The "2DE-Pattern" Database for Inventory of Proteoform Profiles: 2026 Upgrade and Update on Outcomes

Modern proteomics faces a critical bottleneck: the vast discrepancy between the number of genes in the human genome and the exponentially greater variety of functional proteoforms that actually drive biological processes.

Our paper addresses the urgent need for high-resolution systematic mapping of these proteoforms, arguing that the true frontier of molecular biology lies in the precise identification and categorization of protein variants. It centers on the development and expansion of the "2DE-pattern" database, a specialized platform designed to bridge the gap between theoretical protein sequences and the physical reality of proteins as captured through two-dimensional electrophoresis (2DE). The "2DE-pattern" database is based on information obtained by separation of proteoforms using 2DE followed by shotgun ESI LC-MS/MS. It was launched in 2020, contains multiple isoform-centric patterns of proteoforms, and can be freely used.

Here, we report the additional data and all updates that were added into this database. Also, the database was upgraded to be more research-oriented. Tools were incorporated into the database to allow convenient comparative analysis of the data.

New additions and enhancements now allow us to consider our database a knowledge base.