PXD056978-1

PXD056978 is an original dataset announced via ProteomeXchange.

Title	Rapid Tear Proteomics via In-Capillary Digestion for Biomarker Discovery
Description	Tear 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.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_04:19:39.984.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	James Xiao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	6220 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

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-20 04:56:09	ID requested
⏵ 1	2025-05-07 04:19:40	announced

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]

submitter keyword: 1. tear proteomics

2. tear biomarker

3. biomarker discovery

4. point-of-care testing

5. POCT

6. LC-MS/MS

Leanne T. Labriola
contact affiliation	Sewickley Eye Group
contact email	labriola@pghtrials.com
lab head
James Xiao
contact affiliation	Sewickley Eye Group
contact email	jamesxiao039@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD056978

PRIDE project URI

• PRIDE
  1. PXD056978
     1. Label: PRIDE project
     2. Name: Rapid Tear Proteomics via In-Capillary Digestion for Biomarker Discovery