PXD001471

PXD001471 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS: Preparation of more than 4000 native protein maps
Description	Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm X 40 mm area of the CBB-stained slab gel (1.0 mm thick) was cut into 1.1 mm X 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [Jin, et al. Electrophoresis 2014, 35, 2055-2064, PRIDE Project PXD000852]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6 % to 1 X 10-5 % of the total protein quantity in the grid area. Each protein map was characterized by many features, such as the position of quantity peak square, number of detected squares, degree of concentration (focused or dispersed), etc. About 4 percent of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2DE gel, which would further provide information on their interactions.
HostingRepository	PRIDE
AnnounceDate	2015-08-10
AnnouncementXML	Submission_2015-08-10_17:02:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ya Jin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt G2-S HDMS

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-10 02:20:56	ID requested
1	2015-08-10 15:59:24	announced
2	2015-08-10 17:02:00	announced	Updated publication reference for PubMed record(s): 25931155.
⏵ 3	2015-08-10 17:02:33	announced	Updated publication reference for PubMed record(s): 25931155.

Jin Y, Yuan Q, Zhang J, Manabe T, Tan W, Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes. Electrophoresis, 36(17):1991-2001(2015) [pubmed]

Jin Y, Zhang J, Yuan Q, Manabe T, Tan W, Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 1. Preparation of more than 4000 native protein maps. Electrophoresis, 36(15):1711-23(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: cellular proteins, LC-MS/MS, native protein map, nondenaturing micro 2DE, quantitative protein-protein interaction

Ya Jin
contact affiliation	School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, P. R. China
contact email	ya.jin@ymail.com
lab head
Ya Jin
contact affiliation	School of Bioscience and Biotechnology, South China University of Technology
contact email	ya.jin@ymail.com
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/2015/08/PXD001471

PRIDE project URI

• PRIDE
  1. PXD001471
     1. Label: PRIDE project
     2. Name: Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS: Preparation of more than 4000 native protein maps