BSI Publications

If user publications results obtained by PEAKS, please cite:

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

and/or the following paper:

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).

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).

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.
  • 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.
  • 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).


  • 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).

PEAKS de novo sequencing:

  • Hughes, C., Ma, B., Lajoie, G.A. De novo Sequencing Methods in Proteomics. Methods Mol. Biol. 604 (2009).
  • 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.




  • 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).

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).

If you have any questions, please contact us at

2023/10/24A Complete Software Suite for de novo Sequencing and Predicting the Immunogenicity of Class 1 and Class 2 Neoantigens2023-10-24 11:40:22
2023/07/05Integrating Database Search and De Novo Sequencing for Immunopeptidomics with DIA Approach2023-07-05 12:25:17
2022/06/08A streamlined platform for analyzing tera-scale DDA and DIA mass spectrometry data enables highly sensitive immunopeptidomics2022-06-08 17:12:29
2021/03/25Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices2021-03-25 15:42:00
2021/03/16Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines2021-03-16 09:53:47
2019/11/20DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS Map2019-11-20 16:50:31
2018/12/20Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry2018-12-20 15:32:14
2018/11/12AI-based solution for Identification of Immunopeptides with LC-MS2018-11-12 10:24:37
2018/11/01Post-Translational Modification Analysis with PEAKS Studio (Application Note)2018-11-01 14:09:39
2018/11/01MS-based Immunopeptidomics Analysis with PEAKS Studio X (Application Note)2018-11-01 14:08:26
2018/11/01Feature-based Peptide Identifications with PEAKS Studio X (Application Note)2018-11-01 14:07:23
2018/10/01A New Algorithm for Identification of Immunopeptides from LC-MS Data with High Sensitivity2018-10-01 15:17:49
2018/09/10Towards the Comprehensive Mass Spectrometry-based Biopharmaceutical Analysis using PEAKS MAPS2018-09-10 15:18:15
2018/06/07In-Depth Proteomics Analysis Using a TIMS-QTOF with the PASEF Method and Deep Learning2018-06-07 13:49:05
2018/06/07Towards Real-time Proteomics Data Analysis using PEAKS Online 8.52018-06-07 09:06:39
2018/06/07Utility of EThcD and AI-ETD for the Differentiation of Leucine and Isoleucine Residues in Large-Scale Shotgun Proteomic Experiments2018-06-07 09:04:28
2018/06/07Automated de novo Sequencing of Antibodies with Isoleucine/Leucine Differentiation by Using EThcD Fragmentation2018-06-07 09:01:25
2018/03/12Increased Accuracy of Peptide de novo Sequencing Using Complementary AI-ETD and HCD Fragmentation2018-03-12 14:38:31
2018/01/10Complete protein de novo sequencing from antibody mixtures by LC-MS/MS2018-01-10 16:33:01
2018/01/10New Peptide Mapping Approaches for Complete Characterization of Purified Antibodies2018-01-10 14:13:10
2017/09/17Quantitative Profiling of Post-Translational Modifications by SILAC approach with PEAKS2017-09-17 08:43:10
2017/09/13SILAC-based Quantitative Proteome Analysis with PEAKS (Application Note)2017-09-13 08:56:34
2017/07/18De novo peptide sequencing by deep learning2017-07-18 12:56:02
2017/06/08Monoclonal Antibody de novo Sequencing by Deep Learning2017-06-08 14:52:30
2017/06/07Label-free Quantification with PEAKS (Application Note)2017-06-07 08:53:44
2017/06/06N-Linked Glycan Profiling for Monoclonal Antibodies with PEAKS AB Software Platform using LC-MS/MS2017-06-06 14:51:52
2017/06/06Antibody Sequence Validation by Peptide and Disulfide Bond Mapping2017-06-06 14:51:05
2017/06/05Analysis of EThcD Spectra with PEAKS Platform for de novo Sequencing and Peptide Identification2017-06-05 14:45:04
2017/03/20PEAKS AB: A software platform for LC-MS/MS based therapeutic protein characterization2017-03-20 05:39:30
2017/01/07Methionine oxidation analysis in therapeutic protein samples with PEAKS AB software2017-01-07 16:36:43
