David L. Tabb, Ph.D.
Associate Professor of Biochemistry, Biomedical Informatics
Mass Spectrometry Bioinformaticist
Vanderbilt University Medical Center
Learned Lab / MRB III, Room U9211, 465 21st Ave. S.
Nashville, TN 37232-8575
The Tabb Laboratory designs and evaluates algorithms in support of clinical proteomics. In brief, proteomics is the science of identifying and characterizing all proteins in complex mixtures. Since most biological processes involve the action of proteins, knowing which proteins take part can often tell much of the story of a biological process. In most proteomics experiments, we begin by digesting proteins with enzymes, yielding peptides. We generate tandem mass spectra of these peptides that reveal the structure of these molecules. Our software then matches a sequence to each spectrum or deduces the sequence directly from the observed ions. The challenge of identification has been an active area of research for more than a decade, and yet many problems remain.
Our group is also interested in the emerging science of lipidomics, which addresses the problems of identifying lipids in complex mixtures. Lipidomics has huge potential to aid in our understanding of digestive and metabolic disease. This field, however, has not been actively supported by bioinformatics. We hope to build some of the fundamental tools that will support lipid identification and quantification through mass spectrometry.
Identification of peptide or lipid mixtures via tandem mass spectrometry.
Tandem mass spectrometry provides sensitive, high-throughput data from complex mixtures of biomolecules. Individual spectra (ms/ms) show the fragments produced by fragmenting an individual peptide or lipid. Bioinformatic tools reveal the sequences of peptides or the composition of lipid species by analyzing the fragment ions in each spectrum. Likewise, data mining tools assemble the results for collections of spectra to give a higher-level characterization of samples. My laboratory is focused on the creation and improvement of tools to propel systems biology via mass spectrometry.
- Martinez, MN, Emfinger, CH, Overton, MH, Hill, S, Ramaswamy, TS, Cappel, DA, Wu, K, Fazio, S, McDonald, WH, Hachey, DL, Tabb, DL, Stafford, JM Obesity and altered glucose metabolism impact HDL composition in CETP transgenic mice: A role for ovarian hormones. J Lipid Res, 2012.
- Li, J, Su, Z, Ma, ZQ, Slebos, RJ, Halvey, P, Tabb, DL, Liebler, DC, Pao, W, Zhang, B A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics, 10(5), M110.006536, 2011.
- Wang, X, Slebos, RJ, Wang, D, Halvey, PJ, Tabb, DL, Liebler, DC, Zhang, B Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data. J Proteome Res, 2011.
- McConnell, RE, Benesh, AE, Mao, S, Tabb, DL, Tyska, MJ Proteomic analysis of the enterocyte brush border. Am J Physiol Gastrointest Liver Physiol, 300(5), G914-26, 2011.
- Kinsinger, CR, Apffel, J, Baker, M, Bian, X, Borchers, CH, Bradshaw, R, Brusniak, MY, Chan, DW, Deutsch, EW, Domon, B, Gorman, J, Grimm, R, Hancock, W, Hermjakob, H, Horn, D, Hunter, C, Kolar, P, Kraus, HJ, Langen, H, Linding, R, Moritz, RL, Omenn, GS, Orlando, R, Pandey, A, Ping, P, Rahbar, A, Rivers, R, Seymour, SL, Simpson, RJ, Slotta, D, Smith, RD, Stein, SE, Tabb, DL, Tagle, D, Yates, JR, Rodriguez, H Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). Mol Cell Proteomics, 10(12), O111.015446, 2011.
- Kinsinger, CR, Apffel, J, Baker, M, Bian, X, Borchers, CH, Bradshaw, R, Brusniak, MY, Chan, DW, Deutsch, EW, Domon, B, Gorman, J, Grimm, R, Hancock, W, Hermjakob, H, Horn, D, Hunter, C, Kolar, P, Kraus, HJ, Langen, H, Linding, R, Moritz, RL, Omenn, GS, Orlando, R, Pandey, A, Ping, P, Rahbar, A, Rivers, R, Seymour, SL, Simpson, RJ, Slotta, D, Smith, RD, Stein, SE, Tabb, DL, Tagle, D, Yates, JR, Rodriguez, H Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). J Proteome Res, 2011.
- Ma, ZQ, Chambers, MC, Ham, AJ, Cheek, KL, Whitwell, CW, Aerni, HR, Schilling, B, Miller, AW, Caprioli, RM, Tabb, DL ScanRanker: Quality assessment of tandem mass spectra via sequence tagging. J Proteome Res, 10(7), 2896-904, 2011.
