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Items: 1 to 50 of 103

1.

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome.

Duffy FJ, Weiner J 3rd, Hansen S, Tabb DL, Suliman S, Thompson E, Maertzdorf J, Shankar S, Tromp G, Parida S, Dover D, Axthelm MK, Sutherland JS, Dockrell HM, Ottenhoff THM, Scriba TJ, Picker LJ, Walzl G, Kaufmann SHE, Zak DE; GC6-74 Consortium.

Front Immunol. 2019 Mar 22;10:527. doi: 10.3389/fimmu.2019.00527. eCollection 2019.

2.

Proteomic analysis reveals that sulfamethoxazole induces oxidative stress in M. tuberculosis.

Sarkar R, Mdladla C, Macingwana L, Pietersen RD, Ngwane AH, Tabb DL, van Helden PD, Wiid I, Baker B.

Tuberculosis (Edinb). 2018 Jul;111:78-85. doi: 10.1016/j.tube.2018.05.010. Epub 2018 May 17.

PMID:
30029919
3.
4.

A Serum Circulating miRNA Signature for Short-Term Risk of Progression to Active Tuberculosis Among Household Contacts.

Duffy FJ, Thompson E, Downing K, Suliman S, Mayanja-Kizza H, Boom WH, Thiel B, Weiner Iii J, Kaufmann SHE, Dover D, Tabb DL, Dockrell HM, Ottenhoff THM, Tromp G, Scriba TJ, Zak DE, Walzl G; GC6-74 Consortium.

Front Immunol. 2018 Apr 13;9:661. doi: 10.3389/fimmu.2018.00661. eCollection 2018.

5.

Challenges and Opportunities for Biological Mass Spectrometry Core Facilities in the Developing World.

Bell L, Calder B, Hiller R, Klein A, Soares NC, Stoychev SH, Vorster BC, Tabb DL.

J Biomol Tech. 2018 Apr;29(1):4-15. doi: 10.7171/jbt.18-2901-003. Epub 2018 Mar 23.

6.

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.

Zhou JY, Chen L, Zhang B, Tian Y, Liu T, Thomas SN, Chen L, Schnaubelt M, Boja E, Hiltke T, Kinsinger CR, Rodriguez H, Davies SR, Li S, Snider JE, Erdmann-Gilmore P, Tabb DL, Townsend RR, Ellis MJ, Rodland KD, Smith RD, Carr SA, Zhang Z, Chan DW, Zhang H.

J Proteome Res. 2017 Dec 1;16(12):4523-4530. doi: 10.1021/acs.jproteome.7b00362. Epub 2017 Nov 16.

7.

Host blood RNA signatures predict the outcome of tuberculosis treatment.

Thompson EG, Du Y, Malherbe ST, Shankar S, Braun J, Valvo J, Ronacher K, Tromp G, Tabb DL, Alland D, Shenai S, Via LE, Warwick J, Aderem A, Scriba TJ, Winter J, Walzl G, Zak DE; Catalysis TB–Biomarker Consortium.

Tuberculosis (Edinb). 2017 Dec;107:48-58. doi: 10.1016/j.tube.2017.08.004. Epub 2017 Aug 12.

8.

Sipros Ensemble improves database searching and filtering for complex metaproteomics.

Guo X, Li Z, Yao Q, Mueller RS, Eng JK, Tabb DL, Hervey WJ 4th, Pan C.

Bioinformatics. 2018 Mar 1;34(5):795-802. doi: 10.1093/bioinformatics/btx601.

9.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

10.

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.

Heunis T, Dippenaar A, Warren RM, van Helden PD, van der Merwe RG, Gey van Pittius NC, Pain A, Sampson SL, Tabb DL.

J Proteome Res. 2017 Oct 6;16(10):3841-3851. doi: 10.1021/acs.jproteome.7b00483. Epub 2017 Sep 11.

PMID:
28820946
11.

