Jiaxi Wang, Bin Ma, Weiwu Chen Disulfide bonded Dipeptide Analysis with PEAKS and Q-TOF Mass Spectrometry , ASMS 2007 poster MPK . 171 [download 269.152 Kb]
Here we present an algorithmic solution for the analysis of MS/MS data of disulfide bonded dipeptides.

Denis Yuen, Bin Ma, Iain Rogers Peptide Sequence Reconstruction from de novo Sequences and their Homologues, ASMS 2007 poster ThPP . 269 [download 188.051 Kb]
Here we present a technique for constructing the real peptide sequences from de novo sequences derived by PEAKS Studio and homologous entries from a database.

Weijie Yang, Denis Yuen, Bin Ma, Iain Rogers Improving Protein Coverage by de novo Sequence Homology Searching with SPIDER, ASMS 2007 poster MPK . 176 [download 223.669 Kb]
In this work we build and evaluate a workflow involving PEAKS auto de novo sequencing and SPIDER, a unique tool for peptide sequence tag based homology searching.

Denis Yuen, Bin Ma, Iain Rogers Improving de novo Sequencing Accuracy for Ion Trap data in PEAKS Software, ASMS 2007 poster MPK . 175 [download 333.416 Kb]
In this work, the optimal weighting between multiple de novo sequencing score components is trained on a large dataset, and is demonstrated to provide a significant accuracy improvement in PEAKS Studio.

Bin Ma, Iain Rogers, Search for the Undiscovered Peptide; Using de novo sequencing and sequence tag homology search to improve protein characterization, Biotechniques Journal, Vol. 42, No. 5, 2007. [download 255.786 Kb]
A new tool, SPIDER is used to discover hidden peptides. Using a de novo sequence and a homologous sequence from the database, SPIDER reconstructs the real peptide, highlighting mutations and allowing for de novo sequencing error.

Rogers, I., Application Note: New tools for peptide identification on high mass accuracy data. Unpublished, August 2006. [download 63.403 Kb]
A comparative performance analysis on Thermo LTQ Orbitrap data using PEAKS Protein ID search engine, and another popular search engine. PEAKS more than doubles the other's ability to explain spectra. Data will be made available, on request, to anyone wishing to reproduce this test.

Yang, W., Chen, W., Rogers, I., Ma, B., Bendall, S., Lajoie, G., Smith, D., PEAKS Q: Software for MS-based quantification of stable isotope labeled peptides (Bioinformatics Solutions Inc., Genome BC Proteomics Centre, University of Western Ontario) ASMS 2006 poster WP531 [download 620.172 Kb]
In this work we describe a new software, PEAKS-Q, designed to automatically identify and quantify proteins from these ICAT, SILAC and other stable isotope labeling experiments.

Clark Chen, Iain Rogers, Intact Peptide Charge Determination from Ion Trap MS/MS, ASMS 2006 poster MP327 [download 744.905 Kb]
This research presents an algorithm that will allow a researcher to determine a peptide’s charge using MS/MS data alone.

Bin Ma, Gilles Lajoie, Improved positional confidence score in MS/MS peptide de novo sequencing, ASMS 2006 poster MP348 [download 139.391 Kb]
A new “positional confidence score” is developed to indicate which parts of the de novo sequencing results are correct.

Clark Chen, John Morey, Iain Rogers, Filtering out MS/MS spectra of insufficient quality before database searching, ASMS 2006 poster MP329 [download 963.777 Kb]
A method of filtering out the poor quality spectra prior to de novo sequencing or database searching, so as to reduce the risk of false positives and improve search speed.

Rogers, I., Haskins, W., Drastically increased coverage by using four search engines for Protein Identification (Bioinformatics Solutions Inc, Genentech), ASMS 2006 poster MP328 [download 140.836 Kb]
This poster demonstrates the improvement in coverage by using more than one search engine. It should not be viewed as a benchmark comparison of search engines, as the performance shown is dependant on arbitrary score filter values. More important is the low error and high sensitivity when using a sequence tag hybrid approach (PEAKS) and a pure peptide fragment fingerprinting approach (like SEQUEST or MASCOT) together -- regardless of score!

Ma, B., Rogers, I.,Application Note: PEAKS de novo performance on LTQ Orbitrap data Unpublished, June 2006. [download 41.472 Kb]
A demonstration of the accuracy of PEAKS de novo sequencing on a Thermo LTQ Orbitrap mass spectrometer. 97% accuracy is acheived!

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 Bioliogy 3(3):697-716. 2005. [download 145.316 Kb]
In order to identify the protein by searching the de novo sequencing results in a protein database, the database search software must handle the mass gaps and the de novo sequencing errors. Accounting the de novo sequencing errors and the mass gaps, we developed a software system, SPIDER (Software Protein Identifier), for the rapid identification of proteins that contain peptides best matching the given tags. SPIDER is different and superior to the MS Blast system (Altschul et al.) as the latter does not account for the de novo sequencing errors and mass gaps.

Bin Ma; Gilles Lajoie (Departments of Computer Science and Biochemistry at the University of Western Ontario). Improving the de novo Sequencing Accuracy by Combining Two Independent Scoring Functions in PEAKS Software, ASMS 2005. [download 217.6 Kb]
By combining the original PEAKS scoring function and a new scoring function, the accuracy of PEAKS de novo sequencing is remarkably improved.

Iain Rogers. Assessment of an Amalgamative Approach to Protein Identification, ASMS 2005. [download 2034.572 Kb]
The following shows how two or more protein identification tools used in chorus, each confirming the results of the others, can improve quality of and confidence in results.

Jennifer Locke, Jason Rogalski, Lei Guo, Bin Ma, Juergen Kast, Gilles Lajoie (University of British Columbia, Bioinformatics Solutions Inc. & University of Western Ontario). Automated de novo Sequencing Using ToF-ToF MS/MS Data, ASMS 2005. [download 267.776 Kb]
PEAKS software works well for both de novo sequencing (with no protein database) and protein identification (with protein database) with MS/MS data obtained from MALDI ToF/ToF instrument.

Iain Rogers, Christopher Hendrie, Ming Li. Protein ID: Comparing De Novo Based and Database Search Methods, ASMS Poster, 2004. [download 208.207 Kb]
A demonstration of the de novo based protein ID approach used in PEAKS.

Bin Ma, Amanda Doherty-Kirby, Aaron Booy, Bob Olafson, Gilles Lajoie. A Comprehensive Comparison of the de novo Sequencing Accuracies of Peaks, and Other Software ASMS Poster, 2004. [download 33.834 Kb]
A second successful comparison between PEAKS and other de novo software tools.

Chengzhi Liang, Jeffrey C. Smith, Christopher Hendrie, Ming Li, K. W. Michael Siu. A Comparative Study of Peptide Sequencing Software Tools for MS/MS. ASMS Poster, 2003. [download 64.157 Kb]
PEAKS sets a standard in the first of several comparisons against other de novo software

Bin Ma, Kaizhong Zhang, Christopher Hendrie, Chengzhi Liang, Ming Li, Amanda Doherty-Kirby, Gilles Lajoie. PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS. Rapid Communications in Mass Spectrometry, 17(20):2337-2342. 2003. Early version appeared in 50th ASMS Conference 2002. [download 126.345 Kb]
If you plan to cite PEAKS in your research, please refer to this paper. PEAKS has come a long way since the original version, but the principles are the same.