PXD005290

PXD005290 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of culture filtrates from M.tuberculosis H37Rv
Description	In this report, a novel tandem cascade of biomimetic affinity chromatography (BiAC) system was used to fractionate the culture filtrate proteins (CFPs) of M. tuberculosis (MTB) prior to LC-MS/MS analysis. Consequently, in fractionations by 6 BiAC columns, 541 proteins from CFPs were identified using stringent database research by Mascot and scaffold software with ƿ < 0.05, each protein was determined with two distinct peptide sequences. And 248 proteins were identified in un-fractionated culture filtrates. Compared with un-fractionated sample, both proteomic coverage and accuracy of MS analysis were remarkably improved using BiAC fractionations. In 242 identifications by both BiAC fractionations and un-fractionated samples, the average number of matched peptide sequence was increased from 14 hits to 44 hits after BiAC fractionation. The average coverage of peptide sequence of these 242 proteins was also increased from 19.6% (un-fractionation) to 26.1% (fractionation). Compared with previous identifications in CFPs, 11.15% (61/547) identifications in this study have not been reported. The majority of these newly identifications possess extremely biochemical characteristics that usually are not suitable be fractionated by gel-based proteomic approach, of which 12 proteins with Mw<10kDa or Mw>140kDa, 10 with pI<4.0 or pI>10. And 20 membrane proteins, of which have 9 with 2-14 transmembrane domains. Taken together, the BiAC system can enhance the proteomic detection coverage especially by reducing the complexity of sample, improving the low copy and extremely biochemical characteristic proteins.
HostingRepository	PRIDE
AnnounceDate	2018-07-05
AnnouncementXML	Submission_2018-07-05_03:28:13.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD005290
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	guorong ma
SpeciesList	scientific name: Salmonella enterica subsp. enterica serovar Untypable str. 83332; NCBI TaxID: 1192767; scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: 83332;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2016-11-08 02:21:06	ID requested
⏵ 1	2018-07-05 03:28:14	announced

Ma G, Zhang K, Zhou F, Gao L, Sun Z, Deng L, Zhang S, Li R, Improving basic and membrane protein MS detection of the culture filtrate proteins from Mycobacterium tuberculosis H37Rv by biomimetic affinity prefractionation. Proteomics, 17(10):e1600177(2017) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP)

curator keyword: Biological, Biomedical

submitter keyword: Biomimetic affinity chromatography, Culture filtrate proteins of Mycobacterium tuberculosis, low-abundant proteins, Extreme biochemical characteristics proteins

Rongxiu Li
contact affiliation	State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
contact email	rxli@sjtu.edu.cn
lab head
guorong ma
contact affiliation	shanghai jiaotong university
contact email	guorongma8000@sjtu.edu.cn
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/2018/07/PXD005290

PRIDE project URI

• PRIDE
  1. PXD005290
     1. Label: PRIDE project
     2. Name: Proteomic profiling of culture filtrates from M.tuberculosis H37Rv