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David Tabb

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Dong Wang; Matthew C Chambers; Kan Chen; Chang Y Chung; Surendra Dasari; Jerry D Holman; Daniel C Liebler; Matthew E Monroe; Daniel J Orton; Samuel O Purvine; Kristie L Rose; David L Tabb
Basophile: accurate fragment charge state prediction improves Peptide identification rates.
David L Tabb
Quality assessment for clinical proteomics.
Jerry D Holman; Surendra Dasari; David L Tabb
Informatics of Protein and Posttranslational Modification Detection via Shotgun Proteomics.

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All Publications

2013: Dong Wang; Matthew C Chambers; Kan Chen; Chang Y Chung; Surendra Dasari; Jerry D Holman; Daniel C Liebler; Matthew E Monroe; Daniel J Orton; Samuel O Purvine; Kristie L Rose; David L Tabb
Basophile: accurate fragment charge state prediction improves Peptide identification rates.
Genomics, proteomics & bioinformatics 2013;11(2):86-95.
2013: David L Tabb
Quality assessment for clinical proteomics.
Clinical biochemistry 2013;46(6):411-20.
2013: Jerry D Holman; Surendra Dasari; David L Tabb
Informatics of Protein and Posttranslational Modification Detection via Shotgun Proteomics.
Methods in molecular biology (Clifton, N.J.) 2013;1002():167-79.
2012: Lijuan Peng; David L Tabb; Surendra Dasari; Robert J Turesky
Mapping serum albumin adducts of the food-borne carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine by data-dependent tandem mass spectrometry.
Chemical research in toxicology 2012;25(10):2179-93.
2012: David L Tabb
Evaluating protein interactions through cross-linking mass spectrometry.
Nature methods 2012;9(9):879-81.
2012: Yao-Yi Chen; Surendra Dasari; Ming Li; Ze-Qiang Ma; Lorenzo J Vega-Montoto; David L Tabb
Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.
Analytical and bioanalytical chemistry 2012;404(4):1115-25.
2012: John G Gibbons; Jonas G King; Maren A Klich; W Hayes McDonald; Kriston L McGary; David C Rinker; Leonidas Salichos; Jason C Slot; David L Tabb; Antonis Rokas
The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.
Current biology : CB 2012;22(15):1403-9.
2012: Ze-Qiang Ma; Kenneth O Polzin; Birgit Schilling; Matthew C Chambers; Surendra Dasari; Bradford W Gibson; Daniel C Liebler; Bao Q Tran; Lorenzo Vega-Montoto; David L Tabb
QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation.
Analytical chemistry 2012;84(14):5845-50.
2012: Surendra Dasari; Amy-Joan L Ham; Misti A Martinez; Kristin L Carpenter; Matthew C Chambers; Lorenzo J Vega-Montoto; David L Tabb
Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
Journal of proteome research 2012;11(3):1686-95.
2012: Jerry D Holman; Ze-Qiang Ma; David L Tabb
Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2012;Chapter 13():Unit13.17.
2012: Xiaojing Wang; Patrick J Halvey; Daniel C Liebler; Robbert J C Slebos; David L Tabb; Dong Wang; Bing Zhang
Protein identification using customized protein sequence databases derived from RNA-Seq data.
Journal of proteome research 2012;11(2):1009-17.
2011: Ze-Qiang Ma; Michael R Oreto; William C Schultz; Scott M Sobecki; David L Tabb; Tina Y Tsui; Gregory R Wernke; Joseph Burden; Michael J Cantrell; Matthew C Chambers; Matthew B Cox; Amy-Joan L Ham; Michael D Litton; Daniel C Liebler
Supporting tool suite for production proteomics.
Bioinformatics (Oxford, England) 2011;27(22):3214-5.
2011: Jimmy K Eng; Brian C Searle; Karl R Clauser; David L Tabb
A face in the crowd: recognizing peptides through database search.
Molecular & cellular proteomics : MCP 2011;10(11):R111.009522.
2011: Ze-Qiang Ma; Aaron W Miller; Birgit Schilling; Hans Aerni; Richard M Caprioli; Matthew C Chambers; Kristin L Cheek; Amy-Joan L Ham; Corbin W Whitwell; David L Tabb
ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.
Journal of proteome research 2011;10(7):2896-904.
2011: Russell E McConnell; Andrew E Benesh; Suli Mao; David L Tabb; Matthew J Tyska
Proteomic analysis of the enterocyte brush border.
American journal of physiology. Gastrointestinal and liver physiology 2011;300(5):G914-26.
2011: Surendra Dasari; Matthew C Chambers; Simona G Codreanu; Daniel C Liebler; Ben C Collins; Stephen R Pennington; William M Gallagher; David L Tabb
Sequence tagging reveals unexpected modifications in toxicoproteomics.
Chemical research in toxicology 2011;24(2):204-16.
2010: Surendra Dasari; Matthew C Chambers; Robbert J Slebos; Lisa J Zimmerman; Amy-Joan L Ham; David L Tabb
TagRecon: high-throughput mutation identification through sequence tagging.
Journal of proteome research 2010;9(4):1716-26.
2010: Brendan MacLean; Daniela M Tomazela; Nicholas Shulman; Matthew Chambers; Gregory L Finney; Barbara Frewen; Randall Kern; David L Tabb; Daniel C Liebler; Michael J MacCoss
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
Bioinformatics (Oxford, England) 2010;26(7):966-8.
2009: Ze-Qiang Ma; Surendra Dasari; Matthew C Chambers; Michael D Litton; Scott M Sobecki; Lisa J Zimmerman; Patrick J Halvey; Birgit Schilling; Penelope M Drake; Bradford W Gibson; David L Tabb