Quality control in mass spectrometry-based proteomics.

Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K.

Mass Spectrom Rev. 2018 Sep;37(5):697-711. doi: 10.1002/mas.21544. Epub 2017 Sep 7. Review.

PMID:
28802010
12.

The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.

Bittremieux W, Walzer M, Tenzer S, Zhu W, Salek RM, Eisenacher M, Tabb DL.

Anal Chem. 2017 Apr 18;89(8):4474-4479. doi: 10.1021/acs.analchem.6b04310. Epub 2017 Mar 30.

PMID:
28318237
13.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
14.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.

Nat Methods. 2016 Aug;13(8):651-656. Epub 2016 Jun 27.

15.

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.

16.

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam MN, Griss J, Tabb DL.

Anal Chem. 2016 Jun 7;88(11):5733-41. doi: 10.1021/acs.analchem.6b00021. Epub 2016 May 24.

17.

Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data.

Baker MR, Tabb DL, Ching T, Zimmerman LJ, Sakharov IY, Li QX.

J Proteome Res. 2016 Jun 3;15(6):2026-38. doi: 10.1021/acs.jproteome.6b00205. Epub 2016 May 19.

PMID:
27151270
18.

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.

Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B.

Mol Cell Proteomics. 2016 Mar;15(3):1164-75. doi: 10.1074/mcp.M115.052860. Epub 2015 Dec 11.

19.

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res. 2016 Mar 4;15(3):691-706. doi: 10.1021/acs.jproteome.5b00859. Epub 2015 Dec 22.

20.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D.

Mol Cell Proteomics. 2016 Mar;15(3):1060-71. doi: 10.1074/mcp.M115.056226. Epub 2015 Dec 2.

21.

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry.

Basak T, Vega-Montoto L, Zimmerman LJ, Tabb DL, Hudson BG, Vanacore RM.

J Proteome Res. 2016 Jan 4;15(1):245-58. doi: 10.1021/acs.jproteome.5b00767. Epub 2015 Dec 9.

22.

Chronic intermittent alcohol disrupts the GluN2B-associated proteome and specifically regulates group I mGlu receptor-dependent long-term depression.

Wills TA, Baucum AJ 2nd, Holleran KM, Chen Y, Pasek JG, Delpire E, Tabb DL, Colbran RJ, Winder DG.

Addict Biol. 2017 Mar;22(2):275-290. doi: 10.1111/adb.12319. Epub 2015 Nov 8.

23.

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL.

Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.

24.

Correcting systematic bias and instrument measurement drift with mzRefinery.

Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH.

Bioinformatics. 2015 Dec 1;31(23):3838-40. doi: 10.1093/bioinformatics/btv437. Epub 2015 Aug 4.

25.

Corrigendum: Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC.

Sci Data. 2015 Jul 21;2:150037. doi: 10.1038/sdata.2015.37. eCollection 2015. No abstract available.

26.

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V.

J Proteome Res. 2015 Sep 4;14(9):3555-67. doi: 10.1021/acs.jproteome.5b00264. Epub 2015 Jul 21.

27.

The SEQUEST family tree.

Tabb DL.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1814-9. doi: 10.1007/s13361-015-1201-3. Epub 2015 Jun 30.

28.

Proteomic analysis of colon and rectal carcinoma using standard and customized databases.

Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC.

Sci Data. 2015 Jun 23;2:150022. doi: 10.1038/sdata.2015.22. eCollection 2015. Erratum in: Sci Data. 2015;2:150037. Wang, Xaojing [corrected to Wang, Xiaojing].

29.

Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.

French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, Townsend RR, Sherrod SD, Goodwin CR, McLean JA, Tabb DL.

J Proteome Res. 2015 Feb 6;14(2):1299-307. doi: 10.1021/pr500886y. Epub 2014 Dec 2.

30.

A standardized framing for reporting protein identifications in mzIdentML 1.2.