2016/09/19PEAKS AB – A software tool for monoclonal antibody sequencing and characterization with LC-MS/MS2016-09-19 16:41:23
2016/08/26Complete De Novo Assembly of Monoclonal Antibody Sequences2016-08-26 00:00:00
2016/06/05Protein-based PTM Quantitative Analysis by LC-MS/MS with PEAKS (Application Note)2016-06-05 16:42:56
2016/06/05New Cross Experiment Quantification Tool for SILAC/TMT: PEAKS Q2016-06-05 16:40:35
2016/06/05Towards the automated monoclonal antibody sequencing and characterization from LC-MS/MS data2016-06-05 08:48:27
2016/02/20Monoclonal Antibody (mAb) Characterization Using – PEAKS – Data Analysis Overview2016-02-20 16:59:52
2015/09/27PEAKS AB – A Reliable Workflow for Monoclonal Antibody Characterization2015-09-27 00:00:00
2015/06/03Peptide Mapping for Quantitative Profiling of Peptide Variants using PEAKS2015-06-03 00:00:00
2015/03/15Quantitative analysis of endogenous peptides with LC-MS/MS directly from complex secretome samples2015-03-15 00:00:00
2014/06/15Protein Identification and Quantitative Analysis with N-terminal Sequencing by Mass Spectrometry2014-06-15 00:00:00
2014/06/15Comparison of Label Free Quantification Tools2014-06-15 00:00:00
2014/03/31New LC MSMS Analysis Workflow to Discover Endogenous Peptides in Complex Bottom-Up Proteomics Data and Secretome Samples2014-03-31 00:00:00
2014/03/22Integrating de novo Sequencing and Database Search to Improve the Peptide Identification2014-03-22 00:00:00
2014/03/03Integrating Database Search and de novo Sequencing to Improve the Peptide Identification2014-03-03 00:00:00
2013/09/14A New Algorithm for Peptide de novo Sequencing with Multiple Complementary Spectra2013-09-14 15:53:10
2013/09/14PEAKS – A Software Tool for Shotgun Label Free Proteomics with High Sensitivity and High Accuracy2013-09-14 00:00:00
2013/07/15A Combinatorial Approach to the Peptide Feature Matching Problem for Label-Free Quantification2013-07-15 00:00:00
2013/06/11Peptide de novo Sequencing Result Validation2013-06-11 17:11:21
2013/06/10Whole Protein de novo Sequencing from MS/MS2013-06-10 16:33:58
2013/06/09Peptide Identification Using Protein Sequence Databases Derived from RNA-Seq Data2013-06-09 00:00:00
2013/06/09Software for Integrated and Interactive Visualization of LC-MS Data and Peptide Identification Results2013-06-09 00:00:00
2013/06/09Deconvolution of Overlapping Peptide Isotopic Peak Clusters with EM Algorithm for Label-Free Quantification2013-06-09 00:00:00
2013/03/02Integrating de novo Sequencing and Database Search for Monoclonal Antibody Sequencing2013-03-02 00:00:00
2012/10/01PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification2012-10-01 15:38:23
2012/09/09In Depth Analysis of Protein Amino Acid Sequence and PTMs with High-Resolution Mass Spectrometry2012-09-09 08:51:34
2012/09/09Analysis of Post Translational Modifications with AB SCIEX 5600 TripleTOF System2012-09-09 00:00:00
2012/09/09GlycoMaster DB: A Software Tool for Automated Glycopeptide Identification from MS/MS2012-09-09 00:00:00
2012/05/22Peptide Identification with High Mass Accuracy using Lock Mass Calibration2012-05-22 00:00:00
2012/05/22Combine Multiple Database Search Engines with Uniform FDR2012-05-22 00:00:00
2012/05/21Cross-Species Search for Accurate and Sensitive Peptide Identification2012-05-21 00:00:00
2012/05/20Analysis of post translational modifications with AB SCIEX TripleTOF 5600 System2012-05-20 00:00:00
2012/05/19How Useful Is the Product Ion Mass Accuracy for Peptide Identification?2012-05-19 00:00:00
2012/05/19In Depth Analysis of the Spectra Unassigned by Database Search2012-05-19 00:00:00
2012/05/19GlycoMaster: Glycopeptide High-Throughput Identification and Characterization Software2012-05-19 00:00:00
2012/05/19Optimized Database Search Software for Peptide Identification with AB SCIEX TripleTOF 56002012-05-19 00:00:00
2012/03/17Integrating de novo Sequencing and Database Search for Peptide Identification2012-03-17 16:17:26
2012/02/01De Novo Sequencing and Homology Searching2012-02-01 00:00:00
2011/09/04More Accurate Control of the False Discovery Rate in Mass Spectrometry Based Peptide Identification2011-09-04 00:00:00
2011/09/04ETD is Better, Period.2011-09-04 00:00:00
2011/09/03A Robust and Effective Strategy for Combining Results of Multiple Peptide Identification Engines2011-09-03 00:00:00
