Dataset Information

Profiling tear proteomes of patients with unilateral relapsed Behcet's disease-associated uveitis using data-independent acquisition proteomics.

ABSTRACT: Purpose:To explore whether unilateral relapse of Bechet's disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring. Method:To minimize interindividual variations, bilateral tear samples were collected from the same patient (n = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes. Results:A total of 1,797 confident proteins were identified in the tear samples, of which 381 (21.2%) were also highly expressed in various tissues and organs. Fifty-one (2.8%) proteins differed in terms of expression between tears in active and quiescent eyes, 9 (17.6%) of which were functionally related to immunity or inflammation. Alpha-1-acid glycoprotein 1 (fold change = 3.2, p = 0.007) was increased and Annexin A1 (fold change = -1.7, p < 0.001) was decreased in the tears of the active BDU eye compared to the contralateral quiescent eye. Conclusions:A substantial amount of confident proteins were detected in the tears of BDU patients, including proteins that were deferentially expressed in the uveitis-relapsed eyes and the contralateral quiescent eyes. Some of these identified tear proteins play important roles in immune and inflammatory processes. Tear proteome might be a good source of biomarkers for uveitis.

SUBMITTER: Liang A

PROVIDER: S-EPMC7307566 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Profiling tear proteomes of patients with unilateral relapsed Behcet's disease-associated uveitis using data-independent acquisition proteomics.

Liang Anyi A Qin Weiwei W Zhang Meifen M Gao Fei F Zhao Chan C Gao Youhe Y

PeerJ 20200619

<h4>Purpose</h4>To explore whether unilateral relapse of Bechet's disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring.<h4>Method</h4>To minimize interindividual variations, bilateral tear samples were collected from the same patient (<i>n</i> = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identif ...[more]

PMID: 32596040

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Project description:The ultimate aim of proteomics is to fully identify and quantify the entire complement of proteins and post-translational modifications in biological samples of interest. For the last 15 years, liquid chromatography-tandem mass spectrometry (LC-MS/MS) in data-dependent acquisition (DDA) mode has been the standard for proteomics when sampling breadth and discovery were the main objectives; multiple reaction monitoring (MRM) LC-MS/MS has been the standard for targeted proteomics when precise quantification, reproducibility, and validation were the main objectives. Recently, improvements in mass spectrometer design and bioinformatics algorithms have resulted in the rediscovery and development of another sampling method: data-independent acquisition (DIA). DIA comprehensively and repeatedly samples every peptide in a protein digest, producing a complex set of mass spectra that is difficult to interpret without external spectral libraries. Currently, DIA approaches the identification breadth of DDA while achieving the reproducible quantification characteristic of MRM or its newest version, parallel reaction monitoring (PRM). In comparative de novo identification and quantification studies in human cell lysates, DIA identified up to 89% of the proteins detected in a comparable DDA experiment while providing reproducible quantification of over 85% of them. DIA analysis aided by spectral libraries derived from prior DIA experiments or auxiliary DDA data produces identification and quantification as reproducible and precise as that achieved by MRM/PRM, except on low?abundance peptides that are obscured by stronger signals. DIA is still a work in progress toward the goal of sensitive, reproducible, and precise quantification without external spectral libraries. New software tools applied to DIA analysis have to deal with deconvolution of complex spectra as well as proper filtering of false positives and false negatives. However, the future outlook is positive, and various researchers are working on novel bioinformatics techniques to address these issues and increase the reproducibility, fidelity, and identification breadth of DIA.

Dataset Information

Profiling tear proteomes of patients with unilateral relapsed Behcet's disease-associated uveitis using data-independent acquisition proteomics.

Publications

Profiling tear proteomes of patients with unilateral relapsed Behcet's disease-associated uveitis using data-independent acquisition proteomics.

Similar Datasets

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