ProSight Annotator: Complete control and customization of protein entries in UniProt XML files

The effectiveness of any proteomics database search depends on the theoretical candidate information contained in the protein database. Unfortunately, candidate entries from protein databases such as UniProt rarely contain all the post‐translational modifications (PTMs), disulfide bonds, or endogeno...

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Bibliographic Details
Published in:Proteomics (Weinheim) 2022-06, Vol.22 (11-12), p.e2100209-n/a
Main Authors: Greer, Joseph B., Early, Bryan P., Durbin, Kenneth R., Patrie, Steven M., Thomas, Paul M., Kelleher, Neil L., LeDuc, Richard D., Fellers, Ryan T.
Format: Article
Language:English
Subjects:
bottom‐up proteomics
Databases, Protein
Disulfide bonds
Document markup languages
Extensible Markup Language
Language
post‐translational modification
Protein Processing, Post-Translational
Proteins
Proteins - chemistry
proteoforms
Proteomics
proteomics software
Software
top‐down proteomics
UniProt
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Description
Summary:The effectiveness of any proteomics database search depends on the theoretical candidate information contained in the protein database. Unfortunately, candidate entries from protein databases such as UniProt rarely contain all the post‐translational modifications (PTMs), disulfide bonds, or endogenous cleavages of interest to researchers. These omissions can limit discovery of novel and biologically important proteoforms. Conversely, searching for a specific proteoform becomes a computationally difficult task for heavily modified proteins. Both situations require updates to the database through user‐annotated entries. Unfortunately, manually creating properly formatted UniProt Extensible Markup Language (XML) files is tedious and prone to errors. ProSight Annotator solves these issues by providing a graphical interface for adding user‐defined features to UniProt‐formatted XML files for better informed proteoform searches. It can be downloaded from http://prosightannotator.northwestern.edu.
ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.202100209