A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209805%3A_____%2F24%3A00079893" target="_blank" >RIV/00209805:_____/24:00079893 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14310/24:00136596
Result on the web
<a href="https://www.nature.com/articles/s41597-024-03632-2" target="_blank" >https://www.nature.com/articles/s41597-024-03632-2</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s41597-024-03632-2" target="_blank" >10.1038/s41597-024-03632-2</a>
Alternative languages
Result language
angličtina
Original language name
A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Original language description
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
30204 - Oncology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Scientific data
ISSN
2052-4463
e-ISSN
2052-4463
Volume of the periodical
11
Issue of the periodical within the volume
1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
7
Pages from-to
794
UT code for WoS article
001272767500005
EID of the result in the Scopus database
2-s2.0-85199055889