Dear-DIAXMBD: Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics
Qingzu He,
Chuan-Qi Zhong,
Xiang Li,
Huan Guo,
Yiming Li,
Mingxuan Gao,
Rongshan Yu,
Xianming Liu,
Fangfei Zhang,
Donghui Guo,
Fangfu Ye,
Tiannan Guo,
Jianwei Shuai,
Jiahuai Han
Affiliations
Qingzu He
Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research,
Xiamen University, Xiamen 361005, China.
Chuan-Qi Zhong
School of Life Sciences,
Xiamen University, Xiamen 361102, China.
Xiang Li
Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research,
Xiamen University, Xiamen 361005, China.
Huan Guo
Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research,
Xiamen University, Xiamen 361005, China.
Yiming Li
Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research,
Xiamen University, Xiamen 361005, China.
Mingxuan Gao
Department of Computer Science,
Xiamen University, Xiamen 361005, China.
Rongshan Yu
Department of Computer Science,
Xiamen University, Xiamen 361005, China.
Xianming Liu
Bruker (Beijing) Scientific Technology Co. Ltd., Beijing, China.
Fangfei Zhang
Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences,
Westlake University, 18 Shilongshan Road, Hangzhou 310024, China.
Donghui Guo
Department of Electronic Engineering,
Xiamen University, Xiamen 361005, China.
Fangfu Ye
Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health) and Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.
Tiannan Guo
Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences,
Westlake University, 18 Shilongshan Road, Hangzhou 310024, China.
Jianwei Shuai
Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research,
Xiamen University, Xiamen 361005, China.
Jiahuai Han
School of Life Sciences,
Xiamen University, Xiamen 361102, China.
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-DIAXMBD first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms, then uses the k-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-DIAXMBD performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms. Dear-DIAXMBD is publicly available at https://github.com/jianweishuai/Dear-DIA-XMBD.
