If you publish results obtained by PEAKS, please cite PEAKS by:

"PEAKS version_number (Bioinformatics Solutions Inc., Waterloo, Ontario, Canada)"

and/or the following paper:

J. Zhang, L. Xin, B. Shan, W. Chen, M. Xie, D. Yuen, W. Zhang, Z. Zhang, G. Lajoie, and B. Ma. PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics 10.1074/mcp.M111.010587 (2011).

The following is a list of publications on the algorithms used in PEAKS, in case you need to cite a specific algorithm.

	J. Zhang, L. Xin, B. Shan, W. Chen, M. Xie, D. Yuen, W. Zhang, Z. Zhang, G. Lajoie, and B. Ma. PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification. Molecular & Cellular Proteomics 10.1074/mcp.M111.010587 (2011). [Epub ahead of print]

	B. Ma, K. Zhang, C. Hendrie, C. Liang, M. Li, A. Doherty-Kirby, and G. Lajoie. PEAKS: Powerful Software for Peptide De Novo Sequencing by Tandem Mass Spectrometry. Rapid Communication in Mass Spectrometry 17(20): 2337-2342 (2003).

	Y. Han, B. Ma, and K. Zhang. SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error. Journal of Bioinformatics and Computational Biology 3(3):697-716 (2005).

	X. Han, L. He, L. Xin, B. Shan, B. Ma. . PEAKS PTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications. Journal of Proteomics Research 10(7): 2930-2936 (2011).

If you have any questions regarding which paper should be cited in your specific research, please feel free to send an email to This e-mail address is being protected from spambots. You need JavaScript enabled to view it and we will get back to you as soon as possible.