Seymour SL, Farrah T, Binz PA, Chalkley RJ, Cottrell JS, Searle BC, Tabb DL, Vizcaíno JA, Prieto G, Uszkoreit J, Eisenacher M, Martínez-Bartolomé S, Ghali F, Jones AR.

Proteomics. 2014 Nov;14(21-22):2389-99. doi: 10.1002/pmic.201400080. Epub 2014 Sep 23.

31.

Proteogenomic characterization of human colon and rectal cancer.

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC; NCI CPTAC.

Nature. 2014 Sep 18;513(7518):382-7. doi: 10.1038/nature13438. Epub 2014 Jul 20.

32.

Employing ProteoWizard to Convert Raw Mass Spectrometry Data.

Holman JD, Tabb DL, Mallick P.

Curr Protoc Bioinformatics. 2014 Jun 17;46:13.24.1-9. doi: 10.1002/0471250953.bi1324s46.

33.

Neurovascular unit on a chip: implications for translational applications.

Alcendor DJ, Block FE 3rd, 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.

Stem Cell Res Ther. 2013;4 Suppl 1:S18. doi: 10.1186/scrt379. Epub 2013 Dec 20. Review.

34.

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.

Anal Chem. 2014 Mar 4;86(5):2497-509. doi: 10.1021/ac4034455. Epub 2014 Feb 17.

35.

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.

J Biol Chem. 2013 Nov 1;288(44):31458-67. doi: 10.1074/jbc.M113.511337. Epub 2013 Sep 18.

36.

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.

J Proteome Res. 2013 Sep 6;12(9):4111-21. doi: 10.1021/pr400438q. Epub 2013 Aug 12.

37.

Informatics of protein and posttranslational modification detection via shotgun proteomics.

Holman JD, Dasari S, Tabb DL.

Methods Mol Biol. 2013;1002:167-79. doi: 10.1007/978-1-62703-360-2_14.

38.

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.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):86-95. doi: 10.1016/j.gpb.2012.11.004. Epub 2013 Mar 8.

39.

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.

Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20.

PMID:
23448308
40.

Quality assessment for clinical proteomics.

Tabb DL.

Clin Biochem. 2013 Apr;46(6):411-20. doi: 10.1016/j.clinbiochem.2012.12.003. Epub 2012 Dec 12. Review.

41.

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.

Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. No abstract available.

42.

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.

J Proteome Res. 2012 Nov 2;11(11):5265-76. doi: 10.1021/pr300476w. Epub 2012 Oct 5.

43.

Evaluating protein interactions through cross-linking mass spectrometry.

Tabb DL.

Nat Methods. 2012 Sep;9(9):879-81. doi: 10.1038/nmeth.2139. No abstract available.

44.

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.

Chem Res Toxicol. 2012 Oct 15;25(10):2179-93. doi: 10.1021/tx300253j. Epub 2012 Aug 14. Erratum in: Chem Res Toxicol. 2013 Feb 18;26(2):300.

45.

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.

Curr Biol. 2012 Aug 7;22(15):1403-9. doi: 10.1016/j.cub.2012.05.033. Epub 2012 Jul 12.

46.

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.

Anal Chem. 2012 Jul 17;84(14):5845-50. doi: 10.1021/ac300629p. Epub 2012 Jun 27.

47.

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.

Anal Bioanal Chem. 2012 Sep;404(4):1115-25. doi: 10.1007/s00216-012-6011-x. Epub 2012 May 3.

48.

Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.

Holman JD, Ma ZQ, Tabb DL.

Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.17. doi: 10.1002/0471250953.bi1317s37.

49.

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.

J Proteome Res. 2012 Mar 2;11(3):1686-95. doi: 10.1021/pr200874e. Epub 2012 Jan 27.

50.

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.

J Lipid Res. 2012 Mar;53(3):379-89. doi: 10.1194/jlr.M019752. Epub 2012 Jan 3.

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