Summary of Study ST002925

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001817. The data can be accessed directly via it's Project DOI: 10.21228/M8V72T This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002925
Study TitleMetabolite analysis of hepatic Pptc7-ko mice under fed or fasting conditions
Study SummaryHepatic Pptc7 knockout leads to mitochondrial loss under fed conditions in adult mice, which is exacerbated upon fasting. Under fasting conditions, WT liver upregulates Pptc7 levels to repress mitophagy and maintain mitochondrial mass. However, Pptc7-KO liver accumulated higher levels of Bnip3, resulting in mitophagy activation and further mitochondrial loss. To explore the metabolic changes upon Pptc7 knockout under both fed and fasting conditions, we performed a metabolite analysis of wild-type or Pptc7-KO mouse liver samples in this study.
National Institute of Biological Sciences, Beijing
Last NameMa
First NameYan
AddressZhongguancun Life Science Park
Submit Date2023-10-11
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-10-26
Release Version1
Yan Ma Yan Ma application/zip

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Project ID:PR001817
Project DOI:doi: 10.21228/M8V72T
Project Title:A mitophagy sensor PPTC7 integrates homeostatic and physiological signals to regulate mitophagy and mitochondrial mass
Project Summary:Mitophagy mediated by receptors BNIP3 and NIX critically regulates mitochondrial mass under developmental and pathophysiological conditions. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitophagy and lethal disease. Here we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3/NIX-mediated mitophagy in vitro and in vivo. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to mitochondrial outer-membrane, where PPTC7 scaffolds the assembly of the substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer-membrane retention and mitophagy control. Upon starvation, PPTC7 is transcriptionally upregulated in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining proper mitochondrial mass and cellular homeostasis.
Institute:National Institute of Biological Sciences,Beijing
Last Name:Ma
First Name:Yan
Address:Zhongguancun Life Science Park


Subject ID:SU003038
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:10-week


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment
SA317872sample_17Pptc7-KO fasting
SA317873sample_16Pptc7-KO fasting
SA317874sample_14Pptc7-KO fasting
SA317875sample_08Pptc7-KO fasting
SA317876sample_15Pptc7-KO fasting
SA317877sample_06Pptc7-KO fasting
SA317878sample_19Pptc7-KO fasting
SA317879sample_18Pptc7-KO fasting
SA317880sample_05Pptc7-KO fasting
SA317881sample_07Pptc7-KO fasting
SA317882sample_13wild-type fed
SA317883sample_10wild-type fed
SA317884sample_03wild-type fed
SA317885sample_02wild-type fed
SA317886sample_04wild-type fed
SA317887sample_09wild-type fed
SA317888sample_11wild-type fed
SA317889sample_01wild-type fed
SA317890sample_12wild-type fed
Showing results 1 to 19 of 19


Collection ID:CO003031
Collection Summary:Mice were sacrificed and liver samples were dissected out and snap-frozen in liquid nitrogen.
Sample Type:Liver
Storage Conditions:-80℃


Treatment ID:TR003047
Treatment Summary:We performed retro-orbital injection of P28 old Pptc7-flox (GemPharmatech, T011006) mice with 1×10^12 vector genome of the empty vector or Cre AAV8 virus. 42 days post AAV injection, mice were subjected to fasting or left fed as control group respectively. Fasting was done for 18 hours from the beginning of the dark cycle at 7.p.m. to 1.p.m. next day.

Sample Preparation:

Sampleprep ID:SP003044
Sampleprep Summary:Mouse livers were dissected out and snap-frozen in liquid nitrogen. Liver samples were cryo-homogenized on dry ice and 30 mg of homogenized tissue powders were weighed and extracted with 600 μL ice-cold acetonitrile/methanol/water (4/4/2) for 30 min. After centrifugation at 20,000 g for 15 min, supernatant was transferred to a new tube and dried by a Speedvac vacuum concentrator at 30°C. Dried samples were stored at -80°C and subjected to LC-MS analysis within 24 hours.

Combined analysis:

Analysis ID AN004796 AN004797
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish UHPLC Thermo Vanquish UHPLC
Column Merck ZIC-HILIC (2.1x100 mm, 3.5 μm) Merck ZIC-HILIC (2.1x100 mm, 3.5 μm)
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap Thermo Q Exactive HF-X Orbitrap
Units count count


Chromatography ID:CH003627
Instrument Name:Thermo Vanquish UHPLC
Column Name:Merck ZIC-HILIC (2.1x100 mm, 3.5 μm)
Column Temperature:40
Flow Gradient:0-5 min, 99% B; 5-20 min, 99-20% B; 20-21 min, 20-99% B; 21-25 min, 99% B.
Flow Rate:0.5 mL/min
Solvent A:5% acetonitrile/95% water; 10 mM ammonium acetate
Solvent B:95% acetonitrile/5% water; 10 mM ammonium acetate
Chromatography Type:HILIC


MS ID:MS004542
Analysis ID:AN004796
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Comments:-
MS ID:MS004543
Analysis ID:AN004797
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Comments:-