PXD047793

PXD047793 is an original dataset announced via ProteomeXchange.

Title	A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Description	Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in triple negative breast cancer (TNBC) tissues. Primary tumor tissue lysates from 105 TNBC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, were used to generate the spectral library. This project covers raw files from data-dependent acquisition (DDA) – parallel accumulation-serial fragmentation (PASEF) measurements of 12 hydrophilic chromatography (HILIC) fractions of aliquot pool from complete set of 105 samples measured on timsTOF Pro; raw files of 16 individual samples measured in data-independent acquisition (DIA) – PASEF mode and used for hybrid library generation and for demonstrative quantitative DIA data extraction; Pulsar archive generated in Spectronaut 16.0 from 12 DDA-PASEF measurements of HILIC fractions and from 16 data-independent acquisition DIA-PASEF measurements of individual samples. The 16 DIA-PASEF runs of individual samples used for library generation were analyzed using newest versions of Spectronaut (version 18.5) and DIA-NN (version 1.8.1) software tools in library-based setting using the newly generated library as well as in library-free setting showing library-based method to outperform the use of predicted libraries in the terms of identification numbers.
HostingRepository	PRIDE
AnnounceDate	2024-05-31
AnnouncementXML	Submission_2024-05-31_09:44:55.055.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pavel Bouchal
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-13 08:14:32	ID requested
⏵ 1	2024-05-31 09:44:55	announced

Dataset with its publication pending

submitter keyword: proteomics, mass spectrometry,data independent acquisition, assay library, triple-negative breast cancer

Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science
contact email	bouchal@chemi.muni.cz
lab head
Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science
contact email	bouchal@chemi.muni.cz
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/2024/05/PXD047793

PRIDE project URI

• PRIDE
  1. PXD047793
     1. Label: PRIDE project
     2. Name: A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer