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PXD052666-1

PXD052666 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimization of the workflow for deep CSF proteome analysis by enrichment of extracellular vesicles
DescriptionProteome 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-16
AnnouncementXMLSubmission_2024-10-16_13:12:31.934.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterOle Østergaard
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-05-29 02:54:21ID requested
12024-10-16 13:12:32announced
Publication List
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;
Keyword List
submitter keyword: Mass Spectrometry, Extracellular Vesicles, Ultracentrifugation,Cerebrospinal Fluid, Proteome, Data Independent Acquisition, Exploris 480, Biomarkers
Contact List
Jesper Velgaard Olsen
contact affiliationNovo Nordisk Foundation, Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen Blegdamsvej 3B, DK-2200 Copenhagen N Denmark
contact emailjesper.olsen@cpr.ku.dk
lab head
Ole Østergaard
contact affiliationNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
contact emailole.ostergaard@cpr.ku.dk
dataset submitter
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Dataset FTP location
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