Dataset Information

A high-density, organ-specific proteome map for Arabidopsis thaliana

ABSTRACT: Not available

INSTRUMENT(S): instrument model, LTQ

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

TISSUE(S): Carpel, Flower, Cotyledon, Cell Suspension Culture, Root, Seed, Flower Bud, Juvenile Leaf, Silique

SUBMITTER: Katja Baerenfaller

PROVIDER: PRD000044 | Pride | 2008-04-24

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_3321.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_3321.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_3322.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_3322.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_3323.pride.mgf.gz	Mgf

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Publications

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

Baerenfaller Katja K Grossmann Jonas J Grobei Monica A MA Hull Roger R Hirsch-Hoffmann Matthias M Yalovsky Shaul S Zimmermann Philip P Grossniklaus Ueli U Gruissem Wilhelm W Baginsky Sacha S

Science (New York, N.Y.) 20080424 5878

We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptid ...[more]

PMID: 18436743

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Project description:Plant Growth and Treatment. Seedlings of Arabidopsis thaliana GVG::FLAG-NtMEK2DD were grown in 50 ml of half-strength Murashige and Skoog medium at 22°C under continuous light (70 µE/m2/sec). Twelve-day-old seedlings were treated with DEX (1 µM) or ethanol (control) and collected 6 h after treatment. Protein Extraction and MOAC Enrichment of Phosphoproteins. Protein extraction from seedlings and enrichment of phosphoprotein. The concentration of protein in extracts was determined using the Bio-Rad protein assay kit with BSA as the standard. Western Blotting Analysis and Immunodetection. Protein samples were subjected to SDS-PAGE, transferred to nitrocellulose, and used for immunodetection. Mouse monoclonal anti-Flag M2 antibodies were purchased from Sigma-Aldrich; all other antibodies were from New England Biolabs. Chemiluminescence detection of antigen-antibody complexes was done with Immobilon™ Western substrate (Millipore). Enrichment of Phosphopeptides by MOAC. For in-solution protein digestion, total proteins or MOAC-enriched phosphoproteins were predigested for 5 h with endoproteinase Lys-C (1/100 w/w) followed by trypsin digestion (Poroszyme immobilized trypsin (1/100 v/w)) overnight. Protein digests were desalted using a SPEC C-18 96-well plate (Varian) according to the manufacturer’s instructions. TiO2 beads were purchased from Glygen Inc. Mass Spectrometry and Protein Identification. Peptides were analyzed using an Orbitrap XL mass spectrometer (Thermo Scientific). Chromatography was performed using a Chromolith CapRod C18 monolithic column with 0.1% (v/v) formic acid (FA) in ultrapure H2O and 0.1% (v/v) FA in 90% (v/v) acetonitrile (ACN) in ultrapure H20 as mobile phases and a gradient from 10% to 35% organic phase in 120 min with a flow rate of 500 nl/min. Multistage activation/pseudoMS3 was enabled for acquisition of CID tandem MS (MS/MS) mass spectra of phosphopeptides with a neutral loss mass list of 97.97, 48.999, 32.66 and 24.49 Da. Database search was performed with the Proteome Discoverer Software version 1.2. using the SEQUEST algorithm.