posted on 2024-02-27, 19:28authored byLinda Berg Luecke, Roneldine Mesidor, Jack Littrell, Morgan Carpenter, Melinda Wojtkiewicz, Rebekah L. Gundry
Currently, no consensus exists regarding criteria required
to designate
a protein within a proteomic data set as a cell surface protein. Most
published proteomic studies rely on varied ontology annotations or
computational predictions instead of experimental evidence when attributing
protein localization. Consequently, standardized approaches for analyzing
and reporting cell surface proteome data sets would increase confidence
in localization claims and promote data use by other researchers.
Recently, we developed Veneer, a web-based bioinformatic tool that
analyzes results from cell surface N-glycocapture
workflowsthe most popular cell surface proteomics method used
to date that generates experimental evidence of subcellular location.
Veneer assigns protein localization based on defined experimental
and bioinformatic evidence. In this study, we updated the criteria
and process for assigning protein localization and added new functionality
to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate
the importance of applying defined criteria when analyzing cell surface
proteomics data sets and exemplify how Veneer can be used to assess
experimental quality and facilitate data extraction for informing
future biological studies and annotating public repositories.