| Year |
Citation |
Score |
| 2024 |
Tabb DL, Kaniyar MH, Bringas OGR, Shin H, Di Stefano L, Taylor MS, Xie S, Yilmaz OH, LaCava J. Interrogating data-independent acquisition LC-MS/MS for affinity proteomics. Journal of Proteins and Proteomics. 15: 281-298. PMID 39372605 DOI: 10.1007/s42485-024-00166-4 |
0.364 |
|
| 2024 |
Bielow C, Hoffmann N, Jimenez-Morales D, Van Den Bossche T, Vizcaíno JA, Tabb DL, Bittremieux W, Walzer M. Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java. Journal of the American Society For Mass Spectrometry. PMID 38918936 DOI: 10.1021/jasms.4c00174 |
0.32 |
|
| 2023 |
Potgieter MG, Nel AJM, Fortuin S, Garnett S, Wendoh JM, Tabb DL, Mulder NJ, Blackburn JM. MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. Plos Computational Biology. 19: e1011163. PMID 37327214 DOI: 10.1371/journal.pcbi.1011163 |
0.37 |
|
| 2023 |
Tabb DL, Jeong K, Druart K, Gant MS, Brown KA, Nicora C, Zhou M, Couvillion S, Nakayasu E, Williams JE, Peterson HK, McGuire MK, McGuire MA, Metz TO, Chamot-Rooke J. Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection. Journal of Proteome Research. PMID 37235544 DOI: 10.1021/acs.jproteome.2c00673 |
0.309 |
|
| 2020 |
Kriek M, Monyai K, Magcwebeba TU, Plessis ND, Stoychev SH, Tabb DL. Interrogating fractionation and other sources of variability in shotgun proteomes using quality metrics. Proteomics. e1900382. PMID 32415754 DOI: 10.1002/Pmic.201900382 |
0.362 |
|
| 2020 |
Tabb DL, Murugan BD, Okendo J, Nair O, Blackburn JM, Buthelezi SG, Stoychev S. Open search unveils modification patterns in formalin-fixed, paraffin-embedded thermo HCD and SCIEX TripleTOF shotgun proteomes International Journal of Mass Spectrometry. 448: 116266. DOI: 10.1016/J.Ijms.2019.116266 |
0.414 |
|
| 2017 |
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, ... ... Tabb DL, et al. Quality Assessments of Long-term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. Journal of Proteome Research. PMID 29124938 DOI: 10.1021/Acs.Jproteome.7B00362 |
0.439 |
|
| 2016 |
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. In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics. PMID 27498275 DOI: 10.1016/J.Jprot.2016.08.002 |
0.489 |
|
| 2016 |
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. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods. 13: 651-656. PMID 27493588 DOI: 10.1038/Nmeth.3902 |
0.381 |
|
| 2016 |
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, ... ... Tabb DL, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/J.Cell.2016.05.069 |
0.385 |
|
| 2016 |
Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam N, Tabb DL. Greazy: open-source software for automated phospholipid MS/MS identification. Analytical Chemistry. PMID 27186799 DOI: 10.1021/Acs.Analchem.6B00021 |
0.43 |
|
| 2015 |
Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B. proBAMsuite, a bioinformatics framework for genome-based representation and analysis of proteomics data. Molecular & Cellular Proteomics : McP. PMID 26657539 DOI: 10.1074/Mcp.M115.052860 |
0.4 |
|
| 2015 |
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, et al. Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts. Journal of Proteome Research. PMID 26653538 DOI: 10.1021/Acs.Jproteome.5B00859 |
0.432 |
|
| 2015 |
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, et al. An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Molecular & Cellular Proteomics : McP. PMID 26631509 DOI: 10.1074/Mcp.M115.056226 |
0.454 |
|
| 2015 |
Basak T, Vega-Montoto L, Zimmerman LJ, Tabb DL, Hudson BG, Vanacore RM. Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry. Journal of Proteome Research. PMID 26593852 DOI: 10.1021/Acs.Jproteome.5B00767 |
0.352 |
|
| 2015 |
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. The 2012 ABRF Proteomic Research Group Study: Assessing Longitudinal Intra-Laboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses. Molecular & Cellular Proteomics : McP. PMID 26435129 DOI: 10.1074/Mcp.O115.051888 |
0.43 |
|
| 2015 |
Gibbons BC, Chambers MC, Monroe ME, Tabb DL, Payne SH. Correcting systematic bias and instrument measurement drift with mzRefinery. Bioinformatics (Oxford, England). PMID 26243018 DOI: 10.1093/Bioinformatics/Btv437 |
