between differentiating C2C12 skeletal muscle cell in vitro model and between striated muscle types (oxidative and glycolytic skeletal muscle, cardiac muscle) with, and without, exposure to statins.
Sample Description
C2C12 myoblast and myotube cultures Mouse soleus muscle Mouse gastrocnemius muscle Mouse cardiac muscle Mouse liver
Created on 3/4/20, 2:59 PM
Clustergrammer Heatmap
 
Download
NV0001_Mouse-Skin_mProphet_Panorama_2024-03-09_19-20-18.sky.zip2024-03-10 20:30:291,6595,7905,79028,90434 
XW0008_Cas9Myc_DIAassayLIB_OmBcells_17Nov2023_2024-02-24_08-51-18.sky.zip2024-02-24 12:56:485,20383,67483,675605,04024 
XW0009_DIAassayLIB_OmBcells_17Nov2023_2024-02-23_18-35-50.sky.zip2024-02-23 22:06:575,20383,64583,647604,72019 
AutoQC-lumos-SysS-MouAD-PFC-C2-B5-B7.sky.zip2024-02-20 07:53:561889414 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B07.sky.zip2024-02-18 11:31:099,778127,624127,624966,34712 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B06.sky.zip2024-02-18 10:45:259,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B05.sky.zip2024-02-18 09:51:569,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B04.sky.zip2024-02-18 01:14:219,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B03.sky.zip2024-02-18 00:22:039,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B02.sky.zip2024-02-17 23:29:529,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C2_B01.sky.zip2024-02-17 18:20:009,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B28.sky.zip2024-02-17 17:30:039,778127,624127,624966,3476 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B27.sky.zip2024-02-17 16:57:559,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B26.sky.zip2024-02-17 15:06:069,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B25.sky.zip2024-02-17 14:11:069,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B24.sky.zip2024-02-17 13:17:049,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B23.sky.zip2024-02-17 10:45:369,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B22.sky.zip2024-02-17 09:52:589,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B21.sky.zip2024-02-17 09:01:129,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B20.sky.zip2024-02-17 01:24:329,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B19.sky.zip2024-02-17 00:31:539,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B18.sky.zip2024-02-16 23:42:139,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B17.sky.zip2024-02-16 21:59:109,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B16.sky.zip2024-02-16 21:08:449,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B15.sky.zip2024-02-16 19:45:379,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B14.sky.zip2024-02-16 18:50:509,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B13.sky.zip2024-02-16 17:05:369,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B12.sky.zip2024-02-16 16:13:309,778127,624127,624966,34716 
