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.


The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. Employing ProteoWizard to Convert Raw Mass Spectrometry Data. Holman JD, Tabb DL, Mallick P (2014) Curr Protoc Bioinformatics : 13.24.1-9
    › Primary publication · 24939128 (PubMed) · PMC4113728 (PubMed Central)
  2. Neurovascular unit on a chip: implications for translational applications. Alcendor DJ, Block FE, Cliffel DE, Daniels JS, Ellacott KL, Goodwin CR, Hofmeister LH, Li D, Markov DA, May JC, McCawley LJ, McLaughlin B, McLean JA, Niswender KD, Pensabene V, Seale KT, Sherrod SD, Sung HJ, Tabb DL, Webb DJ, Wikswo JP (2013) Stem Cell Res Ther : S18
    › Primary publication · 24564885 (PubMed) · PMC4029462 (PubMed Central)
  3. QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Wang X, Chambers MC, Vega-Montoto LJ, Bunk DM, Stein SE, Tabb DL (2014) Anal Chem 86(5): 2497-509
    › Primary publication · 24494671 (PubMed) · PMC3982976 (PubMed Central)
  4. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, Cortez D (2013) J Biol Chem 288(44): 31458-67
    › Primary publication · 24047897 (PubMed) · PMC3814742 (PubMed Central)
  5. IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification. Chen YY, Chambers MC, Li M, Ham AJ, Turner JL, Zhang B, Tabb DL (2013) J Proteome Res 12(9): 4111-21
    › Primary publication · 23879310 (PubMed) · PMC3804902 (PubMed Central)
  6. Informatics of protein and posttranslational modification detection via shotgun proteomics. Holman JD, Dasari S, Tabb DL (2013) Methods Mol Biol : 167-79
    › Primary publication · 23625403 (PubMed) · PMC4012295 (PubMed Central)
  7. Basophile: accurate fragment charge state prediction improves peptide identification rates. Wang D, Dasari S, Chambers MC, Holman JD, Chen K, Liebler DC, Orton DJ, Purvine SO, Monroe ME, Chung CY, Rose KL, Tabb DL (2013) Genomics Proteomics Bioinformatics 11(2): 86-95
    › Primary publication · 23499924 (PubMed) · PMC3737598 (PubMed Central)
  8. HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V (2013) Anal Chem 85(7): 3515-20
    › Primary publication · 23448308 (PubMed)
  9. Quality assessment for clinical proteomics. Tabb DL (2013) Clin Biochem 46(6): 411-20
    › Primary publication · 23246537 (PubMed) · PMC3602213 (PubMed Central)
  10. A cross-platform toolkit for mass spectrometry and proteomics. Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P (2012) Nat Biotechnol 30(10): 918-20
    › Primary publication · 23051804 (PubMed) · PMC3471674 (PubMed Central)
  11. Proteomic analysis of Chinese hamster ovary cells. Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J, Jacobson E, Tian Y, O'Meally RN, Krag SS, Cole RN, Palsson BO, Zhang H, Betenbaugh M (2012) J Proteome Res 11(11): 5265-76
    › Primary publication · 22971049 (PubMed) · PMC3772721 (PubMed Central)
  12. Evaluating protein interactions through cross-linking mass spectrometry. Tabb DL (2012) Nat Methods 9(9): 879-81
    › Primary publication · 22936167 (PubMed) · PMC3730130 (PubMed Central)
  13. 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. Peng L, Dasari S, Tabb DL, Turesky RJ (2012) Chem Res Toxicol 25(10): 2179-93
    › Primary publication · 22827630 (PubMed) · PMC3544159 (PubMed Central)
  14. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A (2012) Curr Biol 22(15): 1403-9
    › Primary publication · 22795693 (PubMed) · PMC3416971 (PubMed Central)
  15. QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation. Ma ZQ, Polzin KO, Dasari S, Chambers MC, Schilling B, Gibson BW, Tran BQ, Vega-Montoto L, Liebler DC, Tabb DL (2012) Anal Chem 84(14): 5845-50
    › Primary publication · 22697456 (PubMed) · PMC3730131 (PubMed Central)
  16. Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines. Chen YY, Dasari S, Ma ZQ, Vega-Montoto LJ, Li M, Tabb DL (2012) Anal Bioanal Chem 404(4): 1115-25
    › Primary publication · 22552787 (PubMed) · PMC3717168 (PubMed Central)
  17. Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker. Holman JD, Ma ZQ, Tabb DL (2012) Curr Protoc Bioinformatics : Unit13.17
