BSI Publications

If you publish results obtained by PEAKS, please cite:

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

and/or the following papers:

  • Tran NH, Qiao R Xin L, Chen X, Liu C, Zhang X, Shan B, Ghodsi A, Li M. Deep learning enables de novo peptide sequencing from data-independent-acquistion mass spectrometry. Nature Methods. 16(1), 63-66. 20/12/2018.
  • Tran NH, Zhang X, Xin L, Shan B, Li M. De novo peptide sequencing by deep learning. Proceedings of the National Academy of Sciences of the United States of America. 114(29). 18/7/2017.
  • Tran NH, Rahman MZ, He L, Xin L, Shan B, Li M. Complete De Novo Assembly of Monoclonal Antibody Sequences. Scientific Reports. 6(31730). 26/08/2016
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
2014/06/15Comparison of Label Free Quantification Tools2014-06-15 00:00:00
2014/06/15Protein Identification and Quantitative Analysis with N-terminal Sequencing by Mass Spectrometry2014-06-15 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
2013/06/09Deconvolution of Overlapping Peptide Isotopic Peak Clusters with EM Algorithm for Label-Free Quantification2013-06-09 00:00:00
2013/06/09Software for Integrated and Interactive Visualization of LC-MS Data and Peptide Identification Results2013-06-09 00:00:00
2013/06/09Peptide Identification Using Protein Sequence Databases Derived from RNA-Seq Data2013-06-09 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
2012/05/22Combine Multiple Database Search Engines with Uniform FDR2012-05-22 00:00:00
2012/05/22Peptide Identification with High Mass Accuracy using Lock Mass Calibration2012-05-22 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
2012/05/19GlycoMaster: 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
2012/05/19How 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
2012/03/17Integrating 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
2011/09/04ETD is Better, Period.2011-09-04 00:00:00
2011/09/04More Accurate Control of the False Discovery Rate in Mass Spectrometry Based Peptide Identification2011-09-04 00:00:00
2011/09/03Identifying More Peptides at a Lower False Discovery Rate with PEAKS DB Software2011-09-03 00:00:00
2011/09/03A Robust and Effective Strategy for Combining Results of Multiple Peptide Identification Engines2011-09-03 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
2011/06/05De Novo Sequencing vs. Database Search2011-06-05 00:00:00
2011/06/05Improvement in Analytical Software Makes a Difference on the Decision Tree Driven2011-06-05 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
2010/05/23Determining the False Discovery Rate for Peptide Identification without a Decoy Database2010-05-23 00:00:00
2010/05/23Precursor Mono-Isotopic Mass and Charge Determination with Almost 100% Accuracy2010-05-23 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
2009/05/31New Algorithm for Label-Free Protein Quantification2009-05-31 00:00:00
2009/05/31PTM Finder Based on PEAKS De Novo Sequencing Result2009-05-31 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
2008/06/03New Method for the Validation of de novo Sequencing Results2008-06-03 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
2008/06/02New 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
2007/06/03Disulfide bonded Dipeptide Analysis with PEAKS and Q-TOF Mass Spectrometry2007-06-03 00:00:00
2007/06/03Improving Protein Coverage by de novo Sequence Homology Searching with SPIDER2007-06-03 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
2006/05/28Filtering out MS/MS spectra of insufficient quality before database searching2006-05-28 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
2006/05/18Drastically 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