PXD052666

PXD052666 is an original dataset announced via ProteomeXchange.

Title	Optimization of the workflow for deep CSF proteome analysis by enrichment of extracellular vesicles
Description	Proteome analysis of cerebrospinal fluid is associated with many of the same challenges that has to be faced when analyzing other biofluids like plasma or urine. Most importantly is the high dynamic range of protein concentrations, which makes it difficult to quantify more than a thousand proteins in a singleshot analysis of a tryptic digest of a raw sample. In addition, cerebrospinal fluid—especially when collected from children—is a much more scarce and precious sample as compare to urine and plasma. The aim of this work therefore was to find the optimal way to process and analyze cerebrospinal fluid from a minimal amount of sample and still obtain the deepest possible cerebrospinal fluid proteome. The work shows that enrichment of extracellular vesicles by ultracentrifugation increases the complexity of the cerebrospinal fluid proteome by two-fold or more. Thus, by following the enrichment protocol, more than two thousand proteins can routinely be quantified reproducibly by label-free quantification and data independent acquisition (DIA) in single-shot LC-MSMS runs of less than one hour. The project also present an optimized workflow for cerebrospinal fluid proteomics that enables a high-throughput method with a short chromatographic gradient (12 min) allowing analysis of hundred samples per day and still obtaining deep proteome coverage, especially when including a study-specific spectral library generated by repeated injection and gas-phase fractionation of pooled samples.
HostingRepository	PRIDE
AnnounceDate	2024-10-16
AnnouncementXML	Submission_2024-10-16_13:12:31.934.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ole Østergaard
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-29 02:54:21	ID requested
⏵ 1	2024-10-16 13:12:32	announced

Mirian C, Ø, stergaard O, Thastrup M, Modvig S, Foss-Skiftesvik J, Skj, ø, th-Rasmussen J, Berntsen M, Britze J, Yde Nielsen AC, Mathiasen R, Schmiegelow K, Olsen JV, Deep Proteome Analysis of Cerebrospinal Fluid from Pediatric Patients with Central Nervous System Cancer. J Proteome Res, ():(2024) [pubmed]

10.1021/acs.jproteome.4c00471;

submitter keyword: Mass Spectrometry, Extracellular Vesicles, Ultracentrifugation,Cerebrospinal Fluid, Proteome, Data Independent Acquisition, Exploris 480, Biomarkers

Jesper Velgaard Olsen
contact affiliation	Novo Nordisk Foundation, Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Blegdamsvej 3B, DK-2200 Copenhagen N Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Ole Østergaard
contact affiliation	Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
contact email	ole.ostergaard@cpr.ku.dk
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/2024/10/PXD052666

PRIDE project URI

• PRIDE
  1. PXD052666
     1. Label: PRIDE project
     2. Name: Optimization of the workflow for deep CSF proteome analysis by enrichment of extracellular vesicles