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

Abstract

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.

Keywords: UniProt; bottom-up proteomics; post-translational modification; proteoforms; proteomics software; top-down proteomics.

FIGURE 1

ProSight Annotator allows an iterative process of adding, removing, or editing isoform and feature data to create a UniProt formatted Extensible Markup Language (XML) suitable to create a database for top-down or bottom-up searching

FIGURE 2

The ProSight Annotator main window contains five sections: (1) the menu, (2) isoforms table, (3) graphical annotated isoform, (4) point features, and (5) range features. It also contains information regarding currently annotated point features and proteoform counts: total proteoform count (6), selected isoform proteoform count (7), single PTM applied to a residue (8), multiple PTMs applied to a residue (9), cSNP applied to a residue (10), and custom mass modification applied to a residue (11). The main window also contains a button that launches the global feature set editor (12). A locked point feature is designated with a closed lock image (13).

FIGURE 3

The global feature set (GFS) editor allows users to edit the point features included in the GFS and perform global add and remove operations. The point features currently in the GFS are listed in the Included Features table (1). They are organized by feature type. The type can be expanded to display individual PTMs (2). A column with the number of currently applied features is displayed (3). The number of instances that a feature would be applied if added to all the isoforms is included in the potential column (4). Users can globally add or remove features by using the buttons in the global update feature set column (5). Features not currently included in the GFS are listed in the Available Features table (6). Features can be added to the included table by clicking the button in the Include column (7). Custom mass modifications can be added the included table by clicking the “Add Custom Modification” button (8). Features are only applied to isoforms with masses below the max. isoform mass threshold. This threshold can be updated by clicking the Advanced Parameters button (9)