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PXD056978

PXD056978 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRapid Tear Proteomics via In-Capillary Digestion for Biomarker Discovery
DescriptionTear fluid is emerging as a valuable resource for biomarker discovery, but its low sample volume and dynamic composition pose significant challenges for analytical testing. Most tear proteomics studies have focused on samples collected with Schirmer strips, while capillary tube collection has received less attention. To address these challenges, we developed a novel in-capillary trypsin digestion workflow that requires as little as 0.5 μL of tear fluid for bottom-up shotgun proteomics. This method uses liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify a higher number of proteins with enhanced efficiency compared to previously reported methods, which typically required 5-10 μL of pooled tear fluid. Using the same microcentrifuge tube for both tear collection and sample processing, this streamlined workflow simplifies sample handling and minimizes both sample loss and experimental errors associated with sample transfer. This method also efficiently reduced sample processing time to under 2 hours prior to overnight trypsin di-gestion, compared to the 5-8 hours required by other methods. With this workflow, we identified 500-800 proteins per 0.5 μL sample without the need for fractionation, allowing for at least three technical replicates. This optimized workflow greatly enhances the efficiency of tear proteomics for biomarker discovery.
HostingRepositoryPRIDE
AnnounceDate2025-05-07
AnnouncementXMLSubmission_2025-05-07_04:19:39.984.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
02024-10-20 04:56:09ID requested
12025-05-07 04:19:40announced
Publication List
10.3390/ijms252212239;
Xiao J, Frenia K, Garwood KC, Kimmel J, Labriola LT, High-Throughput Tear Proteomics via In-Capillary Digestion for Biomarker Discovery. Int J Mol Sci, 25(22):(2024) [pubmed]
Keyword List
submitter keyword: 1. tear proteomics
2. tear biomarker
3. biomarker discovery
4. point-of-care testing
5. POCT
6. LC-MS/MS
Contact List
Leanne T. Labriola
contact affiliationSewickley Eye Group
contact emaillabriola@pghtrials.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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