PXD001927

PXD001927 is an original dataset announced via ProteomeXchange.

Title	An improved protocol to study the plant cell wall proteome
Description	Cell wall proteins were extracted from alfalfa stems according to a 3-steps extraction procedure using sequentially CaCl2, EGTA and LiCl-complemented buffers. The efficiency of this protocol for extracting cell wall proteins was compared with the 2 previously published methods optimized for alfalfa stem cell wall protein analysis. Following LC-MS/MS analysis the 3-steps extraction procedure resulted in the identification of the highest number of cell wall proteins (242 NCBInr identifiers) and gave the lowest percentage of non-cell wall proteins (about 30%). However, the 3 protocols are rather complementary than substitutive since 43% of the identified proteins were specific to one protocol. This 3-step protocol was therefore selected for a more detailed proteomic characterization using 2D-gel electrophoresis. With this technique, 75% of the identified proteins were shown to be fraction-specific and 72.7% were predicted as belonging to the cell wall compartment. Although being less sensitive than LC-MS/MS approaches in detecting and identifying low-abundant proteins, gel-based approaches are valuable tools for the differentiation and relative quantification of protein isoforms and/or modified proteins. In particular isoforms, having variations in their amino-acid sequence and/or carrying different N-linked glycan chains were detected and characterized. This study highlights how the extracting protocols as well as the analytical techniques devoted to the study of the plant cell wall proteome are complementary and how they may be combined to elucidate the dynamism of the plant cell wall proteome in biological studies.
HostingRepository	PRIDE
AnnounceDate	2015-04-14
AnnouncementXML	Submission_2015-04-14_02:02:49.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001927
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	kjell sergeant
SpeciesList	scientific name: Medicago sativa (Alfalfa); NCBI TaxID: 3879;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-13 02:00:26	ID requested
⏵ 1	2015-04-14 02:02:50	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: proteomics, alfalfa, stem, cell wall, LC-MSMS, 2D-gel electrophoresis

Jenny Renaut
contact affiliation	Luxembourg Institute of Science and Technology “Environmental Research and Innovation” (ERIN) department
contact email	jenny.renaut@list.lu
lab head
kjell sergeant
contact affiliation	Luxembourg Institute of Science and Technology (LIST) Environmental Research and Innovation (ERIN)
contact email	kjell.sergeant@list.lu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/04/PXD001927

PRIDE project URI

• PRIDE
  1. PXD001927
     1. Label: PRIDE project
     2. Name: An improved protocol to study the plant cell wall proteome