PXD055555

PXD055555 is an original dataset announced via ProteomeXchange.

Title	Rhythmic variation in proteomics: challenges and opportunities for statistical power and biomarker identification
Description	Time-of-day variation in the molecular profile of biofluids and 􀆟ssues is a well-described phenomenon, but – especially for proteomics – is rarely considered in terms of the challenges this presents to reproducible biomarker identification. In this work we demonstrate these confounding issues using a small-scale proteomics analysis of male participants in a constant routine protocol following an 8-day laboratory study, in which sleep-wake, light-dark and meal timings were controlled. We provide a case study analysis of circadian and ultradian rhythmicity in proteins in the complement and coagulation cascades, as well as apolipoproteins, and demonstrate that rhythmicity increases the risk of Type II errors due to the reduction in statistical power from increased variance.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_02:55:39.242.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lee Gethings
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-04 09:59:25	ID requested
⏵ 1	2025-05-07 02:55:40	announced

10.1038/s44323-024-00020-2;

Spick M, Isherwood CM, Gethings LA, Hughes CJ, Daly ME, Hassanin H, van der Veen DR, Skene DJ, Johnston JD, Challenges and opportunities for statistical power and biomarker identification arising from rhythmic variation in proteomics. NPJ Biol Timing Sleep, 2(1):3(2025) [pubmed]

submitter keyword: Circadian Rhythm DIA QToF Biomarkers

Lee Gethings
contact affiliation	Discovery, Characterisation & Imaging, Waters Corp
contact email	lee_gethings@waters.com
lab head
Lee Gethings
contact affiliation	Waters Corporation
contact email	lee_gethings@waters.com
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/2025/05/PXD055555

PRIDE project URI

• PRIDE
  1. PXD055555
     1. Label: PRIDE project
     2. Name: Rhythmic variation in proteomics: challenges and opportunities for statistical power and biomarker identification