Biomedical Research Education & Training
Faculty Member

Tabb, David L., Ph.D.
Associate Professor of Biomedical Informatics
Associate Professor of Biochemistry

Lab Url: http://fenchurch.mc.vanderbilt.edu

Phone Number: (615)936-0380

Email Address: david.l.tabb@vanderbilt.edu

Tabb, David's picture
Academic history
B.S., University of Arkansas
Ph.D., University of Washington
Post-doc, Oak Ridge National Laboratory

Office Address   Mailing Address

MRB III / Learned Lab U9211

465 21st Ave. S. Learned Lab / MRB III, room U9211 37232-8575


Research Keywords
bioinformatics, lipidomics, biomolecular fragmentation, data mining, biomolecular identification,Mass spectroscopy,Proteomics

Research Specialty
Identification of peptide or lipid mixtures via tandem mass spectrometry.

Research Description
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.

Publications
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

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 PMCID:3042045

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

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 PMCID:3098595

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 PMCID:3128668

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 PMCID:3208394

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 PMCID:3094140

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

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

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 PMCID:2836977

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

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 PMCID:2836977

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, 5, 303, 2009 PMCID:2736651

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 PMCID:2696559

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 PMCID:2810655

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 PMCID:2712962

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 PMCID:2577210

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 PMCID:2811579

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 PMCID:2528074

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 PMCID:2669493

Tabb, DL. What''s driving false discovery rates. J Proteome Res, 7(1), 45-6, 2008 PMCID:2810656

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 PMCID:2810657

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 PMCID:2525619

Zhang, B, Chambers, MC, Tabb, DL. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res, 6(9), 3549-57, 2007

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

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

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, 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

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

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, Narasimhan, C, Strader, MB, Hettich, RL. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem, 77(8), 2464-74, 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

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

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

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

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, 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

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


Postdoctoral Position Available
Yes

Postdoctoral Position Details
A postdoctoral position to develop new algorithms for proteomic tandem mass spectrometry is available immediately. A Ph.D. in analytical chemistry, biochemistry, biotechnology, computer science, mathematics, electrical engineering, or a related field is required. Programming experience and exposure to statistics and mass spectrometry are preferred. Please send curriculum vitae and names of three references to:
David L. Tabb
Mass Spectrometry Research Center
Learned Lab / MRB III U9211
465 21st Ave S
Nashville, TN 37232-8575

Updated Date
01/06/2012