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PXD060101

PXD060101 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlePrecision in Tear Fluid Biomarker Discovery: Quantitative Proteomic Profiling of Small-Volume, Individual Samples Using Capillary Tube Collection
DescriptionTear fluid, a complex biofluid that contains thousands of proteins and can be collected non-invasively, has emerged as a promising source of biomarkers for ocular and systemic health. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is currently the primary method for discovering novel biomarkers in tear fluid. However, the method of tear collection can sig-nificantly impact LC-MS/MS analysis outcomes. Tear fluid is commonly collected using either Schirmer strips or capillary tubes. While capillary tubes offer distinct advantages, such as reduced extracellular contamination and reflex tearing, most LC-MS/MS protocol development has focused on optimizing protocols for Schirmer strips. This study addresses this gap by evaluating digestion protocols for tear fluid collected with capillary tubes, focusing on biomarker discovery using small-volume samples. In this study, we evaluated multiple digestion protocols for the shotgun quantitative LC-MS/MS analysis of small-volume tear fluid samples collected using glass capillary tubes. Protocol optimization was performed using pooled samples and then compared with the analysis of individual samples. Using the optimized protocol, 0.5μL were processed using a timsTOF Pro 2 mass spectrometer (Bruker) coupled online with an Evosep One liquid chroma-tography system (Evosep), leading to the identification of an average of 368 ± 87 proteins in pooled samples and 502 ± 127 proteins in individual small-volume tear fluid samples. This protocol highlights the practicality of using glass capillary tubes for comprehensive LC-MS/MS-based tear proteomics analysis, paving the way for detailed proteomics characterization of individual tear fluid samples rather than pooled samples. By shifting from pooled to individual samples, this approach greatly accelerates tear biomarker discovery, advancing precision and personalized medicine.
HostingRepositoryPRIDE
AnnounceDate2025-05-07
AnnouncementXMLSubmission_2025-05-07_07:28:21.548.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJames Xiao
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
Instrument6220 Time-of-Flight LC/MS; MALDI Synapt MS; Synapt MS; Q Exactive HF; LCQ Classic; TripleTOF 5600; 6410 Triple Quadrupole LC/MS; Q Exactive; LTQ Orbitrap; 4800 Proteomics Analyzer; 6340 Ion Trap LC/MS; Orbitrap Fusion Lumos; LTQ; LTQ Orbitrap Velos; Q TRAP; Q-Tof Ultima; timsTOF Pro 2; maXis; LTQ FT; autoflex; ultraflex; QSTAR; 4700 Proteomics Analyzer; Orbitrap Fusion; 6520A Quadrupole Time-of-Flight LC/MS; LTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02025-01-23 01:03:24ID requested
12025-05-07 07:28:22announced
Publication List
10.3390/biomedicines13020386;
Frenia K, Fu Y, Beatty MA, Garwood KC, Kimmel J, Raiji V, Pan D, Bartlett D, Labriola LT, Xiao K, Precision in Tear Fluid Biomarker Discovery: Quantitative Proteomic Profiling of Small-Volume, Individual Samples Using Capillary Tube Collection. Biomedicines, 13(2):(2025) [pubmed]
Keyword List
submitter keyword: 1. tear proteomics
2. tear biomarker
3. biomarker discovery
4. capillary collection
5. LC-MS/MS
Contact List
Kunhong Xiao
contact affiliationAllegheny Health Network
contact emailkevin.kh.xiao@gmail.com
lab head
James Xiao
contact affiliationSewickley Eye Group
contact emailjamesxiao039@gmail.com
dataset submitter
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Dataset FTP location
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