[1] CHEN C,HOU J,TANNER J J,et al. Bioinformatics methods for mass spectrometry-based proteomics data analysis[J]. International Journal of Molecular Sciences,2020,21(8):No. 2873. [2] PERKINS D N,PAPPIN D J C,CREASY D M,et al. Probabilitybased protein identification by searching sequence databases using mass spectrometry data[J]. Electrophoresis,1999,20(18):3551-3567. [3] ENG J K,HOOPMANN M R,JAHAN T A,et al. A deeper look into Comet-implementation and features[J]. Journal of The American Society for Mass Spectrometry,2015,26(11):1865-1874. [4] TYANOVA S,TEMU T,COX J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics[J]. Nature Protocols,2016,11(12):2301-2319. [5] CHI H,HE K,YANG B,et al. pFind-Alioth:a novel unrestricted database search algorithm to improve the interpretation of highresolution MS/MS data[J]. Journal of Proteomics,2015,125:89-97. [6] CHI H,LIU C,YANG H,et al. Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine[J]. Nature Biotechnology,2018,36(11):1059-1061. [7] MA B,ZHANG K Z,HENDRIE C,et al. PEAKS:powerful software for peptide de novo sequencing by tandem mass spectrometry[J]. Rapid Communications in Mass Spectrometry, 2003,17(20):2337-2342. [8] FRANK A,PEVZNER P. PepNovo:de novo peptide sequencing via probabilistic network modeling[J]. Analytical Chemistry, 2005,77(4):964-973. [9] CHI H,SUN R X,YANG B,et al. pNovo:de novo peptide sequencing and identification using HCD spectra[J]. Journal of Proteome Research,2010,9(5):2713-2724. [10] CHI H,CHEN H F,HE K,et al. pNovo+:de novo peptide sequencing using complementary HCD and ETD tandem mass spectra[J]. Journal of Proteome Research, 2013, 12(2):615-625. [11] YANG H,CHI H,ZHOU W J,et al. Open-pNovo:de novo peptide sequencing with thousands of protein modifications[J]. Journal of Proteome Research,2017,16(2):645-654. [12] YANG H,CHI H,ZENG W F,et al. pNovo 3:precise de novo peptide sequencing using a learning-to-rank framework[J]. Bioinformatics,2019(14):i183-i190. [13] FISCHER B,ROTH V,ROOS F,et al. NovoHMM:a hidden Markov model for de novo peptide sequencing[J]. Analytical Chemistry,2005,77(22):7265-7273. [14] MA B. Novor:real-time peptide de novo sequencing software[J]. Journal of The American Society for Mass Spectrometry,2015,26(11):1885-1894. [15] TRAN N H,ZHANG X L L,XIN L,et al. De novo peptide sequencing by deep learning[J]. Proceedings of the National Academy of Sciences of the United States of America,2017,114(31):8247-8252. [16] 赵新元, 秦伟捷, 钱小红. 深度学习方法在生物质谱及蛋白质组学中的应用[J]. 生物化学与生物物理进展,2018,45(12):1214-1223.(ZHAO X Y,QIN W J,QIAN X H. Application of deep learning in biological mass spectrometry and proteomics[J]. Progress in Biochemistry and Biophysics,2018,45(12):1214-1223.) [17] WEN B, ZENG W F, LIAO Y X, et al. Deep learning in proteomics[J]. Proteomics,2020,20(21/22):No. 1900335. [18] 徐冰冰, 岑科廷, 黄俊杰, 等. 图卷积神经网络综述[J]. 计算机学报,2020,43(5):755-780.(XU B B,CEN K T,HUANG J J, et al. A survey on graph convolutional neural network[J]. Chinese Journal of Computers,2020,43(5):755-780.) [19] KIPF T N,WELLING M. Semi-supervised classification with graph convolutional networks[EB/OL](2017-02-22)[2020-09-09]. https://arxiv.org/pdf/1609.02907.pdf. [20] DEFFERRARD M, BRESSON X, VANDERGHEYNST P. Convolutional neural networks on graphs with fast localized spectral filtering[C]//Proceedings of the 30th International Conference on Neural Information Processing Systems. Red Hook, NY:Curran Associates Inc.,2016:3844-3852. [21] MICHALSKI A,NEUHAUSER N,COX J,et al. A systematic investigation into the nature of tryptic HCD spectra[J]. Journal of Proteome Research,2012,11(11):5479-5491. [22] LIN T Y,GOYAL P,GIRSHICK R,et al. Focal loss for dense object detection[C]//Proceedings of the 2017 IEEE International Conference on Computer Vision. Piscataway:IEEE,2017:2999-3007. [23] ZOLG D P,WILHELM M,SCHNATBAUM K,et al. Building ProteomeTools based on a complete synthetic human proteome[J]. Nature Methods,2017,14(3):259-262. [24] GESSULAT S,SCHMIDT T,ZOLG D P,et al. Prosit:proteomewide prediction of peptide tandem mass spectra by deep learning[J]. Nature Methods,2019,16(6):509-518. |