Proteomics

Dataset Information

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Optimization of the workflow for deep CSF proteome analysis by enrichment of extracellular vesicles


ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cerebrospinal Fluid

DISEASE(S): Acute Leukemia

SUBMITTER: Ole Østergaard  

LAB HEAD: Jesper Velgaard Olsen

PROVIDER: PXD052666 | Pride | 2024-10-16

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
12m_E_DDA_peptides.txt Txt
12m_E_DDA_proteinGroups.txt Txt
12m_M_DDA__proteinGroups.txt Txt
12m_M_DDA_peptides.txt Txt
12m_R_DDA_peptides.txt Txt
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Publications


The cerebrospinal fluid (CSF) is a key matrix for discovery of biomarkers relevant for prognosis and the development of therapeutic targets in pediatric central nervous system malignancies. However, the wide range of protein concentrations and age-related differences in children makes such discoveries challenging. In addition, pediatric CSF samples are often sparse and first prioritized for clinical purposes. The present work focused on optimizing each step of the proteome analysis workflow to e  ...[more]

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