Dataset Information

Arabidopsis cell LC-MSMS - Proteomics analysis reveals a highly heterogeneous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants

ABSTRACT: 26S proteasome was affinity-purified with anti-FLAG beads and separated by 2-DE method. Each spot was cut and digested by Trypsin enzyme, which finaly applied for LC-MS/MS nalysis using a LTQ-Orbitrap XL (Thermo Scientific). The obtained spectra were compared against 35,386 sequences in The Arabidopsis Information Resource 10 (TAIR10; http://www.arabidopsis.org/) using the MASCOT server (version 2.4; Matrix Science) with the following search parameters: threshold set-off at 0.05 in the ion-score cut-off; protein identification cut-off set to two assigned spectra per predicted protein; peptide tolerance at 10 ppm; MS/MS tolerance at +/- 0.5 Da; peptide charge of 2+ or 3+; trypsin as the enzyme and allowing up to one missed cleavage; carboxymethylation on cysteines as a fixed modification and oxidation on methionine as a variable modification.

INSTRUMENT(S): LTQ Orbitrap

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

TISSUE(S): Plant Cell, Cell Culture

SUBMITTER: Takeo Sato

LAB HEAD: Takeo Sato

PROVIDER: PXD000417 | Pride | 2014-07-28

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_30610.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_30610.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_30610.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_30611.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_30611.pride.mztab.gz	Mztab

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Publications

Proteomics analysis reveals a highly heterogeneous proteasome composition and the post-translational regulation of peptidase activity under pathogen signaling in plants.

Sun Hui H HH Fukao Yoichiro Y Ishida Sakiko S Yamamoto Hiroko H Maekawa Shugo S Fujiwara Masayuki M Sato Takeo T Yamaguchi Junji J

Journal of proteome research 20130920 11

The proteasome is a large multisubunit complex that plays a crucial role in the removal of damaged or selective ubiquitinated proteins, thereby allowing quality control of cellular proteins and restricted regulation of diverse cellular signaling in eukaryotic cells. Proteasome-dependent protein degradation is involved in almost all aspects of plant growth and responses to environmental stresses including pathogen resistance. Although the molecular mechanism for specifying targets by ubiquitin li ...[more]

PMID: 23991809

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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.