PXD039414 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition |
Description | Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nano and micro flow regimes, but they often lack throughput and chromatographic robustness, which is critical for large-scale studies. In this context, we have developed, optimized and benchmarked LC-MS methods combining the robustness and throughput of analytical flow chromatography with the added sensitivity provided by the Zeno trap across a wide range of cynomolgus monkey and human matrices of interest for toxicological studies and clinical biomarker discovery. SWATH data independent acquisition (DIA) experiments with Zeno trap activated (Zeno SWATH DIA) provided a clear advantage over conventional SWATH DIA in all sample types tested with improved sensitivity, quantitative robustness and signal linearity as well as increased protein coverage by up to 9-fold. Using a 10-min gradient chromatography, up to 3,300 proteins were identified in tissues at 2 µg peptide load. Importantly, the performance gains with Zeno SWATH translated into better biological pathway representation and improved the ability to identify dysregulated proteins and pathways associated with two metabolic diseases in human plasma. Finally, we demonstrate that this method is highly stable over time with the acquisition of reliable data over the injection of 1,000+ samples (14.2 days of uninterrupted acquisition) without the need for human intervention or normalization. Altogether, Zeno SWATH DIA methodology allows fast, sensitive and robust proteomic workflows using analytical flow and is amenable to large-scale studies. This work provides detailed method performance assessment on a variety of relevant biological matrices and serves as a valuable resource for the proteomics community. |
HostingRepository | PRIDE |
AnnounceDate | 2023-05-09 |
AnnouncementXML | Submission_2023-05-08_20:01:46.009.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | KevinContrepois |
SpeciesList | scientific name: Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey); NCBI TaxID: 9541; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | TripleTOF 6600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-01-13 06:48:35 | ID requested | |
⏵ 1 | 2023-05-08 20:01:47 | announced | |
2 | 2023-11-14 08:45:39 | announced | 2023-11-14: Updated project metadata. |
Publication List
Sun W, Lin Y, Huang Y, Chan J, Terrillon S, Rosenbaum AI, Contrepois K, Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices With Zeno SWATH Data-Independent Acquisition. Mol Cell Proteomics, 22(6):100562(2023) [pubmed] |
Keyword List
submitter keyword: DIA, biofluids, 7600 ZenoTOF,Tissues, Zeno SWATH |
Contact List
KevinContrepois |
contact affiliation | Group Director OMICS, Integrated Bioanalysis AstraZeneca R&D / Clinical Pharmacology & Safety Sciences 121 Oyster Point Blvd. South San Francisco, CA 94080, USA |
contact email | kevin.contrepois@astrazeneca.com |
lab head | |
KevinContrepois |
contact affiliation | AstraZeneca |
contact email | kevin.contrepois@astrazeneca.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039414
- Label: PRIDE project
- Name: Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition