Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction. In this paper, we proposed an untargeted analysis method, Dear-DIAXMBD, for direct analysis of DIA data. Dear-DIAXMBDfirst integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms, then uses thek-means clustering algorithm to aggregate fragments with similar representations into the same classes, and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides. We show that Dear-DIAXMBDperforms superiorly with the highly complicated DIA data of different species obtained by different instrument platforms. Dear-DIAXMBDis publicly available athttps://github.com/jianweishuai/Dear-DIA-XMBD.