TANDEM

TANDEM: matching proteins with tandem mass spectra. 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.


References in zbMATH (referenced in 10 articles )

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  1. D.C.L. Handler, P.A. Haynes: PeptideMind - Applying machine learning algorithms to assess replicate quality in shotgun proteomic data (2021) not zbMATH
  2. Mitra, Riten; Gill, Ryan; Sikdar, Sinjini; Datta, Susmita: Bayesian hierarchical model for protein identifications (2019)
  3. Canan Has; Jens Allmer: PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization (2017) not zbMATH
  4. Chen, Chuming; McGarvey, Peter B.; Huang, Hongzhan; Wu, Cathy H.: Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput “omics” data (2010) ioport
  5. Karpievitch, Yuliya V.; Polpitiya, Ashoka D.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.: Liquid chromatography mass spectrometry-based proteomics: biological and technological aspects (2010)
  6. Fu, Yan; Jia, Wei; Lu, Zhuang; Wang, Haipeng; Yuan, Zuofei; Chi, Hao; Li, You; Xiu, Liyun; Wang, Wenping; Liu, Chao; Wang, Leheng; Sun, Ruixiang; Gao, Wen; Qian, Xiaohong; He, Simin: Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences (2009) ioport
  7. Loevenich, Sandra N.; Brunner, Erich; King, Nichole L.; Deutsch, Eric W.; Stein, Stephen E.; Aebersold, Ruedi; Hafen, Ernst: The drosophila melanogaster peptideatlas facilitates the use of peptide data for improved fly proteomics and genome annotation (2009) ioport
  8. Ma, Bin: Challenges in computational analysis of mass spectrometry data for proteomics (2009) ioport
  9. Wong, Jason W. H.; Schwahn, Alexander B.; Downard, Kevin M.: ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics (2009) ioport
  10. Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G.; Kohlbacher, Oliver: Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics (2007) ioport