ArticleScientific data2024
A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer.
Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A porcine spectral assay library to quantify brain proteome by DIA-MS.Scientific data · 2026Article
- Carafe2 enables high qualitybioRxiv : the preprint server for biology · 2026Article
- Creatine kinase B, a downstream effector of c-Myb, controls migration of osteosarcoma cells via regulation of N-cadherin.Cancer cell international · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.Nature communications · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.bioRxiv : the preprint server for biology · 2024Article
- A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer.Scientific data · 2024Article
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Authors and funding
7 authors.
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Abstract
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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