Summary of Study ST001062

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 PR000712. The data can be accessed directly via it's Project DOI: 10.21228/M8N965 This work is supported by NIH grant, U2C- DK119886.


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Study IDST001062
Study TitleArabidopsis Nit1 knockout metabolomics
Study SummaryGlutathione (GSH) is a tripeptide that is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1-10 millimolar range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has efficient amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons were used and subcellular localization of GFP fusions confirmed both cytosolic and plastidial localization. Further, we show that Arabidopsis enzymes convert GSH to dGSH at a rate of 2.8 pmol min-1 mg-1 in vitro. Our data demonstrate that plants have a dGSH repair system that is directed to at least two subcellular compartments via the use of alternative translation start sites.
University of California, Davis
Last NameFolz
First NameJacob
Address451 Health Sciences Dr., Davis, CA, 95616
Submit Date2018-09-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-03-06
Release Version1
Jacob Folz Jacob Folz application/zip

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Combined analysis:

Analysis ID AN001736 AN001737 AN001738
Analysis type MS MS MS
Chromatography type HILIC HILIC Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS instrument type Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Units AU AU AU


Chromatography ID:CH001228
Chromatography Summary:HILIC chromatography 17 minute run. Positive and Negative mode.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:The gradient started at 100% B for 2 minutes, then brought to 70% B by 7.7 minutes, 40% B by 9.5 minutes, back to 100% B by 12.75 minutes and held at 100% B until 17 minutes.
Flow Rate:0.4 mL/min
Internal Standard:5ug Val-Tyr-Val+
Sample Injection:5uL
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Washing Buffer:Water:ACN 50:50
Target Sample Temperature:4
Chromatography Type:HILIC
Chromatography ID:CH001229
Chromatography Summary:CSH C18 lipidomics run. Positive mode. As in Cajka et al. 2017 "Validating Quantitative untargeted lipidomics across nine liquid chromatography-High-Resolution Mass spectrometry platforms"
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Column Temperature:65
Flow Gradient:: 0 min 15% (B); 0−2 min 30% (B); 2−2.5 min 48% (B); 2.5−11 min 82% (B); 11−11.5 min 99% (B); 11.5−12 min 99% (B); 12−12.1 min 15% (B); and 12.1−15 min 15% (B)
Flow Rate:0.6 mL/min
Internal Standard:[LPE(17:1), LPC(17:0), PC(12:0/13:0), PE(17:0/17:0), PG(17:0/17:0), d7-cholesterol, SM(d18:1/17:0), Cer(d18:1/17:0), sphingosine (d17:1), DG(12:0/12:0/0:0), DG(18:1/2:0/0:0), and d5-TG- (17:0/17:1/17:0)]
Sample Injection:3uL
Solvent A:60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Washing Buffer:IPA
Target Sample Temperature:4
Chromatography Type:Reversed phase