PXD043925

PXD043925 is an original dataset announced via ProteomeXchange.

Title	Urine-HILIC – An automated sample preparation for bottom-up urinary proteome profiling in clinical proteomics
Description	Urine provides a diverse source of information related to health status and is ideal for clinical proteomics because of its ease of collection. To date, there is no standard operating procedure for reproducible and robust urine sample processing for mass spectrometry-based clinical proteomics. To address this need, a novel workflow was developed based on an on-bead protein capture, clean up, and digestion without the requirement from pre-processing steps such as precipitation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample were subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using a novel urine-HILIC (uHLC) approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analysed by LCMS in DIA mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. Data was searched in Spectronaut™ 17. Following statistical analysis, candidate protein markers were filtered at ≥ 2-fold change in abundance, ≥ 2 uniques peptides and ≤ 1% false discovery rate. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method. With fewer manuel processiing steps, a lower peptide and protein CV was observed in the uHLC technical replicates. Analysis of clinical samples revealed many significant, differentially abundant kidney injury-associated urinary proteins. The pilot data derived using this novel workflow provides information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:27:33.986.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Previn Naicker
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 14:05:07	ID requested
1	2024-01-26 10:32:56	announced
⏵ 2	2024-10-22 06:27:34	announced	2024-10-22: Updated project metadata.

Govender IS, Mokoena R, Stoychev S, Naicker P, Urine-HILIC: Automated Sample Preparation for Bottom-Up Urinary Proteome Profiling in Clinical Proteomics. Proteomes, 11(4):(2023) [pubmed]

10.3390/proteomes11040029;

submitter keyword: automated sample preparation

clinical proteomics

SWATH-MS (DIA)

urinary proteomics

HILIC

Previn Naicker
contact affiliation	NextGen Health, CSIR, South Africa
contact email	pnaicker1@csir.co.za
lab head
Previn Naicker
contact affiliation	Council for Scientific and Industrial Research
contact email	pnaicker1@csir.co.za
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/2024/01/PXD043925

PRIDE project URI

• PRIDE
  1. PXD043925
     1. Label: PRIDE project
     2. Name: Urine-HILIC – An automated sample preparation for bottom-up urinary proteome profiling in clinical proteomics