2011/09/03Identifying More Peptides at a Lower False Discovery Rate with PEAKS DB Software2011-09-03 00:00:00
2011/06/08New Computational Method for Identifying Peptides with Unspecified Post-Translational Modifications2011-06-08 00:00:00
2011/06/05PEAKS DB: New Software for Substantially Improved Peptide Identification from Orbitrap ETD Mass Spectrometry2011-06-05 16:39:37
2011/06/05Improvement in Analytical Software Makes a Difference on the Decision Tree Driven2011-06-05 00:00:00
2011/06/05De Novo Sequencing vs. Database Search2011-06-05 00:00:00
2011/05/24PeaksPTM: Mass Spectrometry-Based Identification of Peptides with Unspecified Modifications2011-05-24 00:00:00
2011/01/20PEAKS DB – Substantially Improved Peptide Identification.2011-01-20 00:00:00
2010/12/01ADEPTS: advanced peptide de novo sequencing with a pair of tandem mass spectra2010-12-01 00:00:00
2010/05/26Systematic Assessment of the Reproducibility of Relative Quantification Based on LC-MS with Replicates2010-05-26 00:00:00
2010/05/24No News is Good News: de novo Determination of Amino Acids when Peaks are Missing2010-05-24 16:35:46
2010/05/23Precursor Mono-Isotopic Mass and Charge Determination with Almost 100% Accuracy2010-05-23 00:00:00
2010/05/23Determining the False Discovery Rate for Peptide Identification without a Decoy Database2010-05-23 00:00:00
2010/01/18Better score function for peptide identification with ETD MS/MS spectra2010-01-18 00:00:00
2009/09/01Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy2009-09-01 00:00:00
2009/06/03Automated Multiple Round Searches to Increase Coverage of Peptide-Protein Identification2009-06-03 00:00:00
2009/06/03Modeling ETD Fragmentation with Bayesian Network for Peptide Identification2009-06-03 00:00:00
2009/05/31PTM Finder Based on PEAKS De Novo Sequencing Result2009-05-31 00:00:00
2009/05/31New Algorithm for Label-Free Protein Quantification2009-05-31 00:00:00
2009/03/01De Novo Interpretation of Tandem Mass Spectra2009-03-01 15:35:45
2008/06/04SPIDER: Novel Scoring Function Improves Homology Searches using MS/MS de novo Sequencing Results2008-06-04 00:00:00
2008/06/03PEAKS Online: A Free MS/MS de novo Sequencing and Protein ID Online Public Server2008-06-03 00:00:00
2008/06/03New Method for the Validation of de novo Sequencing Results2008-06-03 00:00:00
2008/06/02New Quantitation Software Package Based on PEAKS Protein ID2008-06-02 00:00:00
2007/06/06Peptide Sequence Reconstruction from de novo Sequences and their Homologues2007-06-06 00:00:00
2007/06/03Improving Protein Coverage by de novo Sequence Homology Searching with SPIDER2007-06-03 00:00:00
2007/06/03Disulfide bonded Dipeptide Analysis with PEAKS and Q-TOF Mass Spectrometry2007-06-03 00:00:00
2007/05/01Search for the Undiscovered Peptide, Using de novo sequencing and sequence tag homology search to improve protein characterization2007-05-01 00:00:00
2006/07/01Software for computational peptide identification from MS-MS data2006-07-01 00:00:00
2006/06/01PEAKS de novo performance on LTQ Orbitrap data2006-06-01 00:00:00
2006/05/30PEAKS Q: Software for MS-based quantification of stable isotope labeled peptides2006-05-30 00:00:00
2006/05/28Improved positional confidence score in MS/MS peptide de novo sequencing2006-05-28 00:00:00
2006/05/28Intact Peptide Charge Determination from Ion Trap MS/MS2006-05-28 00:00:00
2006/05/28Filtering out MS/MS spectra of insufficient quality before database searching2006-05-28 00:00:00
2006/05/18Drastically increased coverage by using four search engines for Protein Identification2006-05-18 00:00:00
2005/07/01SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error2005-07-01 00:00:00
2005/06/06Assessment of an Amalgamative Approach to Protein Identification2005-06-06 00:00:00
2005/06/05Improving the de novo Sequencing Accuracy by Combining Two Independent Scoring Functions in PEAKS Software2005-06-05 00:00:00
2004/05/24Protein ID: Comparing De Novo Based and Database Search Methods2004-05-24 00:00:00
2003/08/21PEAKS: Powerful software for peptide de novo sequencing by tandem mass spectrometry2003-08-21 00:00:00
2003/06/08A Comparative Study of Peptide Sequencing Software Tools for MS/MS2003-06-08 00:00:00