- Dasari, S, Chambers, MC, Codreanu, SG, Liebler, DC, Collins, BC, Pennington, SR, Gallagher, WM, Tabb, DL Sequence tagging reveals unexpected modifications in toxicoproteomics. Chem Res Toxicol, 24(2), 204-16, 2011.
- Ma, ZQ, Tabb, DL, Burden, J, Chambers, MC, Cox, MB, Cantrell, MJ, Ham, AJ, Litton, MD, Oreto, MR, Schultz, WC, Sobecki, SM, Tsui, TY, Wernke, GR, Liebler, DC Supporting tool suite for production proteomics. Bioinformatics, 27(22), 3214-5, 2011.
- Benesh, AE, Nambiar, R, McConnell, RE, Mao, S, Tabb, DL, Tyska, MJ Differential localization and dynamics of class I myosins in the enterocyte microvillus. Mol Biol Cell, 21(6), 970-8, 2010.
- Baucum, AJ, Jalan-Sakrikar, N, Jiao, Y, Gustin, RM, Carmody, LC, Tabb, DL, Ham, AJ, Colbran, RJ Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach. Mol Cell Proteomics, 9(6), 1243-59, 2010.
- Tabb, DL, Vega-Montoto, L, Rudnick, PA, Variyath, AM, Ham, AJ, Bunk, DM, Kilpatrick, LE, Billheimer, DD, Blackman, RK, Cardasis, HL, Carr, SA, Clauser, KR, Jaffe, JD, Kowalski, KA, Neubert, TA, Regnier, FE, Schilling, B, Tegeler, TJ, Wang, M, Wang, P, Whiteaker, JR, Zimmerman, LJ, Fisher, SJ, Gibson, BW, Kinsinger, CR, Mesri, M, Rodriguez, H, Stein, SE, Tempst, P, Paulovich, AG, Liebler, DC, Spiegelman, C Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res, 9(2), 761-76, 2010.
- Dasari, S, Chambers, MC, Slebos, RJ, Zimmerman, LJ, Ham, AJ, Tabb, DL TagRecon: high-throughput mutation identification through sequence tagging. J Proteome Res, 9(4), 1716-26, 2010.
- Ma, ZQ, Dasari, S, Chambers, MC, Litton, MD, Sobecki, SM, Zimmerman, LJ, Halvey, PJ, Schilling, B, Drake, PM, Gibson, BW, Tabb, DL IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. J Proteome Res, 8(8), 3872-81, 2009.
- Li, J, Zimmerman, LJ, Park, BH, Tabb, DL, Liebler, DC, Zhang, B Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol, 5303, 2009.
- Loecken, EM, Dasari, S, Hill, S, Tabb, DL, Guengerich, FP The bis-electrophile diepoxybutane cross-links DNA to human histones but does not result in enhanced mutagenesis in recombinant systems. Chem Res Toxicol, 22(6), 1069-76, 2009.
- McConnell, RE, Higginbotham, JN, Shifrin, DA, Tabb, DL, Coffey, RJ, Tyska, MJ The enterocyte microvillus is a vesicle-generating organelle. J Cell Biol, 185(7), 1285-98, 2009.
- Arnett, DR, Jennings, JL, Tabb, DL, Link, AJ, Weil, PA A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol Cell Proteomics, 7(11), 2090-106, 2008.
- Tabb, DL, Ma, ZQ, Martin, DB, Ham, AJ, Chambers, MC DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res, 7(9), 3838-46, 2008.
- Slebos, RJ, Brock, JW, Winters, NF, Stuart, SR, Martinez, MA, Li, M, Chambers, MC, Zimmerman, LJ, Ham, AJ, Tabb, DL, Liebler, DC Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res, 7(12), 5286-94, 2008.
- Burgess, EF, Ham, AJ, Tabb, DL, Billheimer, D, Roth, BJ, Chang, SS, Cookson, MS, Hinton, TJ, Cheek, KL, Hill, S, Pietenpol, JA Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes. Proteomics Clin Appl, 2(9), 1223-1233, 2008.
- Cao, Z, Li, C, Higginbotham, JN, Franklin, JL, Tabb, DL, Graves-Deal, R, Hill, S, Cheek, K, Jerome, WG, Lapierre, LA, Goldenring, JR, Ham, AJ, Coffey, RJ Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. Mol Cell Proteomics, 7(9), 1651-67, 2008.
- Tabb, DL What''s driving false discovery rates. J Proteome Res, 7(1), 45-6, 2008.
