Computational protocol: Dye-Free Porcine Model of Experimental Branch Retinal Vein Occlusion: A Suitable Approach for Retinal Proteomics

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Protocol publication

[…] Data obtained by mass spectrometry were searched against a pig isoform database optimized from Uniprot using MaxQuant (version 1.5.0.22). The label-free algorithm was activated in MaxQuant. The peptide and protein false discovery rates were set to 1%. A two-tailed, heteroscedastic t-test was used to calculate p values.Identified proteins were uploaded onto Perseus (version 1.5.0.9). Technical replicates were averaged by mean and proteins identified by less than two unique peptides were removed from the dataset. Perseus was used to search for proteins that were identified from peptides that were found to be part of a protein derived from the reversed part of the decoy database. These proteins were also removed from the dataset. All identified proteins were exported to Excel (Microsoft Office Standard 2007). Remaining keratins in the dataset were removed. Proteins with no assigned gene name in the identification were searched for on http://www.uniprot.com/ and gene names corresponding to the identified proteins were added.A bioinformatic analysis was conducted using GeneCodis3 [–]. Gene names corresponding to the identified proteins were entered in GeneCodis3 to conduct Gene Ontology cellular component analysis. Homo sapiens was selected as organism to ensure that all gene names were recognized by GeneGodis3. p values were obtained by hypergeometric analysis corrected by a false discovery rate method. […]

Pipeline specifications

Software tools MaxQuant, Perseus, GeneCodis
Application MS-based untargeted proteomics
Diseases Retinal Vein Occlusion
Chemicals Argon