WISB '06 Proceedings of the 2006 workshop on Intelligent systems for bioinformatics - Volume 73
ISNN '07 Proceedings of the 4th international symposium on Neural Networks: Part II--Advances in Neural Networks
Classification of Proteomic Signals by Block Kriging Error Matching
ICISP '08 Proceedings of the 3rd international conference on Image and Signal Processing
Classification of Mass Spectrometry Based Protein Markers by Kriging Error Matching
MDA '08 Proceedings of the 3rd international conference on Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry
A Clustering Based Hybrid System for Mass Spectrometry Data Analysis
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Computational prediction models for cancer classification using mass spectrometry data
International Journal of Data Mining and Bioinformatics
Peak detection using peak tree approach for mass spectrometry data
International Journal of Hybrid Intelligent Systems - Computational Models for Life Sciences
A time series representation model for accurate and fast similarity detection
Pattern Recognition
Efficient Peak-Labeling Algorithms for Whole-Sample Mass Spectrometry Proteomics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
AI'07 Proceedings of the 20th Australian joint conference on Advances in artificial intelligence
Mass spectrometry based cancer classification using fuzzy fractal dimensions
CIARP'07 Proceedings of the Congress on pattern recognition 12th Iberoamerican conference on Progress in pattern recognition, image analysis and applications
Computer Methods and Programs in Biomedicine
Chemical profiling of the plant cell wall through Raman microspectroscopy
ISBI'10 Proceedings of the 2010 IEEE international conference on Biomedical imaging: from nano to Macro
Bayesian peptide peak detection for high resolution TOF mass spectrometry
IEEE Transactions on Signal Processing
Feature detection techniques for preprocessing proteomic data
Journal of Biomedical Imaging - Special issue on mathematical methods for images and surfaces
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Feature extraction from mass spectra for classification of pathological states
PKDD'05 Proceedings of the 9th European conference on Principles and Practice of Knowledge Discovery in Databases
Gaussian mixture decomposition in the analysis of MALDI-TOF spectra
Expert Systems: The Journal of Knowledge Engineering
Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data
Information Sciences: an International Journal
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Motivation: Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantifications. Feature extraction and quantification involves a number of interrelated steps. It is important to perform these steps well, since subsequent analyses condition on these determinations. Also, it is difficult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known. Results: In this paper, we introduce a new method for feature extraction in mass spectrometry data that uses translation-invariant wavelet transforms and performs peak detection using the mean spectrum. We examine the method's performance through examples and simulation, and demonstrate the advantages of using the mean spectrum to detect peaks. We also describe a new physics-based computer model of mass spectrometry and demonstrate how one may design simulation studies based on this tool to systematically compare competing methods. Availability: MATLAB scripts to implement the methods described in this paper and R code for the virtual mass spectrometer are available at http://bioinformatics.mdanderson.org/software.html Contact: jefmorris@mdanderson.org Supplementary information: http://bioinformatics.mdanderson.org/supplements.html