Mining Mass Spectrometry Database Search Results--A Rough Set Approach
RSEISP '07 Proceedings of the international conference on Rough Sets and Intelligent Systems Paradigms
Protein identification as an information retrieval problem
Proceedings of the 32nd international ACM SIGIR conference on Research and development in information retrieval
Protein Identification from Tandem Mass Spectra with Probabilistic Language Modeling
ECML PKDD '09 Proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases: Part II
Improved ranking functions for protein and modification-site identifications
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
A high-throughput bioinformatics platform for mass spectrometry-based proteomics
DILS'07 Proceedings of the 4th international conference on Data integration in the life sciences
A fragmentation event model for peptide identification by mass spectrometry
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
A Bayesian approach to protein inference problem in shotgun proteomics
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
A Partial Set Covering Model for Protein Mixture Identification Using Mass Spectrometry Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ECML PKDD'11 Proceedings of the 2011 European conference on Machine learning and knowledge discovery in databases - Volume Part II
A new approach to protein identification
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Peptide Reranking with Protein-Peptide Correspondence and Precursor Peak Intensity Information
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Neural network-based method for peptide identification in proteomics
ITIB'12 Proceedings of the Third international conference on Information Technologies in Biomedicine
A Combinatorial Perspective of the Protein Inference Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary: Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. Availability: The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.