在基于质谱分析（MS）的蛋白质组学中，从已鉴定的肽段（蛋白质碎片）推断蛋白质是关键的一步。我们提出了一种新颖的蛋白质组装方法，名为ProInfer（蛋白质推断），利用生物网络中的信息。ProInfer能够恢复仅由不确定性肽段（映射到多个蛋白质候选物的肽段）支持的蛋白质，并增强由唯一肽段和不确定性肽段同时支持的蛋白质的统计置信度。因此，ProInfer能够挽救支持较弱的蛋白质，从而提高蛋白组覆盖率。在THP1细胞系、肺癌和RAW267.4数据集上的评估中，与流行的蛋白质推断工具Fido、EPIFANY和PIA相比，ProInfer总是推断出最多的真阳性。ProInfer还擅长检索差异表达的蛋白质，标志着它在功能分析和表型分析方面的有用性。ProInfer的源代码可在https://github.com/PennHui2016/ProInfer获得。版权所有：©2023 Peng等人。本文是一篇开放获取文章，依照创作共用许可，允许在任何媒介上无限制使用、分发及复制，前提是保留原作者和出处的署名。

In mass spectrometry (MS)-based proteomics, protein inference from identified peptides (protein fragments) is a critical step. We present ProInfer (Protein Inference), a novel protein assembly method that takes advantage of information in biological networks. ProInfer assists recovery of proteins supported only by ambiguous peptides (a peptide which maps to more than one candidate protein) and enhances the statistical confidence for proteins supported by both unique and ambiguous peptides. Consequently, ProInfer rescues weakly supported proteins thereby improving proteome coverage. Evaluated across THP1 cell line, lung cancer and RAW267.4 datasets, ProInfer always infers the most numbers of true positives, in comparison to mainstream protein inference tools Fido, EPIFANY and PIA. ProInfer is also adept at retrieving differentially expressed proteins, signifying its usefulness for functional analysis and phenotype profiling. Source codes of ProInfer are available at https://github.com/PennHui2016/ProInfer.Copyright: © 2023 Peng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.