Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis seedling FFE-purified plasma membrane LC-MS/MS

ABSTRACT: Plasma membranes from 7-day old wild type Arabidopsis seedlings were enriched by two-phase partitioning and further purified by free-flow electrophoresis prior to analysis of fractions by LC-MS/MS. Data from two independent replicates were analyzed, with two fractions analyzed from each replicate.

INSTRUMENT(S):

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

TISSUE(S): Plant Cell, Seedling

SUBMITTER: Joshua Heazlewood

LAB HEAD: Joshua Heazlewood

PROVIDER: PXD001795 | Pride | 2015-12-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AtPM1-53.dat-pride-filtered.pride.mgf.gz	Mgf
	AtPM1-53.dat-pride-filtered.pride.mztab.gz	Mztab
	AtPM1-53.dat-pride-filtered.xml.gz	Xml
	AtPM1-53.wiff	Wiff
	AtPM1-53.wiff.mtd	Wiff

Items per page:

1 - 5 of 24

Publications

Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings.

de Michele Roberto R McFarlane Heather E HE Parsons Harriet T HT Meents Miranda J MJ Lao Jeemeng J González Fernández-Niño Susana M SM Petzold Christopher J CJ Frommer Wolf B WB Samuels A Lacey AL Heazlewood Joshua L JL

Journal of proteome research 20160204 3

The plant plasma membrane is the interface between the cell and its environment undertaking a range of important functions related to transport, signaling, cell wall biosynthesis, and secretion. Multiple proteomic studies have attempted to capture the diversity of proteins in the plasma membrane using biochemical fractionation techniques. In this study, two-phase partitioning was combined with free-flow electrophoresis to produce a population of highly purified plasma membrane vesicles that were ...[more]

PMID: 26781341

Similar Datasets

A novel tool, Multiple Marker Abundance Profiling, uses Selected Reaction Monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.

Project description:Methods were investigated that would deliver rapid and semi-quantitative analysis of the subcellular composition of Arabidopsis samples, as the standard technique for this i.e. immunoblotting is difficult to quantify and relies on a very few protein targets, whose responses to developmental or environmental cues are often not known. Spectral counts from shotgun analysis of different Arabidopsis tissues, cells or growth stages were compared to selected reaction monitoring (SRM) analyses of the same samples. Results were further compared to a novel protein abundance scoring method, MASCP Gator scoring, described in this study for the first time. The latter is reliant on previously collated public proteomics data and so provides an estimate of protein abundance even in the absence of de-novo experimentation. This scoring method is presented as an online tool, Multiple Marker Abundance Profiling (MMAP), available at http:SUBA.live. This submission comprises the shotgun data from this study. SRM results are available in a separate submission: http://www.peptideatlas.org/PASS/PASS00906

2018-10-26 | PXD005408 | Pride

Maize and Arabidopsis Golgi proteome

Project description:Comparative proteomics of ER-Golgi membranes from etiolated coleoptiles of maize (Zea mays) and young leaves of Arabidopsis (Arabidopsis thaliana) isolated by flotation centrifugation demonstrate differences in the complement of synthases and glycosyl transferases unique to the type of wall made. Additionally, maize Golgi membranes enriched by flotation were separated further by free-flow electrophoresis (FFE), yielding 3009 proteins, of which 229 were known to function in cell wall synthesis or metabolism. A subset of proteins identified after flotation centrifugation were identified in Golgi membranes but failed to enrich in them. Individual classes of proteins associated with cell wall synthesis were asymmetrically distributed across the fractions of Golgi membranes separated by FFE.

2019-04-11 | PXD007612 | Pride

ZNF322A_lung cancer_iTRAQ_LC-MSMS

Project description:ZNF322A, a transcription factor, has been identified as a novel putative oncogene in lung cancer. There are over 50% of amplification rates in both Asia and Caucasian lung cancer patients. This study is to use proteomics approach to establish the protein interaction network of ZNF322A.

