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PXD070173-1
PXD070173 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients |
| Description | Recent advances in liquid chromatography–mass spectrometry (LC-MS) have accelerated the adoption of high-throughput workflows that deliver deep proteome coverage using minimal sample amounts. This trend is largely driven by single-cell proteomics, where sensitivity and reproducibility are essential. Here, we extend our previous benchmark dataset (PXD028735) that was generated using next-generation LC-MS platforms optimized for rapid proteome analysis. With shorter LC gradients and lower sample amounts, we generated an extensive DDA/DIA dataset on a standardized human-yeast-E. coli hybrid proteome. This new dataset includes data acquired by the Orbitrap Astral, which combines an Orbitrap with a time-of-flight (TOF) mass analyzer, and features new scanning quadrupole-based implementations, extending coverage across different instruments and acquisition strategies. Our comprehensive evaluation highlights how technological advances and reduced LC gradients affect proteome depth, quantitative precision, and cross-instrument consistency. The release of this benchmark dataset via ProteomeXchange (PXD070049), allows for the acceleration of cross-platform algorithm development, enhance data mining strategies, and support the continued standardization of short-gradient, high-throughput LC-MS-based proteomics.  |
| HostingRepository | PanoramaPublic |
| AnnounceDate | 2025-10-31 |
| AnnouncementXML | Submission_2025-10-31_17:05:44.799.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Bart Van Puyvelde |
| SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; |
| ModificationList | Carbamidomethyl |
| Instrument | ZenoTOF 7600+; ZenoTOF 8600; timsTOF Ultra; timsTOF Ultra 2; Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-10-31 16:12:40 | ID requested | |
| ⏵ 1 | 2025-10-31 17:05:45 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: DDA, DIA, Label-free quantification, Benchmarking dataset |
Contact List
| Maarten Dhaenens | |
|---|---|
| contact affiliation | ProGenTomics, Laboratory of Pharmaceutical Biotechnology |
| contact email | maarten.dhaenens@ugent.be |
| lab head | |
| Bart Van Puyvelde | |
| contact affiliation | ProGenTomics, Laboratory of Pharmaceutical Biotechnology |
| contact email | bart.vanpuyvelde@ugent.be |
| dataset submitter | |
Full Dataset Link List
| Panorama Public dataset URI |
