PXD045472-1

PXD045472 is an original dataset announced via ProteomeXchange.

Title	High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH
Description	We investigated the combined sensitivity of micro-flow liquid chromatography with a ZenoTOF mass spectrometer for high throughput proteomic and phosphoproteomic analysis of rat tissues. Comparing the proteomes acquired using data-independent acquisition (DIA) on the ZenoTOF 7600 with the previous generation TripleTOF 6600, more proteins were quantified using a fifth of the sample load and a third of the instrument time. Zeno SWATH data was evaluated using replicate injections of rat organ digests to compare FragPipe and DIA-NN computational pipelines. FragPipe identified more proteins in 7 of the 8 rat organs, with an extra 12% and 17% observed in heart and muscle tissue respectively. The number of identified peptides per protein were higher with FragPipe and the precision of missing values across replicate injections was more consistent. Single-shot phosphopeptide enrichment from 100 µg rat tissue, without fractionation, was acquired using data-dependent acquisition (DDA) on both instruments. A total of 5,108 phosphosites were quantified with a negligible increase in phosphosites found using the ZenoTOF 7600 relative to the 6600. Using DIA on the ZenoTOF, 8,013 phosphosites were quantified using Spectronaut.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:18:38.976.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erin Humphries
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	phosphorylated residue; iodoacetamide derivatized residue
Instrument	SCIEX instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-18 11:43:14	ID requested
⏵ 1	2024-10-08 11:18:39	announced

10.1021/ACS.JPROTEOME.4C00010;

submitter keyword: proteomics,rat, phosphoproteomics, Zeno SWATH

Phillip J.
contact affiliation	ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia.
contact email	probinson@cmri.org.au
lab head
Erin Humphries
contact affiliation	The University of Sydney
contact email	ehum9128@uni.sydney.edu.au
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD045472

PRIDE project URI

• PRIDE
  1. PXD045472
     1. Label: PRIDE project
     2. Name: High-throughput proteomics and phosphoproteomics of rat tissues using micro-flow Zeno SWATH