XW0008-Myc248_DIAassayLIB_OmBcells_17Nov2023_2024-02-16_10-02-13.sky.zip2024-02-16 15:02:065,20383,67483,675605,04024 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B11.sky.zip2024-02-16 11:03:589,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B10.sky.zip2024-02-16 10:07:519,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B09.sky.zip2024-02-16 09:14:539,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B08.sky.zip2024-02-16 08:20:059,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B07.sky.zip2024-02-16 01:08:409,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B06.sky.zip2024-02-16 00:17:379,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B05.sky.zip2024-02-15 23:29:389,778127,624127,624966,34716 
XW0008_nanos3_DIAassayLIB_OmBcells_17Nov2023_2024-02-15_17-02-46.sky.zip2024-02-15 21:13:165,20383,67483,675605,04024 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B04.sky.zip2024-02-15 16:37:369,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B03.sky.zip2024-02-15 14:42:299,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B02.sky.zip2024-02-15 13:44:359,778127,624127,624966,34716 
Lumos-Jax-Cortex-DIA-ind-8mz-ovlp-400to1000-C1_B01.sky.zip2024-02-15 12:45:409,778127,624127,624966,34716 
AutoQC-lumos-PCs-MouAD-PFC-C2-B5-B7.sky.zip2024-02-14 16:42:502141417344 
AutoQC-lumos-PCs-MouAD-PFC-C2-B1-B4.sky.zip2024-02-14 16:42:332141417364 
AutoQC-lumos-PCs-MouAD-PFC-C1-B9-B12.sky.zip2024-02-14 16:42:152141417364 
AutoQC-lumos-PCs-MouAD-PFC-C1-B4-B8.sky.zip2024-02-14 16:42:002141417380 
AutoQC-lumos-PCs-MouAD-PFC-C1-B25-B28.sky.zip2024-02-14 16:41:372141417354 
AutoQC-lumos-PCs-MouAD-PFC-C1-B21-B24.sky.zip2024-02-14 16:41:002141417364 
AutoQC-lumos-PCs-MouAD-PFC-C1-B17-B20.sky.zip2024-02-14 16:40:442141417365 
AutoQC-lumos-PCs-MouAD-PFC-C1-B13-B16.sky.zip2024-02-14 16:40:282141417364 
AutoQC-lumos-PCs-MouAD-PFC-C1-B1-B3.sky.zip2024-02-14 16:40:082141417347 
AutoQC-lumos-SysS-MouAD-PFC-C2-B1-B4.sky.zip2024-02-14 16:10:161889417 
AutoQC-lumos-SysS-MouAD-PFC-C1-B9-B12.sky.zip2024-02-14 16:06:251889416 
AutoQC-lumos-SysS-MouAD-PFC-C1-B4-B8.sky.zip2024-02-14 16:02:231889422 
AutoQC-lumos-SysS-MouAD-PFC-C1-B1-B3.sky.zip2024-02-14 15:59:501889418 
AutoQC-lumos-SysS-MouAD-PFC-C1-B17-B20.sky.zip2024-02-14 14:48:381889410 
ZipChip_HR_Metabolomics_2024Protocol_2024-02-05_17-24-05.sky.zip2024-02-05 14:24:28100821594 
22AminoAcids_Fully13CLabeled_2024-01-29_14-30-52.sky.zip2024-01-29 11:32:1410444936 
RBD_M_Glyco_2024-01-25_15-29-41.sky.zip2024-01-26 17:23:2672923972,3829 
20240104_Neg_FMT_MCBAs_isoRemove_Cleaned_Final_2024-01-25_21-40-19.sky.zip2024-01-26 16:43:471010030056 
20231220_Neg_FMT_BA_Full_reduce_Res50_High_final_2024-01-04_15-44-59.sky.zip2024-01-26 16:43:47405112176 
P179_UNCSet1_ACE_v0p3_2024-01-24_22-42-18.sky.zip2024-01-24 19:51:4423034963724 
P179_UNCSet2_ACE_v0p3_2024-01-24_22-37-25.sky.zip2024-01-24 19:40:1117021336726 
New_iRBD2024-01-15 23:30:5233474794292 
Paired_CSF_Plasma_Serum2024-01-15 23:30:523347479460 
Initial_Targeted_Proteomics2024-01-15 23:30:5233474794441 
TPAD_VL_CSF_PRTC_APOA1_2024-01-07_23-01-46.sky.zip2024-01-07 23:08:493464642412 
TPAD-CSF-SP3_1-5.sky.zip2024-01-05 06:03:432,90823,74323,743189,895396 
