recent publications

• academic article

  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. P., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) Proteomics  2012 12:11-20  DOI:10.1002/pmic.201100562  PMID:22069307
  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles) Molecular & Cellular Proteomics  2011 10:O111.015446  DOI:10.1074/mcp.O111.015446  PMID:22052993  PMCID:PMC3237091
  • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. P., Borchers, C. H., Bradshaw, R., Brusniak, M. Y., Chan, D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles) Proteomics Clinical Applications  2011 5:580-589  DOI:10.1002/prca.201100097  PMID:22213554
  • Cociorva, D., Tabb, D. L., Yates, J. R. Validation of tandem mass spectrometry database search results using DTASelect Current Protocols in Bioinformatics  2007 16:13.4.1-13.4.14  DOI:10.1002/0471250953.bi1304s16  PMID:18428785
  • Tabb, D. L., Huang, Y. Y., Wysocki, V. H., Yates, J. R. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides Analytical Chemistry  2004 76:1243-1248  DOI:10.1021/ac0351163  PMID:14987077  PMCID:PMC2813199
  • McDonald, W. H., Tabb, D. L., Sadygov, R. G., MacCoss, M. J., Venable, J., Graumann, J., Johnson, J. R., Cociorva, D., Yates, J. R. MS1, MS2, and SQT: three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications Rapid Communications in Mass Spectrometry  2004 18:2162-2168  DOI:10.1002/rcm.1603  PMID:15317041
  • Tabb, D. L., Saraf, A., Yates, J. R. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model Analytical Chemistry  2003 75:6415-6421  DOI:10.1021/ac0347462  PMID:14640709  PMCID:PMC2915448
  • Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., Yates, J. R. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility Analytical Chemistry  2003 75:2470-2477  DOI:10.1021/ac026424o  PMID:12918992
  • Breci, L. A., Tabb, D. L., Yates, J. R., Wysocki, V. H. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra Analytical Chemistry  2003 75:1963-1971  DOI:10.1021/ac026359i  PMID:12720328
  • Lin, D., Tabb, D. L., Yates, J. R. Large-scale protein identification using mass spectrometry Biochimica et Biophysica Acta-Proteins and Proteomics  2003 1646:1-10  DOI:10.1016/s1570-9639(02)00546-0  PMID:12637006
  • Tabb, D. L., Smith, L. L., Breci, L. A., Wysocki, V. H., Lin, D., Yates, J. R. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides Analytical Chemistry  2003 75:1155-1163  DOI:10.1021/ac026122m  PMID:12641236  PMCID:PMC2819022
  • Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., Witney, A. A., Wolters, D., et al. A proteomic view of the Plasmodium falciparum life cycle Nature  2002 419:520-526  DOI:10.1038/nature01107  PMID:12368866
  • Huang, Y. Y., Wysocki, V. H., Tabb, D. L., Yates, J. R. The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides International Journal of Mass Spectrometry  2002 219:233-244  DOI:10.1016/s1387-3806(02)00660-7
  • Tabb, D. L., McDonald, W. H., Yates, J. R. DTASelect and contrast: tools for assembling and comparing protein identifications from shotgun proteomics Journal of Proteome Research  2002 1:21-26  DOI:10.1021/pr015504q  PMID:12643522  PMCID:PMC2811961
  • Krahmer, M. T., Walters, J. J., Fox, K. F., Fox, A., Creek, K. E., Pirisi, L., Wunschel, D. S., Smith, R. D., Tabb, D. L., Yates, J. R. MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products Analytical Chemistry  2000 72:4033-4040  DOI:10.1021/ac000142b  PMID:10994962