PXD018830

PXD018830 is an original dataset announced via ProteomeXchange.

Title	DIA-MS analysis of 21 breast cancer tissues
Description	In recent years genomic and proteomic technologies have been employed in a combined effort to extrapolate key clinical and biological information of complex diseases such as cancer. Most integrative studies employ DNA and/or RNA sequencing technologies coupled to mass spectrometry-derived information to achieve deep information extraction levels, resulting in massive experimental efforts. In this context the employment of data independent acquisition (DIA) methods, which generally do not rely on fractionation, has seldom been tested. In this study, we evaluated the ability of DIA and data dependent acquisition (DDA) MS in determining key biological features of a set of 21 breast cancer tissues for whose RNA-sequencing data was also collected. We evaluated how proteomic data layers matched RNA analysis-derived genomic information, their degree of consensus, and their discrepancies.
HostingRepository	PRIDE
AnnounceDate	2021-04-26
AnnouncementXML	Submission_2021-04-25_21:43:18.044.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tommaso De Marchi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-27 06:27:02	ID requested
⏵ 1	2021-04-25 21:43:18	announced

De Marchi T, Pyl PT, Sj, ö, str, ö, m M, Klasson S, Sartor H, Tran L, Pekar G, Malmstr, ö, m J, Malmstr, ö, m L, Nim, é, us E, Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance. J Proteome Res, 20(5):2983-3001(2021) [pubmed]

submitter keyword: Breast cancer, human, proteome, data independent acquisition

Emma Niméus
contact affiliation	Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences. Biomedical Center – Lund University, Solvegatan 19, 223 62, Lund, Sweden
contact email	emma.nimeus@med.lu.se
lab head
Tommaso De Marchi
contact affiliation	Lund University
contact email	tommaso.de_marchi@med.lu.se
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/2021/04/PXD018830

PRIDE project URI

• PRIDE
  1. PXD018830
     1. Label: PRIDE project
     2. Name: DIA-MS analysis of 21 breast cancer tissues