A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer

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Publikace nespadá pod Fakultu sportovních studií, ale pod Přírodovědeckou fakultu. Oficiální stránka publikace je na webu muni.cz.
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LAPČÍK Petr SYNKOVÁ Klára JANÁČOVÁ Lucia BOUCHALOVÁ Pavla POTĚŠIL David NENUTIL Rudolf BOUCHAL Pavel

Rok publikování 2024
Druh Článek v odborném periodiku
Časopis / Zdroj Scientific Data
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www https://www.nature.com/articles/s41597-024-03632-2
Doi http://dx.doi.org/10.1038/s41597-024-03632-2
Klíčová slova Biochemical networks; Predictive markers
Přiložené soubory
Popis 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).
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