173_peptides_iRTs_chromatogram_library_2023-12-22_00-47-19.sky.zip2023-12-22 01:06:36311833561,0822 
Figure_8B_Freiburg_ALG1-CDG-Patients_Comparison_2023-12-22_02-34-55.sky.zip2023-12-22 01:06:2022691284006 
Figures_4_5_6_7_8A_Heidelberg_CDG-Patients_2023-12-22_02-32-43.sky.zip2023-12-22 01:06:20206712439014 
Figure_S5_Freiburg_ALG11_I-CDG_Natural_Variant_2023-12-22_01-59-41.sky.zip2023-12-22 01:06:2021112146 
Figure_9_Freiburg_ALG11_I-CDG_Natural_Variant_2023-12-22_01-53-52.sky.zip2023-12-22 01:06:2021418404 
Figures_3_and_S3_HEK_293T_Fibroblasts_HeLa_2023-12-22_01-03-03.sky.zip2023-12-22 01:06:2023701303989 
20210301 Calibration Dev_DilutionOil_2023-12-11_10-57-35.sky.zip2023-12-20 00:34:263482654 
20210607 Calibration Curve_DilutionDigest_2023-12-11_10-50-40.sky.zip2023-12-20 00:34:2634824108 
20210212 Low range exploration 140K-fragmod_Pub_2023-12-08_16-04-13.sky.zip2023-12-20 00:34:263482456 
HeatedOilSpike-LowTemp_HighTemp_Combined_Final_2022-05-26_12-00-47.sky.zip2023-12-20 00:34:26591548204 
20200715_PeptideSpecificity_SignalRatio_2022-05-25_16-33-02.sky.zip2023-12-20 00:34:2611202212044 
20200622_PeptideSpecificityTest_2022-05-25_16-30-20.sky.zip2023-12-20 00:34:2614252713545 
20191112_Diff-TempConc_Oil-Spike_24pep_2022-05-25_14-24-35.sky.zip2023-12-20 00:34:2611242715040 
20191007_HeatedOilSpike_Extraction_method_24pep_2022-05-25_14-16-21.sky.zip2023-12-20 00:34:2611242715032 
20190904_Organic_Aqueous_Extraction_Oil_Spike_24pep_2022-05-25_14-12-26.sky.zip2023-12-20 00:34:2611242715636 
September 21 Import V1 (Samples with IS) w Cal Curve_Blanks Deleted_2023-12-01_11-40-59.sky.zip2023-12-02 23:51:3320262687 
September 21 Kaylie New Molecule Import v1 (Filtered)_2023-12-01_11-40-01.sky.zip2023-12-02 23:51:3310161698 
September 21 Import V1 all samples (Neg mode only)_2023-12-01_11-35-34.sky.zip2023-12-02 23:51:338014514598 
THP1_IFN_PRM_Skyline_2023-11-14_14-22-42.sky.zip2023-11-16 13:26:09711771771,5148 
CCS_library_v2.sky.zip2023-11-15 14:36:301061,86361,8630 
IdentExpression_2023-09-25_14-39-47.sky.zip2023-10-02 20:45:1381581941,16419 
2DGel_II_2023-09-25_14-37-39.sky.zip2023-10-02 20:45:13897408805,28034 
2DGel_I_2023-09-25_14-36-13.sky.zip2023-10-02 20:45:13252142321,39232 
InGelDigest_Der_p_SEA_II_2023-09-18_10-01-52.sky.zip2023-09-21 11:03:445004,0584,42026,52051 
InGelDigest_Der_p_SEA_I_2023-09-15_16-14-11.sky.zip2023-09-21 11:03:443272,3822,52115,12652 
FASP_Der_p_SEA_2023-09-15_14-24-26.sky.zip2023-09-21 11:03:445504,2964,77128,6261 
230504_Myllys_231247ff_2023-09-20_13-22-59.sky.zip2023-09-21 10:31:2410434398 
230512MyllysUrea_231247ff_2023-09-21_15-27-13.sky.zip2023-09-21 10:31:24102292 
230511Myllys231247ff_AA_Crea_2023-09-20_13-36-24.sky.zip2023-09-21 10:31:242044166126 
AutoQC-lumos-SysS-MouAD-C2-B8-10.sky.zip2023-09-17 11:22:321889414 
AutoQC-lumos-SysS-MouAD-C2-B5-B7.sky.zip2023-09-17 11:22:301889415 
AutoQC-lumos-SysS-MouAD-C2-B1-B4.sky.zip2023-09-17 11:22:281889419 
AutoQC-lumos-SysS-MouAD-C1-B9-B12.sky.zip2023-09-17 11:22:261889413 

This data is available under the CC BY 4.0 license.