Dataset Information

Arabidopsis mitochondrial proteome during a diurnal cycle

ABSTRACT: We surveyed the heterogeneity of the mitochondrial proteome and its function during a typical night and day cycle in Arabidopsis shoots. This used a staged, quantitative analysis of the proteome across 10 time points covering 24 h of the life of 3-week-old Arabidopsis shoots grown under 12-h dark and 12-h light conditions. Results were queried against an in-house Arabidopsis database comprising ATH1.pep (release 7) from The Arabidopsis Information Resource and the Arabidopsis mitochondrial and plastid protein sets (the combined database contained a total of 30,700 protein sequences with 12,656,682 residues) using the Mascot search engine version 2.2 and utilizing error tolerances of +-1.2 Da for MS and +-0.6 Da for MS/MS, 'enzyme' set to trypsin, 'maximum missed cleavages' set to 1, variable modifications of oxidation (Met) and carbamidomethyl (Cys), instrument set to ESI-TRAP, and peptide charge set at 2+ and 3+. ATH1.pep is a non-redundant database with systematically named protein sequences based on Arabidopsis genome sequencing and annotation. PRIDE XML files with accession numbers 10471–10525 and without peptide/protein identifications have already been made public.

INSTRUMENT(S): 1200 series LC/MSD VL

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Shoot

SUBMITTER: Chun Pong Lee

LAB HEAD: Chun Pong Lee

PROVIDER: PXD000500 | Pride | 2013-10-09

REPOSITORIES: Pride

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Publications

Diurnal changes in mitochondrial function reveal daily optimization of light and dark respiratory metabolism in Arabidopsis.

Lee Chun Pong CP Eubel Holger H Millar A Harvey AH

Molecular & cellular proteomics : MCP 20100702 10

Biomass production by plants is often negatively correlated with respiratory rate, but the value of this rate changes dramatically during diurnal cycles, and hence, biomass is the cumulative result of complex environment-dependent metabolic processes. Mitochondria in photosynthetic plant tissues undertake substantially different metabolic roles during light and dark periods that are dictated by substrate availability and the functional capacity of mitochondria defined by their protein compositio ...[more]

PMID: 20601493

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Project description:Two datasets: StREM1.3: methyl-beta cyclodextrin-dependent distribution of StREM1.3 to detergent resistant and detergent soluble membrane fractions. SLAH3: localization of SLAH3 to detergent resistant and detergent soluble fractions dependent on co-expression with CPK21 and ABI1. Data analysis: Protein identiﬁcation and ion intensity quantitation was carried out by MaxQuant version 1.3.0.5. Spectra were matched against the Arabidopsis proteome (TAIR10, 35,386 entries) using Andromeda. Thereby, carbamidomethylation of cysteine was set as a ﬁxed modiﬁcation; oxidation of methionine as well as phosphorylation of serine, threonine, and tyrosine was set as variable modiﬁcations. Because label-free quantitation based on ion intensities was used, multiplicity was set to 1. Mass tolerance for the database search was set to 20 ppm on full scans and 0.5 Da for fragment ions. Retention time matching between runs was chosen within a time window of 2 min. Peptide false discovery rate (FDR), protein FDR was set to 0.01, and site FDR was set to 0.05. Contaminants and reverse hits identiﬁed by MaxQuant were excluded from further analys Protein identiﬁcation and ion intensity quantitation was carried out by MaxQuant version 1.3.0.5. Spectra were matched against the Arabidopsis proteome (TAIR10, 35,386 entries) using Andromeda. Thereby, carbamidomethylation of cysteine was set as a ﬁxed modiﬁcation; oxidation of methionine as well as phosphorylation of serine, threonine, and tyrosine was set as variable modiﬁcations. Because label-free quantitation based on ion intensities was used, multiplicity was set to 1. Mass tolerance for the database search was set to 20 ppm on full scans and 0.5 Da for fragment ions. Retention time matching between runs was chosen within a time window of 2 min. Peptide false discovery rate (FDR), protein FDR was set to 0.01, and site FDR was set to 0.05. Contaminants and reverse hits identiﬁed by MaxQuant were excluded from further analysis. PXD000211 is also assoicated with the same study/paper.

			Action	DRS
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	DIURNAL_14.mgf	Mgf
	DIURNAL_15.mgf	Mgf
	DIURNAL_16.mgf	Mgf
	DIURNAL_17.mgf	Mgf