Proteomics

Dataset Information

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Human PDR Vitreous Variability Study, TMT-MS

ABSTRACT: Control (n=27) and proliferative diabetic retinopathy (n=23) vitreous samples were treated as biologically distinct individuals or pooled together and aliquoted into technical replicates. Quantitative mass spectrometry with tandem mass tag labeling was used to identify proteins in individual or pooled control samples to determine technical and biological variability. To determine effect size and perform power analysis, control and proliferative diabetic retinopathy samples were analyzed across four 10plexes. Pooled samples were used to normalize the data across plexes and generate a single data matrix for downstream analysis.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Vitreous Humor

DISEASE(S): Proliferative Diabetic Retinopathy,Macular Holes

SUBMITTER: Sarah Weber  

LAB HEAD: Jeffrey M. Sundstrom

PROVIDER: PXD025986 | Pride | 2022-02-14

REPOSITORIES: pride

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Dataset's files

Source:
Action DRS
2020-02-04-decoys-reviewed-contam-UP000005640.fas Other
PRF_F_2019_T_GARD_253_48580_48589_1.mzML Mzml
PRF_F_2019_T_GARD_253_48580_48589_1.pepXML Pepxml
PRF_F_2019_T_GARD_253_48580_48589_2.mzML Mzml
PRF_F_2019_T_GARD_253_48580_48589_2.pepXML Pepxml
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Publications

A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy.

Weber Sarah R SR   Zhao Yuanjun Y   Ma Jingqun J   Gates Christopher C   da Veiga Leprevost Felipe F   Basrur Venkatesha V   Nesvizhskii Alexey I AI   Gardner Thomas W TW   Sundstrom Jeffrey M JM  

Clinical proteomics 20211203 1

<h4>Background</h4>Vitreous is an accessible, information-rich biofluid that has recently been studied as a source of retinal disease-related proteins and pathways. However, the number of samples required to confidently identify perturbed pathways remains unknown. In order to confidently identify these pathways, power analysis must be performed to determine the number of samples required, and sample preparation and analysis must be rigorously defined.<h4>Methods</h4>Control (n = 27) and prolifer  ...[more]

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