HuPEX®-Powered Proteomics Research Published in Journal of Proteome Research
Tokyo, Japan – July 25, 2025 – ProteoBridge Inc. (Head Office: Tokyo, President & CEO: Ryo Kumagai) is pleased to announce that groundbreaking findings from its joint research with Kumamoto University have been published in the prestigious international journal Journal of Proteome Research. By leveraging the company’s proprietary HuPEX® human protein expression library, the study demonstrates significant advancements in proteomics research using mass spectrometry.
In recent years, in silico spectral libraries powered by deep learning have attracted increasing attention, and the “library-free search” approach has been widely adopted in data-independent acquisition (DIA) analysis. However, managing the false discovery rate (FDR) has remained a challenge due to the vast volume of peptide data contained in these libraries.
In this study, researchers proposed a novel methodology to rigorously evaluate FDR control in DIA software. Human proteins synthesized via a cell-free expression system using HuPEX® were analyzed with liquid chromatography–mass spectrometry (LC-MS) and DIA software, and the resulting data were compared against known protein sequences to quantify FDR. A comparative analysis of DIA-NN versions 1.8.1, 1.9.2, and 2.1.0 revealed that versions 1.9.2 and 2.1.0 achieved higher peptide identification accuracy and significantly improved FDR control compared with version 1.8.1.
This achievement is expected to advance the accuracy of DIA-based proteomics and support bioinformaticians, pharmaceutical companies, and life science researchers in their pursuit of more reliable and precise data analysis.
Publication Information
Title: Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using In Vitro Human Proteome
Authors: Kongxin Gu, Masanaga Kenko, Koji Ogawa, Naoki Goshima, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki
Journal: Journal of Proteome Research
Publication Date: July 18, 2025
DOI: https://doi.org/10.1021/acs.jproteome.5c00036
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