    › Primary publication · 22389012 (PubMed) · PMC4547833 (PubMed Central)
  18. Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. Dasari S, Chambers MC, Martinez MA, Carpenter KL, Ham AJ, Vega-Montoto LJ, Tabb DL (2012) J Proteome Res 11(3): 1686-95
    › Primary publication · 22217208 (PubMed) · PMC3292681 (PubMed Central)
  19. Obesity and altered glucose metabolism impact HDL composition in CETP transgenic mice: a role for ovarian hormones. Martinez MN, Emfinger CH, Overton M, Hill S, Ramaswamy TS, Cappel DA, Wu K, Fazio S, McDonald WH, Hachey DL, Tabb DL, Stafford JM (2012) J Lipid Res 53(3): 379-389
    › Primary publication · 22215797 (PubMed) · PMC3276461 (PubMed Central)
  20. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). 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 (2011) Proteomics Clin Appl 5(11-12): 580-9
    › Primary publication · 22213554 (PubMed)
  21. Protein identification using customized protein sequence databases derived from RNA-Seq data. Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B (2012) J Proteome Res 11(2): 1009-17
    › Primary publication · 22103967 (PubMed) · PMC3727138 (PubMed Central)
  22. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). 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 (2012) Proteomics 12(1): 11-20
    › Primary publication · 22069307 (PubMed)
  23. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). 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 (2012) J Proteome Res 11(2): 1412-9
    › Primary publication · 22053864 (PubMed) · PMC3272102 (PubMed Central)
  24. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). 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 (2011) Mol Cell Proteomics 10(12): O111.015446
    › Primary publication · 22052993 (PubMed) · PMC3237091 (PubMed Central)
  25. Supporting tool suite for production proteomics. 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 (2011) Bioinformatics 27(22): 3214-5
    › Primary publication · 21965817 (PubMed) · PMC3208394 (PubMed Central)
  26. A face in the crowd: recognizing peptides through database search. Eng JK, Searle BC, Clauser KR, Tabb DL (2011) Mol Cell Proteomics 10(11): R111.009522
    › Primary publication · 21876205 (PubMed) · PMC3226415 (PubMed Central)
  27. ScanRanker: Quality assessment of tandem mass spectra via sequence tagging. Ma ZQ, Chambers MC, Ham AJ, Cheek KL, Whitwell CW, Aerni HR, Schilling B, Miller AW, Caprioli RM, Tabb DL (2011) J Proteome Res 10(7): 2896-904
    › Primary publication · 21520941 (PubMed) · PMC3128668 (PubMed Central)
  28. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B (2011) Mol Cell Proteomics 10(5): M110.006536
    › Primary publication · 21389108 (PubMed) · PMC3098595 (PubMed Central)
  29. Proteomic analysis of the enterocyte brush border. McConnell RE, Benesh AE, Mao S, Tabb DL, Tyska MJ (2011) Am J Physiol Gastrointest Liver Physiol 300(5): G914-26
    › Primary publication · 21330445 (PubMed) · PMC3094140 (PubMed Central)
  30. Sequence tagging reveals unexpected modifications in toxicoproteomics. Dasari S, Chambers MC, Codreanu SG, Liebler DC, Collins BC, Pennington SR, Gallagher WM, Tabb DL (2011) Chem Res Toxicol 24(2): 204-16
    › Primary publication · 21214251 (PubMed) · PMC3042045 (PubMed Central)
  31. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ (2010) Bioinformatics 26(7): 966-8
    › Primary publication · 20147306 (PubMed) · PMC2844992 (PubMed Central)
  32. TagRecon: high-throughput mutation identification through sequence tagging. Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJ, Tabb DL (2010) J Proteome Res 9(4): 1716-26
    › Primary publication · 20131910 (PubMed) · PMC2859315 (PubMed Central)
  33. Identification and validation of novel spinophilin-associated proteins in rodent striatum using an enhanced ex vivo shotgun proteomics approach. Baucum AJ, Jalan-Sakrikar N, Jiao Y, Gustin RM, Carmody LC, Tabb DL, Ham AJ, Colbran RJ (2010) Mol Cell Proteomics 9(6): 1243-59
    › Primary publication · 20124353 (PubMed) · PMC2877984 (PubMed Central)
