PXD039414

PXD039414 is an original dataset announced via ProteomeXchange.

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	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:45:34.427.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kevin Contrepois
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

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.

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]

submitter keyword: DIA, biofluids, 7600 ZenoTOF,Tissues, Zeno SWATH

Kevin Contrepois
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
Kevin Contrepois
contact affiliation	AstraZeneca
contact email	kevin.contrepois@astrazeneca.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD039414
     1. Label: PRIDE project
     2. Name: Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition