Name: Systematic Investigation of Targeted Analysis of Metabolites and Proteins in Tear Fluid
Keywords: Tear fluid

OmicsDI

Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic Investigation of Targeted Analysis of Metabolites and Proteins in Tear Fluid

ABSTRACT: Since the sampling of tear fluid seems rather variable we sought to evaluate a protocol for combined metabolomic and proteomic analyses with regard to clinical applicability. Tear fluid was taken from twelve human volunteers at different time points using specially designed Schirmer strips. Following liquid extraction of metabolites from standardized punchesthe remaining material was processed for bottom-up proteomics. The targeted proteomic analysis of 15 tear proteins revealed a mean intra-individual variation of 23 % merely for the three most abundant proteins. Overall, our newly established workflow opens perspectives for clinical and routine diagnostic applications using well accessible tear fluid.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Tear

SUBMITTER: Janina D'Alvise

LAB HEAD: Sascha Dammeier

PROVIDER: PXD008536 | Pride | 2019-11-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Combined Targeted Analysis of Metabolites and Proteins in Tear Fluid With Regard to Clinical Applications.

Dammeier Sascha S Martus Peter P Klose Franziska F Seid Michael M Bosch Dario D D'Alvise Janina J Ziemssen Focke F Dimopoulos Spyridon S Ueffing Marius M

Translational vision science & technology 20181101 6

<h4>Purpose</h4>To establish a robust workflow for combined mass spectrometry-based analysis of metabolites and proteins in tear fluid with regard to clinical applicability.<h4>Methods</h4>Tear fluid was taken from 12 healthy volunteers at different time points using specially designed Schirmer strips. Following the liquid extraction of metabolites from standardized punches, the remaining material was processed for bottom-up proteomics. Targeted metabolite profiling was performed adapting a meta ...[more]

PMID: 30564511

Similar Datasets

Investigation of inter- and intra-day variability of tear fluid regarding flow rate, protein concentration as well as protein composition

Project description:Purpose: Determination of inter- and intra-day variations in tear flow rate, tear fluid protein concentration as well as protein composition regarding their impact for future biomarker studies.Methods: Tear fluid was collected non-invasively from 18 healthy subjects performing Schirmer tests at four different time points repetitive in a period of two days. The tear flow rate with Schirmer test strips was measured. Proteins were extracted from strips and quantified using amino acid analysis. Protein composition was analyzed by data-independent (DIA) based mass spectrometry. To exclude any impairments to health, volunteers underwent a detailed neurological as well as an ophthalmological examination.Results: Whether tear fluid was collected from OS or OD did not affect the tear flow rate (p ≈ 0.63) or protein concentration (p ≈ 0.97) of individual subjects. Moreover, protein concentration was independent from the tear volume, so that a change in volume would only have an effect on total protein amount. When the examination days were compared, investigation of tear flow rate (p ≈ 0.001) and protein concentration (p ≈ 0.0003) indicated significant differences. Further mass spectrometric analysis of tear fluid revealed eleven differentially regulated proteins when comparing both examination days. Conclusion: Our findings provide evidence of inter-day variation in tear flow rate, tear proteome concentration and composition in healthy subjects, suggesting that inter-day variation need to be taken into consideration in biomarker research of tear fluid. Identified proteins were assigned to functions in the immune response, oxidative and reducing processes, as well as mannose metabolism.

