<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ProteomeXchangeDataset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="PXD045192" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" formatVersion="1.4.0">
  <CvList>
    <Cv id="MS" fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-Cv/master/psi-ms.obo"/>
    <Cv id="MOD" fullName="PSI-MOD" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo"/>
    <Cv id="UNIMOD" fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo"/>
  </CvList>
  <DatasetSummary announceDate="2023-10-20" hostingRepository="jPOST" title="Hands-free Proteomic Profiling of Urinary Extracellular Vesicles with a High-throughput Automated Workflow">
    <Description>Extracellular vesicles (EVs) have emerged as a promising source of disease biomarkers for non-invasive early-stage diagnoses, but a bottleneck in EV sample processing restricts their immense potential in clinical applications. Existing methods are limited by low EV yield and integrity, slow processing speeds, low sample capacity, and poor recovery efficiency. We aimed to address these issues with a high-throughput, automated workflow for EV isolation, EV lysis, protein extraction, and protein denaturation. The automation can process clinical urine samples in parallel, resulting in protein-covered beads ready for various analytical methods, including immunoassays, protein quantitation assays, and mass spectrometry. Compared to the standar&#xAD;&#xAD;&#xAD;d manual lysis method for contamination levels, efficiency, and consistency of EV isolation, the automated protocol shows reproducible and robust proteomic quantitation with less than 10% median coefficient of variation. When we applied the method to clinical samples, we identified a total 3,793 unique proteins and 40,380 unique peptides, with 992 significantly upregulated proteins in kidney cancer patients versus healthy controls. These upregulated proteins were found to be involved in several important kidney cancer metabolic pathways also identified with a manual control. This hands-free workflow represents a practical EV extraction and profiling approach that can benefit both clinical and research applications, streamlining biomarker discovery, tumor monitoring, and early cancer diagnoses.</Description>
    <ReviewLevel>
      <cvParam cvRef="MS" accession="MS:1002855" name="Non peer-reviewed dataset"/>
    </ReviewLevel>
    <RepositorySupport>
      <cvParam cvRef="MS" accession="MS:1002857" name="Unsupported dataset by repository"/>
    </RepositorySupport>
  </DatasetSummary>
  <DatasetIdentifierList>
    <DatasetIdentifier>
      <cvParam accession="MS:1001919" cvRef="MS" name="ProteomeXchange accession number" value="PXD045192"/>
      <cvParam accession="MS:1001921" cvRef="MS" name="ProteomeXchange accession number version number" value="1"/>
    </DatasetIdentifier>
    <DatasetIdentifier>
      <cvParam accession="MS:1002632" cvRef="MS" name="jPOST dataset identifier" value="JPST002311"/>
    </DatasetIdentifier>
  </DatasetIdentifierList>
  <DatasetOriginList>
    <DatasetOrigin>
      <cvParam cvRef="MS" accession="MS:1002868" name="Original data"/>
    </DatasetOrigin>
  </DatasetOriginList>
  <SpeciesList>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Homo sapiens (Human)"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9606"/>
    </Species>
    <Species>
      <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="cellular organisms"/>
      <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="131567"/>
    </Species>
  </SpeciesList>
  <InstrumentList>
    <Instrument id="Instrument_1">
      <cvParam cvRef="MS" accession="MS:1000463" name="instrument"/>
    </Instrument>
  </InstrumentList>
  <ModificationList>
    <cvParam cvRef="MOD" accession="MOD:01060" name="S-carboxamidomethyl-L-cysteine"/>
    <cvParam cvRef="MOD" accession="MOD:00719" name="L-methionine sulfoxide"/>
  </ModificationList>
  <ContactList>
    <Contact id="project_submitter">
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Marco Hadisurya"/>
      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Purdue University"/>
      <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
    </Contact>
    <Contact id="project_lab_head">
      <cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="W. Andy Tao"/>
    </Contact>
  </ContactList>
  <PublicationList>
    <Publication id="pending">
      <cvParam cvRef="MS" accession="MS:1002858" name="Dataset with its publication pending"/>
    </Publication>
  </PublicationList>
  <KeywordList>
    <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="kidney cancer, proteomics, urine, renal cell carcinoma, DIA, automation, TimsTOF, high-throughput, EVtrap, extracellular vesicles, exosomes"/>
  </KeywordList>
  <FullDatasetLinkList>
    <FullDatasetLink>
      <cvParam accession="MS:1002633" cvRef="MS" name="jPOST dataset URI" value="https://repository.jpostdb.org/entry/JPST002311"/>
    </FullDatasetLink>
    <FullDatasetLink>
      <cvParam cvRef="MS" accession="MS:1002852" name="Dataset FTP location" value="ftp://ftp.jpostdb.org/JPST002311/"/>
    </FullDatasetLink>
  </FullDatasetLinkList>
</ProteomeXchangeDataset>