  34. Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes. Burgess EF, Ham AJ, Tabb DL, Billheimer D, Roth BJ, Chang SS, Cookson MS, Hinton TJ, Cheek KL, Hill S, Pietenpol JA (2008) Proteomics Clin Appl 2(9): 1223
    › Primary publication · 20107526 (PubMed) · PMC2811579 (PubMed Central)
  35. Differential localization and dynamics of class I myosins in the enterocyte microvillus. Benesh AE, Nambiar R, McConnell RE, Mao S, Tabb DL, Tyska MJ (2010) Mol Biol Cell 21(6): 970-8
    › Primary publication · 20089841 (PubMed) · PMC2836977 (PubMed Central)
  36. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. 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 (2010) J Proteome Res 9(2): 761-76
    › Primary publication · 19921851 (PubMed) · PMC2818771 (PubMed Central)
  37. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Paulovich AG, Billheimer D, Ham AJ, Vega-Montoto L, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR, Zimmerman LJ, Fenyo D, Carr SA, Fisher SJ, Gibson BW, Mesri M, Neubert TA, Regnier FE, Rodriguez H, Spiegelman C, Stein SE, Tempst P, Liebler DC (2010) Mol Cell Proteomics 9(2): 242-54
    › Primary publication · 19858499 (PubMed) · PMC2830837 (PubMed Central)
  38. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE (2010) Mol Cell Proteomics 9(2): 225-41
    › Primary publication · 19837981 (PubMed) · PMC2830836 (PubMed Central)
  39. Network-assisted protein identification and data interpretation in shotgun proteomics. Li J, Zimmerman LJ, Park BH, Tabb DL, Liebler DC, Zhang B (2009) Mol Syst Biol : 303
    › Primary publication · 19690572 (PubMed) · PMC2736651 (PubMed Central)
  40. The enterocyte microvillus is a vesicle-generating organelle. McConnell RE, Higginbotham JN, Shifrin DA, Tabb DL, Coffey RJ, Tyska MJ (2009) J Cell Biol 185(7): 1285-98
    › Primary publication · 19564407 (PubMed) · PMC2712962 (PubMed Central)
  41. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA (2009) Nat Biotechnol 27(7): 633-41
    › Primary publication · 19561596 (PubMed) · PMC2855883 (PubMed Central)
  42. IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL (2009) J Proteome Res 8(8): 3872-81
    › Primary publication · 19522537 (PubMed) · PMC2810655 (PubMed Central)
  43. The bis-electrophile diepoxybutane cross-links DNA to human histones but does not result in enhanced mutagenesis in recombinant systems. Loecken EM, Dasari S, Hill S, Tabb DL, Guengerich FP (2009) Chem Res Toxicol 22(6): 1069-76
    › Primary publication · 19364102 (PubMed) · PMC2696559 (PubMed Central)
  44. Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC (2008) J Proteome Res 7(12): 5286-94
    › Primary publication · 18939861 (PubMed) · PMC2669493 (PubMed Central)
  45. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC (2008) J Proteome Res 7(9): 3838-46
    › Primary publication · 18630943 (PubMed) · PMC2810657 (PubMed Central)
  46. A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Arnett DR, Jennings JL, Tabb DL, Link AJ, Weil PA (2008) Mol Cell Proteomics 7(11): 2090-106
    › Primary publication · 18596064 (PubMed) · PMC2577210 (PubMed Central)
  47. Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. 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 (2008) Mol Cell Proteomics 7(9): 1651-67
    › Primary publication · 18504258 (PubMed) · PMC2528074 (PubMed Central)
  48. What's driving false discovery rates? Tabb DL (2008) J Proteome Res 7(1): 45-6
    › Primary publication · 18081243 (PubMed) · PMC2810656 (PubMed Central)
  49. Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences. Padliya ND, Garrett WM, Campbell KB, Tabb DL, Cooper B (2007) Proteomics 7(21): 3932-42
    › Primary publication · 17922518 (PubMed) · PMC2810652 (PubMed Central)
  50. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Zhang B, Chambers MC, Tabb DL (2007) J Proteome Res 6(9): 3549-57
    › Primary publication · 17676885 (PubMed) · PMC2810678 (PubMed Central)
  51. Verification of automated peptide identifications from proteomic tandem mass spectra. Tabb DL, Friedman DB, Ham AJ (2006) Nat Protoc 1(5): 2213-22
    › Primary publication · 17406459 (PubMed) · PMC2819013 (PubMed Central)
