BSI Algorithm Publications:

PEAKS Online and PEAKS Studio DDA and DIA Workflows:

• Xin, L., Qiao, R., Chen, X. et al. A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics. Nat Commun 13, 3108 (2022). https://doi.org/10.1038/s41467-022-30867-7

Deep learning-enabled de novo sequencing:

• Tran, N. H., Zhang, X., Xin, L., Shan, B., & Li, M. (2017). De novo peptide sequencing by deep learning. Proceedings of the National Academy of Sciences of the United States of America, 114(31), 8247–8252. https://doi.org/10.1073/pnas.1705691114
• Tran, N. H., Qiao, R., Xin, L., Chen, X., Liu, C., Zhang, X., Shan, B., Ghodsi, A., & Li, M. (2019). Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry. Nature methods, 16(1), 63–66. https://doi.org/10.1038/s41592-018-0260-3
• Qiao, R., Tran, N.H., Xin, L. Chen, X., Li, M., & Shan. B. (2020) . Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices. Nat Mach Intell 3, 420–425 (2021). https://doi.org/10.1038/s42256-021-00304-3

PEAKS DB:

• Zhang J, Xin L, Shan B, Chen W, Xie M, Yuen D, Zhang W, Zhang Z, Lajoie G.A., Ma B, PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Mol. Cell. Proteomics. 11, M111.010587 (2012). https://doi.org/10.1074/mcp.M111.010587

PEAKS de novo sequencing:

• Hughes, C., Ma, B., Lajoie, G.A. De novo Sequencing Methods in Proteomics. Methods Mol. Biol. 604 (2009). https://doi.org/10.1007/978-1-60761-444-9_8
• Ma, B., Zhang, K., Hendrie, C., Liang, C., Li, M., Doherty-Kirby, A., & Lajoie, G. (2003). PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid communications in mass spectrometry : RCM, 17(20), 2337–2342. https://doi.org/10.1002/rcm.1196

PEAKS PTM:

• Han X, Xin L. Shan B. Ma B. PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications. J. Proteome Res., 10, 2930-2936 (2011). https://pubs.acs.org/doi/10.1021/pr200153k

SPIDER:

• Han, Y., Ma, B., Zhang, K. SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error. J. Bioinform. Comput. Biol., 3, 697-716 (2005). https://doi.org/10.1142/S0219720005001247
• Ma, B. & Johnson, R. De novo Sequencing and Homology Searching. Mol. Cell. Proteomics. 11 O111.01490 (2012). https://doi.org/10.1074/mcp.O111.014902

PEAKS AB:

• Tran NH, Rahman MZ, He L, Xin L, Shan B, Li M. Complete De Novo Assembly of Monoclonal Antibody Sequences. Sci. Rep., 6, 31730 (2016). https://doi.org/10.1038/srep31730

PEAKS GlycanFinder:

• Sun, W., Zhang, Q., Zhang, X. et al. Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics. Nat Commun 14, 4046 (2023). https://doi.org/10.1038/s41467-023-39699-5

If you have any questions, please contact us at peaks@bioinfor.com.