2023-10-24 | PXD037811 | Pride

Human Tear using MALDI-TOF-MS for Dry Eye syndrome

Project description:Tears are a biological fluid that has diagnostic potential for ocular diseases. Extracellular vesicles (EVs), wildly detected in various biofluids including tears, are nanoparticles released by living cells and considered as promising detection sources for non-invasive liquid biopsy. Understanding the roles of tears and tear-EVs in ocular diseases such as dry eye can facilitate the studies of clinical diagnosis, which usually entails detecting such liquid objects with a rapid and effective method. In this study, we utilized a mass spectrometry based strategy to analyze peptidome/proteome profiles of tear and EVs for rapid dry eye diagnosis. Nano-sized EVs were isolated from tears of either healthy control (HC) individuals or dry eye syndrome (DES) patients, and the tear compositions were further analyzed by tracking their fingerprints with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS). The fingerprints of tear-EVs could be observed in a dose-dependent manner as well as tears, allowing comparing their discriminant peaks between tears and EVs. By analyzing these peaks, the fingerprints of both tear and tear-EVs were showed to have a capability of distinguishing DES patients from HC donors, and providing an efficient way for screening potential DES biomarkers. The proposed tear and EV fingerprinting approach is expected to be a potential tool in rapid diagnosis of ocular disease and in-depth researches of pathogenesis.

2020-08-20 | PXD020217 | Pride

Comparison of Different Mass-Spectrometry Workflows for the Proteomic Analysis of Tear Fluid

Project description:Proteomic analysis of tear fluid is challenging mainly due to a wide dynamic range of proteins and small sample volume. However, recent advancements in mass spectrometry have revolutionized the field of proteomics through its unprecedented depth, speed, and accuracy even with small sample volumes. In this study using the Orbitrap Fusion Tribrid mass spectrometer, we compared four different mass-spectrometry workflows for proteomic analysis of human tear fluid.

2022-04-04 | PXD030990 | Pride

Human tear fluid proteome dataset for usage as a spectral library and for protein modeling

Project description:This article provides a detailed dataset of human tear fluid proteins. Samples were fractionated by sodium dodecyl sulfate (SDS) gel electrophoresis resulting in 48 fractions that were spiked with an indexed retention time (iRT) peptide standard. These data are based on a data-dependent acquisition (DDA) mass spectrometric approach and can be used for example as a spectral library for tear fluid proteome analysis by data-independent acquisition (DIA). Moreover, the provided data set can be used with optimized HPLC as well as mass spectrometric settings for proteins/peptides of interest. Besides these aspects, this dataset can serve as a protein overview for gene ontology enrichment analysis as well as for modeling and benchmarking of multiple signaling pathways associated with the ocular surface in healthy or disease stages.

2019-08-15 | PXD011075 | Pride

microRNA expression data from human corneal epithelial cells exposed to media, human tear, media + P. aeruginosa antigens, tear + P. aeruginosa antigens

Project description:Exposure to tear fluid can enhance corneal epithelial cells' ability to resist bacterial virulence mechanisms by upregulating epithelial-derived innate defense genes. The aim of this study was to further elucidate the mechanisms by which tear fluid modulates epithelial cell susceptibility to P. aeruginosa internalization and the relationship to known to be upregulated genes with tear fluid exposure. The hypothesis tested was that tear fluid effects on epithelial cells involve the induction of microRNA expression to modify innate defense gene responses to bacterial challenge. Human corneal epithelial cells were incubated in either 40 ul of fresh human tear fluid or high calcium KGM without antibiotics for 16 hours before extraction or before incubation with P. aeruginosa antigens for 3 h then extraction.

2012-07-13 | E-GEOD-39341 | biostudies-arrayexpress

Dog tear film proteome in-depth analysis

Project description:In this study, mass spectrometry was used to explore the canine tear proteome. Tear samples were obtained from six healthy dogs, and one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis (1D SDS-PAGE) was used as a first step to separate intact proteins into 17 bands. Each fraction was then trypsin digested and analysed by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS) to characterize the protein components in each fraction. In total, 125 tear proteins were identified, with MCA (Major Canine Allergen), Serum albumin, UPF0557 protein C10orf119 homolog, Collagen alpha-2(I) chain, Tyrosine -protein kinase Fer, Keratine type II cytoskeletal, Beta-crystallin B2, Interleukin-6 and Desmin occuring as the most confident ones with the highest scores. The results showed that the proteomic strategy used in this study was successful in the analysis of the dog tear proteome. To the best of our knowledge, this study is the first to report the comprehensive proteome profile of tears from healthy dogs by 1D SDS PAGE and MALDI-TOF.

