PXD036822

PXD036822 is an original dataset announced via ProteomeXchange.

Title	High-quality and robust protein quantification in large clinical cohort of serum samples with IonStar
Description	Robust, reliable quantification of large sample cohorts is often essential for meaningful clinical or pharmaceutical proteomics investigations, but it is technically challenging. When analyzing very large numbers of samples, isotope labeling approaches may suffer from substantial batch effects; and even with label-free methods, it becomes evident that low-abundance proteins are not reliably measured due to missing data peaks. The MS1-based quantitative proteomics pipeline, IonStar, was designed to address these challenges. To demonstrate the capability of IonStar to achieve highly reproducible and robust proteomics quantification in large sample cohorts, we applied IonStar to proteomics investigation in serum samples collected from 60 human subjects with moderate acute respiratory distress syndrome (ARDS).
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:05:53.911.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD036822
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xiaoyu Zhu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 15:10:53	ID requested
1	2023-10-12 13:14:46	announced
⏵ 2	2023-11-14 09:05:54	announced	2023-11-14: Updated project metadata.

Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J, High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc, 18(3):700-731(2023) [pubmed]

10.6019/PXD036822;

submitter keyword: large-cohort clinical study

quantitative proteomics

IonStar

liquid chromatography-mass spectrometry

high-resolution mass spectrometry

Jun Qu
contact affiliation	Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, United States
contact email	junqu@buffalo.edu
lab head
Xiaoyu Zhu
contact affiliation	University at Buffalo
contact email	xzhu27@buffalo.edu
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/2023/10/PXD036822

PRIDE project URI

• PRIDE
  1. PXD036822
     1. Label: PRIDE project
     2. Name: High-quality and robust protein quantification in large clinical cohort of serum samples with IonStar