PXD001928

PXD001928 is an original dataset announced via ProteomeXchange.

Title	Near complete quantitative proteomics for Yeast
Description	In this study, we attempted to achieve to date the most comprehensive coverage of the yeast proteome during log-phase growth and in the K11R mutant ubiquitin yeast strain with a combination of (1) extensive gel molecular weight fractionation and use of either of two digestion enzymes to improve coverage by addressing the issue of dynamic range via decreased sample complexity, (2) use of a more sensitive and faster LC-MS/MS platform than available for many of the previous experiments (Orbitrap Velos coupled to a nanoAcquity UPLC). By this approach, we identified with high confidence a new fungal conserved gene expressed in S. cerevisiae and achieved the highest coverage of the yeast proteome (83.5%) to date. Besides that, we also extended our experimental workflow incorporating the same advantages to identify and quantify proteins in a K11R/reference SILAC/control total yeast lysate mixture.
HostingRepository	PRIDE
AnnounceDate	2021-01-18
AnnouncementXML	Submission_2021-01-17_23:19:44.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001928
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Zhang Chengpu Zhang Chengpu
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	Oxidation; Label:13C(6); Carbamidomethyl
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-03-13 02:19:55	ID requested
1	2019-08-26 00:57:35	announced
⏵ 2	2021-01-17 23:19:45	announced	2021-01-18: Updated publication reference for PubMed record(s): 31444107, 33443437.

Gao Y, Ping L, Duong D, Zhang C, Dammer EB, Li Y, Chen P, Chang L, Gao H, Wu J, Xu P, Proteome. J Proteome Res, 20(2):1328-1340(2021) [pubmed]

Li Y, Dammer EB, Gao Y, Lan Q, Villamil MA, Duong DM, Zhang C, Ping L, Lauinger L, Flick K, Xu Z, Wei W, Xing X, Chang L, Jin J, Hong X, Zhu Y, Wu J, Deng Z, He F, Kaiser P, Xu P, Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation. Mol Cell, 76(1):126-137.e7(2019) [pubmed]

curator keyword: Biological

submitter keyword: Yeast, LC-MS/MS, High coverage, proteome, SILAC

Ping Xu
contact affiliation	Beijing proteome research center, Beijing, China
contact email	xuping_bprc@126.com
lab head
Zhang Chengpu Zhang Chengpu
contact affiliation	Beijing proteome research center
contact email	zhangchengpu0203@163.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/2019/08/PXD001928

PRIDE project URI

• PRIDE
  1. PXD001928
     1. Label: PRIDE project
     2. Name: Near complete quantitative proteomics for Yeast