  52. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Tabb DL, Fernando CG, Chambers MC (2007) J Proteome Res 6(2): 654-61
    › Primary publication · 17269722 (PubMed) · PMC2525619 (PubMed Central)
  53. ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Pan C, Kora G, McDonald WH, Tabb DL, VerBerkmoes NC, Hurst GB, Pelletier DA, Samatova NF, Hettich RL (2006) Anal Chem 78(20): 7121-31
    › Primary publication · 17037911 (PubMed)
  54. Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics. Pan C, Kora G, Tabb DL, Pelletier DA, McDonald WH, Hurst GB, Hettich RL, Samatova NF (2006) Anal Chem 78(20): 7110-20
    › Primary publication · 17037910 (PubMed)
  55. Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra. Tabb DL, Shah MB, Strader MB, Connelly HM, Hettich RL, Hurst GB (2006) J Am Soc Mass Spectrom 17(7): 903-915
    › Primary publication · 16713712 (PubMed)
  56. Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. 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 (2006) J Proteome Res 5(2): 287-98
    › Primary publication · 16457594 (PubMed)
  57. Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Strader MB, Tabb DL, Hervey WJ, Pan C, Hurst GB (2006) Anal Chem 78(1): 125-34
    › Primary publication · 16383319 (PubMed)
  58. MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence. Narasimhan C, Tabb DL, Verberkmoes NC, Thompson MR, Hettich RL, Uberbacher EC (2005) Anal Chem 77(23): 7581-93
    › Primary publication · 16316165 (PubMed)
  59. MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. Tabb DL, Thompson MR, Khalsa-Moyers G, VerBerkmoes NC, McDonald WH (2005) J Am Soc Mass Spectrom 16(8): 1250-61
    › Primary publication · 15979332 (PubMed)
  60. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Tabb DL, Narasimhan C, Strader MB, Hettich RL (2005) Anal Chem 77(8): 2464-74
    › Primary publication · 15828782 (PubMed)
  61. Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach. Strader MB, Verberkmoes NC, Tabb DL, Connelly HM, Barton JW, Bruce BD, Pelletier DA, Davison BH, Hettich RL, Larimer FW, Hurst GB (2004) J Proteome Res 3(5): 965-78
    › Primary publication · 15473684 (PubMed)
  62. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR (2004) Rapid Commun Mass Spectrom 18(18): 2162-8
    › Primary publication · 15317041 (PubMed)
  63. Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Tabb DL, Huang Y, Wysocki VH, Yates JR (2004) Anal Chem 76(5): 1243-8
    › Primary publication · 14987077 (PubMed) · PMC2813199 (PubMed Central)
  64. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Tabb DL, Saraf A, Yates JR (2003) Anal Chem 75(23): 6415-21
    › Primary publication · 14640709 (PubMed) · PMC2915448 (PubMed Central)
  65. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR (2003) Anal Chem 75(10): 2470-7
    › Primary publication · 12918992 (PubMed)
  66. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Breci LA, Tabb DL, Yates JR, Wysocki VH (2003) Anal Chem 75(9): 1963-71
    › Primary publication · 12720328 (PubMed)
  67. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. Tabb DL, McDonald WH, Yates JR (2002) J Proteome Res 1(1): 21-6
    › Primary publication · 12643522 (PubMed) · PMC2811961 (PubMed Central)
  68. Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Tabb DL, Smith LL, Breci LA, Wysocki VH, Lin D, Yates JR (2003) Anal Chem 75(5): 1155-63
    › Primary publication · 12641236 (PubMed) · PMC2819022 (PubMed Central)
  69. Large-scale protein identification using mass spectrometry. Lin D, Tabb DL, Yates JR (2003) Biochim Biophys Acta 1646(1-2): 1-10
    › Primary publication · 12637006 (PubMed)
  70. A proteomic view of the Plasmodium falciparum life cycle. 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 (2002) Nature 419(6906): 520-6
    › Primary publication · 12368866 (PubMed)
  71. MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products. Krahmer MT, Walters JJ, Fox KF, Fox A, Creek KE, Pirisi L, Wunschel DS, Smith RD, Tabb DL, Yates JR (2000) Anal Chem 72(17): 4033-40
    › Primary publication · 10994962 (PubMed)