2015-11-23 | PXD003124 | Pride

Putative tear fluid biomarkers of diabetic retinopathy

Project description:Identification of tear fluid biomarkers may offer a non-invasive strategy for detecting diabetic patients with increased risk of developing diabetic retinopathy (DR) or increased disease progression, thus helping both improving diagnostic accuracy and understanding the pathophysiology of the disease. The goal of this study was to characterize the proteomic profile of human tear fluid and examine changes in proteins expression in different stages of diabetic retinopathy.

2022-05-31 | PXD033101 | Pride

Tear proteomics of young patients wearing glasses, orthokeratology lenses, and soft contact lenses

Project description:Contact lens-related ocular surface complications occur more often in teenagers and young adults. The purpose of this study was to determine changes in tear proteome of young patients wearing glasses (GL), orthokeratology lenses (OK), and soft contact lenses (SCL). Twenty-two young patients (10-26 years of age) who were established (> 3 years) GL (n=10), OK (n=6), and SCL (n=6) wearers were recruited. Tears were collected via Schirmer strips. Proteomic data were collected using a data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) workflow. Tear proteome composition and abundance were compared across different correction groups and between the children (age <18 years) and young adults (age 18 years) GL wearers. We identified 3406 protein groups in tears. Among proteins identified in 80% of tear samples, 8 proteins were upregulated, and 11 proteins were down-regulated in the SCL group compared to the OK group. Eighty-two proteins were differentially expressed in children and young adults GL wearers, among which 67 proteins were upregulated, and 15 proteins were downregulated in children. These 82 proteins were involved in 1 inflammation, 9 immune, and 1 glycoprotein metabolic biological processes. As teenagers and young adults have the highest risk of developing contact lens-related complications, this work highlights the importance of understanding ocular responses to contact lens wear across different ages.

2022-11-07 | PXD029188 | Pride

Potential tear biomarkers for the early diagnosis of Parkinson's disease- A pilot study

Project description:Parkinson's disease (PD) is the second most common neurodegenerative disease after Alzheimer's disease. The purpose of this study was to analyze the profile of the tear proteome of patients with idiopathic PD (iPD), carriers of the E46K-SNCA mutation and healthy subjects (CT) and to identify biomarkers for the early diagnosis of PD. An observational, prospective and case-control pilot study was carried out in 24 patients with iPD, 3 carriers of the E46K-SNCA mutation and 27 CT subjects. The patients' neurological involvement was scored and their tear samples were analyzed using nano-liquid chromatography-mass spectrometry (nLC-MS/MS). These analyses led to the identification of 560 tear proteins in which some of the deregulated proteins were involved in immune response, apoptosis, collagen degradation, protein synthesis, defense and altered lysosomal function. Of these proteins, six related to neurodegenerative processes, showed a good capacity to classify patients and controls. These findings revealed that some proteins were upregulated in the tears of PD patients, mainly those involved in lysosomal function. It is worth highlighting the importance of this study in identifying tear proteins implicated in neurodegeneration and its relationship with PD patients with an aggressive disease phenotype.

2022-02-14 | PXD028811 | Pride

Proteomic Analysis of Human Conjunctival Cells and Tears Collected with Schirmer Strips Using TimsTOF Pro

Project description:This study aimed to investigate the human tear proteins extracted from whole (W) Schirmer strips (ScS) and their two parts, the bulb (B) and the rest of the strip (R) with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at 4 different visits to be separated into three batches: 4W, 4B and 4R. In total, 1582 proteins were identified in the W, B and R batches. Among all iden-tified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cel-lular processes (31.2%), metabolic processes (20.8%) and biological regulation (13.1%). Enzymes were the most represented protein class (41 %), consisting mainly of hydrolases (47.5%), oxi-doreductases (22.1%) and transferases (16.7%). The bulb (B), which is in contact with the conjunc-tiva, might collect both tear and cell proteins and therefore promote identification of more pro-teins. Processing B and R separately before MS analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.

2022-01-27 | PXD030334 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data