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
Journal of proteome research 2009;8(8):3872-81.
2009: Elisabeth M Loecken; Surendra Dasari; Salisha Hill; David L Tabb; F Peter Guengerich
The bis-electrophile diepoxybutane cross-links DNA to human histones but does not result in enhanced mutagenesis in recombinant systems.
Chemical research in toxicology 2009;22(6):1069-76.
2008: Diana R Arnett; Jennifer L Jennings; David L Tabb; Andrew J Link; P Anthony Weil
A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism.
Molecular & cellular proteomics : MCP 2008;7(11):2090-106.
2008: David L Tabb; Ze-Qiang Ma; Daniel B Martin; Amy-Joan L Ham; Matthew C Chambers
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.
Journal of proteome research 2008;7(9):3838-46.
2008: David L Tabb
What's driving false discovery rates?
Journal of proteome research 2008;7(1):45-6.
2006: Chongle Pan; Guruprasad Kora; W Hayes McDonald; David L Tabb; Nathan C VerBerkmoes; Gregory B Hurst; Dale A Pelletier; Nagiza F Samatova; Robert L Hettich
ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation.
Analytical chemistry 2006;78(20):7121-31.
2006: Chongle Pan; Guruprasad Kora; David L Tabb; Dale A Pelletier; W Hayes McDonald; Gregory B Hurst; Robert L Hettich; Nagiza F Samatova
Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics.
Analytical chemistry 2006;78(20):7110-20.
2006: David L Tabb; Manesh B Shah; Michael Brad Strader; Heather M Connelly; Robert L Hettich; Gregory B Hurst
Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra.
Journal of the American Society for Mass Spectrometry 2006;17(7):903-15.
2006: Nathan C VerBerkmoes; Manesh B Shah; Patricia K Lankford; Dale A Pelletier; Michael Brad Strader; David L Tabb; W Hayes McDonald; John W Barton; Gregory B Hurst; Loren Hauser; Brian H Davison; J Thomas Beatty; Caroline S Harwood; F Robert Tabita; Robert L Hettich; Frank W Larimer
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states.
Journal of proteome research 2006;5(2):287-98.
2006: Michael Brad Strader; David L Tabb; W Judson Hervey; Chongle Pan; Gregory B Hurst
Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems.
Analytical chemistry 2006;78(1):125-34.
2005: Chandrasegaran Narasimhan; David L Tabb; Nathan C VerBerkmoes; Melissa R Thompson; Robert L Hettich; Edward C Uberbacher
MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence.
Analytical chemistry 2005;77(23):7581-93.
2005: David L Tabb; Melissa R Thompson; Gurusahai Khalsa-Moyers; Nathan C VerBerkmoes; W Hayes McDonald
MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.
Journal of the American Society for Mass Spectrometry 2005;16(8):1250-61.
2005: David L Tabb; Chandrasegaran Narasimhan; Michael Brad Strader; Robert L Hettich
DBDigger: reorganized proteomic database identification that improves flexibility and speed.
Analytical chemistry 2005;77(8):2464-74.
2004: Michael Brad Strader; Nathan C VerBerkmoes; David L Tabb; Heather M Connelly; John W Barton; Barry D Bruce; Dale A Pelletier; Brian H Davison; Robert L Hettich; Frank W Larimer; Gregory B Hurst
Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach.
Journal of proteome research 2004;3(5):965-78.
2004: David L Tabb; Yingying Huang; Vicki H Wysocki; John R Yates
Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.
Analytical chemistry 2004;76(5):1243-8.
2004: W Hayes McDonald; David L Tabb; Rovshan G Sadygov; Michael J MacCoss; John D Venable; Johannes Graumann; Jeff R Johnson; Daniel Cociorva; John R Yates
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 : RCM 2004;18(18):2162-8.
2003: David L Tabb; Anita Saraf; John R Yates
GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.
Analytical chemistry 2003;75(23):6415-21.
2003: David L Tabb; Michael J MacCoss; Christine C Wu; Scott D Anderson; John R Yates
Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility.
Analytical chemistry 2003;75(10):2470-7.
2003: Linda Breci; David L Tabb; John R Yates; Vicki H Wysocki
Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra.
Analytical chemistry 2003;75(9):1963-71.
2003: Dayin Lin; David L Tabb; John R Yates
Large-scale protein identification using mass spectrometry.
Biochimica et biophysica acta 2003;1646(1-2):1-10.
2003: David L Tabb; Lori L Smith; Linda Breci; Vicki H Wysocki; Dayin Lin; John R Yates
Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides.
Analytical chemistry 2003;75(5):1155-63.
2002: Laurence Florens; Michael Washburn; J Dale Raine; Robert M Anthony; Munira Grainger; J David Haynes; J Kathleen Moch; Nemone Muster; John B Sacci; David L Tabb; Adam A Witney; Dirk Wolters; Yimin Wu; Malcolm J Gardner; Anthony A Holder; Robert E Sinden; John R Yates; Daniel J Carucci
A proteomic view of the Plasmodium falciparum life cycle.
Nature 2002;419(6906):520-6.
2002: David L Tabb; W Hayes McDonald; John R Yates
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.
Journal of proteome research 2002;1(1):21-6.