- Tabb, DL, Fernando, CG, Chambers, MC MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res, 6(2), 654-61, 2007.
- Zhang, B, Chambers, MC, Tabb, DL Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res, 6(9), 3549-57, 2007.
- VerBerkmoes, NC, Shah, MB, Lankford, PK, Pelletier, DA, Strader, MB, Tabb, DL, McDonald, WH, Barton, JW, Hurst, GB, Hauser, L, Davison, BH, Beatty, JT, Harwood, CS, Tabita, FR, Hettich, RL, Larimer, FW Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J Proteome Res, 5(2), 287-98, 2006.
- Tabb, DL, Shah, MB, Strader, MB, Connelly, HM, Hettich, RL, Hurst, GB Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra. J Am Soc Mass Spectrom, 17(7), 903-15, 2006.
- Strader, MB, Tabb, DL, Hervey, WJ, Pan, C, Hurst, GB Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Anal Chem, 78(1), 125-34, 2006.
- Pan, C, Kora, G, McDonald, WH, Tabb, DL, VerBerkmoes, NC, Hurst, GB, Pelletier, DA, Samatova, NF, Hettich, RL ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Anal Chem, 78(20), 7121-31, 2006.
- Pan, C, Kora, G, Tabb, DL, Pelletier, DA, McDonald, WH, Hurst, GB, Hettich, RL, Samatova, NF Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics. Anal Chem, 78(20), 7110-20, 2006.
- Tabb, DL, Friedman, DB, Ham, AJ Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006.
- Tabb, DL, Narasimhan, C, Strader, MB, Hettich, RL DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem, 77(8), 2464-74, 2005.
- Narasimhan, C, Tabb, DL, Verberkmoes, NC, Thompson, MR, Hettich, RL, Uberbacher, EC MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Anal Chem, 77(23), 7581-93, 2005.
- Tabb, DL, Thompson, MR, Khalsa-Moyers, G, Verberkmoes, NC, McDonald, WH MS2Grouper: Group Assessment and Synthetic Replacement of Duplicate Proteomic Tandem Mass Spectra. J Am Soc Mass Spectrom, 16(8), 1250-61, 2005.
- Strader, MB, Verberkmoes, NC, Tabb, DL, Connelly, HM, Barton, JW, Bruce, BD, Pelletier, DA, Davison, BH, Hettich, RL, Larimer, FW, Hurst, GB Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. J Proteome Res, 3(5), 965-78, 2004.
- Tabb, DL, Huang, Y, Wysocki, VH, Yates, JR Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal Chem, 76(5), 1243-8, 2004.
- McDonald, WH, Tabb, DL, Sadygov, RG, MacCoss, MJ, Venable, J, Graumann, J, Johnson, JR, Cociorva, D, Yates, JR MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom, 18(18), 2162-8, 2004.
- Breci, LA, Tabb, DL, Yates, JR, Wysocki, VH Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem, 75(9), 1963-71, 2003.
- Tabb, DL, McDonald, WH, Yates, JR DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res, 1(1), 21-6, 2003.
- Tabb, DL, Saraf, A, Yates, JR GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal Chem, 75(23), 6415-21, 2003.
- Lin, D, Tabb, DL, Yates, JR Large-scale protein identification using mass spectrometry. Biochim Biophys Acta, 1646(1-2), 1-10, 2003.
- Tabb, DL, MacCoss, MJ, Wu, CC, Anderson, SD, Yates, JR Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem, 75(10), 2470-7, 2003.
- Tabb, DL, Smith, LL, Breci, LA, Wysocki, VH, Lin, D, Yates, JR Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem, 75(5), 1155-63, 2003.
- Florens, L, Washburn, MP, Raine, JD, Anthony, RM, Grainger, M, Haynes, JD, Moch, JK, Muster, N, Sacci, JB, Tabb, DL, Witney, AA, Wolters, D, Wu, Y, Gardner, MJ, Holder, AA, Sinden, RE, Yates, JR, Carucci, DJ A proteomic view of the Plasmodium falciparum life cycle. Nature, 419(6906), 520-6, 2002.
- Krahmer, MT, Walters, JJ, Fox, KF, Fox, A, Creek, KE, Pirisi, L, Wunschel, DS, Smith, RD, Tabb, DL, Yates, JR MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products. Anal Chem, 72(17), 4033-40, 2000.
- Ph.D. Molecular Biotechnology from University of Washington
- B.S. Major: Biology, Minor: Computer Science from University of Arkansas