2016-07-07 | PXD001123 | Pride

Proteomics of Fuchs Endothelial Corneal Dystrophy support that the extracellular matrix of Descemet¹s membrane is Disordered

Project description:Fuchs’ endothelial corneal dystrophy is major corneal disorder in the western world affecting the innermost part of the cornea, which leads to visual impairment. The morphological changes observed in Fuchs’ endothelial corneal dystrophy is well described, however, much less in known of the pathology at the molecular level. As the morphological changes observed in the cornea is profound in the extracellular matrix we sought to determine in protein profiles and changes herein in the Descement’s membrane and endothelium layer of Fuchs’ endothelial conrneal dystrophy patients when compared to healthy control tissue. Using the extracted ion chromatogram label-free MS based quantification method we quantified approximately the 50 most abundant proteins of the Descemet’s membrane and endothelial layer in in patient and control tissue. In addition, using the isobaric tag for relative and absolute quantification MS method resulted in a total of 22 regulated proteins of which the majority were extracellular proteins known to be involved in proper assembly and modulation of the basement membrane in other tissues. Many of the regulated proteins were furthermore among the most abundant proteins quantified. The two MS methods performed here suggest altered arrangement of the extracellular matrix in Fuchs’ endothelial corneal dystrophy and provide new candidate proteins that may be involved in molecular mechanism of this disease.

2014-05-27 | PXD000746 | Pride

Root iTRAQ protein profile analysis of two Citrus species differing in aluminum-tolerance in response to long-term aluminum-toxicity

Project description:After long-term aluminum treatment, thereafter, we investigated Citrus root protein profiles using isobaric tags for relative and absolute quantification (iTRAQ).

2017-10-26 | PXD002301 | Pride

Phosphorus-mediated alleviation of aluminum toxicity revealed by iTRAQ technique in Citrus grandis roots

Project description:Citrus grandis seedlings were irrigated with nutrient solutions containing two levels of aluminium (Al; 0 mM and 1.2 mM AlCl3•6H2O) and two levels of phosphorus (P; 0 μM and 200 μM KH2PO4) combinations for 18 weeks, respectively. The proteome profile of Citrus root submitted to different P-Al interactions were investigated by using isobaric tags for relative and absolute quantification (iTRAQ).

2019-11-13 | PXD012534 | Pride

Proteomic analysis in Arabidopsis tissues reveals hydrogen cyanide regulation of intracellular processes through posttranslational modification of proteins by S-cyanylation

Project description:Hydrogen cyanide (HCN) is co-produced with ethylene in plant cell and enzymatically detoxified mainly by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alteration in the plant that point to the function of HCN as a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from wild type and cas-c1 mutant reveled significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins only present or more abundant in the mutant background. Gene onthology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered inmune response observed in cas-c1 mutant. The mechanism of action of cyanide as signaling molecule has been addressed by two proteomic approaches focused on identifying S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and direct untargeted analysis of proteins by LC-MS/MS identified a set of 163 proteins susceptibles to be S-cyanylated that include sedoheptulose 1, 7 biphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified this modification in SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues that affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways as glycolysis, and the Calvin and S-adenosylmethionine cicles.

2019-01-09 | PXD009812 | Pride

Agron-omics Long Day Optimal Watering (LOW) experiment

Project description:Plants adapt to the prevailing photoperiod by optimally adjusting growth and flowering to the availability of energy. When Arabidopsis thaliana plants are grown in long days individual leaf growth is favoured, whereas whole plant leaf area is decreased because of the rapid shift to floral stages and, consequently, the low number of total leaves. To understand the molecular profiles of adaptation to long-day conditions we profiled Arabidopsis leaf number six of plants grown in 16 hours of light at four developmental stages both at the end of the day and the end of the night and compared the profiles to those acquired in short day conditions.

2015-12-14 | PXD000908 | Pride

PTMs in yeast complexes - We investigate the roles of natively present PTMs on stability of interactions in three large and essential yeast Saccharomyces cerevisiae complexes: exosome, RNA polymerase II and 26S proteasome.

Project description:We investigate the roles of natively present PTMs on stability of interactions in three large and essential yeast Saccharomyces cerevisiae complexes: exosome, RNA polymerase II and 26S proteasome.

2018-09-13 | PXD008324 | Pride

Protein accumulation post-LASIK surgery in granular corneal dystrophy type II patients involves altered proteolytic processing of transforming growth factor beta-induced protein (TGFBIp)

Project description:his study present the protein profile of diseased cornea from granular corneal dystrophy patients developing protein accumulation after LASIK surgery. Extracted ion chromatography (XIC) label free quantification was perform using Mascot Distiller software. In addition, 2D-PAGE followed by western blot against the mutated protein TGFBIp that cause the protein accumulation in the cornea, was examined and compared to normal corneal tissue.

2016-02-19 | PXD001997 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data