PXD060101

PXD060101 is an original dataset announced via ProteomeXchange.

Title	Precision in Tear Fluid Biomarker Discovery: Quantitative Proteomic Profiling of Small-Volume, Individual Samples Using Capillary Tube Collection
Description	Tear 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.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_07:28:21.548.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	2025-01-23 01:03:24	ID requested
⏵ 1	2025-05-07 07:28:22	announced

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]

submitter keyword: 1. tear proteomics

2. tear biomarker

3. biomarker discovery

4. capillary collection

5. LC-MS/MS

Kunhong Xiao
contact affiliation	Allegheny Health Network
contact email	kevin.kh.xiao@gmail.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/PXD060101

PRIDE project URI

• PRIDE
  1. PXD060101
     1. Label: PRIDE project
     2. Name: Precision in Tear Fluid Biomarker Discovery: Quantitative Proteomic Profiling of Small-Volume, Individual Samples Using Capillary Tube Collection