0.309 |
|
| 2015 |
Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC. Corrigendum: Proteomic analysis of colon and rectal carcinoma using standard and customized databases. Scientific Data. 2: 150037. PMID 26217491 DOI: 10.1038/Sdata.2015.37 |
0.321 |
|
| 2015 |
Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. Journal of Proteome Research. 14: 3555-67. PMID 26139413 DOI: 10.1021/Acs.Jproteome.5B00264 |
0.397 |
|
| 2015 |
Tabb DL. The SEQUEST Family Tree. Journal of the American Society For Mass Spectrometry. PMID 26122518 DOI: 10.1007/S13361-015-1201-3 |
0.318 |
|
| 2015 |
Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC. Proteomic analysis of colon and rectal carcinoma using standard and customized databases. Scientific Data. 2: 150022. PMID 26110064 DOI: 10.1038/Sdata.2015.22 |
0.374 |
|
| 2015 |
French WR, Zimmerman LJ, Schilling B, Gibson BW, Miller CA, Townsend RR, Sherrod SD, Goodwin CR, McLean JA, Tabb DL. Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert. Journal of Proteome Research. 14: 1299-307. PMID 25411686 DOI: 10.1021/Pr500886Y |
0.465 |
|
| 2014 |
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. A standardized framing for reporting protein identifications in mzIdentML 1.2. Proteomics. 14: 2389-99. PMID 25092112 DOI: 10.1002/Pmic.201400080 |
0.429 |
|
| 2014 |
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, ... ... Tabb DL, et al. Proteogenomic characterization of human colon and rectal cancer. Nature. 513: 382-7. PMID 25043054 DOI: 10.1038/Nature13438 |
0.377 |
|
| 2014 |
Holman JD, Tabb DL, Mallick P. Employing ProteoWizard to Convert Raw Mass Spectrometry Data. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 46: 13.24.1-9. PMID 24939128 DOI: 10.1002/0471250953.Bi1324S46 |
0.424 |
|
| 2014 |
Wang X, Chambers MC, Vega-Montoto LJ, Bunk DM, Stein SE, Tabb DL. QC metrics from CPTAC raw LC-MS/MS data interpreted through multivariate statistics. Analytical Chemistry. 86: 2497-509. PMID 24494671 DOI: 10.1021/Ac4034455 |
0.451 |
|
| 2013 |
Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, Cortez D. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. The Journal of Biological Chemistry. 288: 31458-67. PMID 24047897 DOI: 10.1074/Jbc.M113.511337 |
0.329 |
|
| 2013 |
Chen YY, Chambers MC, Li M, Ham AJ, Turner JL, Zhang B, Tabb DL. IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification. Journal of Proteome Research. 12: 4111-21. PMID 23879310 DOI: 10.1021/Pr400438Q |
0.474 |
|
| 2013 |
Holman JD, Dasari S, Tabb DL. Informatics of protein and posttranslational modification detection via shotgun proteomics. Methods in Molecular Biology (Clifton, N.J.). 1002: 167-79. PMID 23625403 DOI: 10.1007/978-1-62703-360-2_14 |
0.461 |
|
| 2013 |
Wang D, Dasari S, Chambers MC, Holman JD, Chen K, Liebler DC, Orton DJ, Purvine SO, Monroe ME, Chung CY, Rose KL, Tabb DL. Basophile: accurate fragment charge state prediction improves peptide identification rates. Genomics, Proteomics & Bioinformatics. 11: 86-95. PMID 23499924 DOI: 10.1016/J.Gpb.2012.11.004 |
0.353 |
|
| 2013 |
Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, VizcaÃno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, et al. HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions. Analytical Chemistry. 85: 3515-20. PMID 23448308 DOI: 10.1021/Ac303239G |
0.449 |
|
| 2013 |
Tabb DL. Quality assessment for clinical proteomics. Clinical Biochemistry. 46: 411-20. PMID 23246537 DOI: 10.1016/J.Clinbiochem.2012.12.003 |
0.398 |
|
| 2012 |
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, ... ... Tabb DL, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology. 30: 918-20. PMID 23051804 DOI: 10.1038/Nbt.2377 |
0.469 |
|
| 2012 |
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, et al. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research. 11: 5265-76. PMID 22971049 DOI: 10.1021/Pr300476W |
0.512 |
|
| 2012 |
Tabb DL. Evaluating protein interactions through cross-linking mass spectrometry. Nature Methods. 9: 879-81. PMID 22936167 DOI: 10.1038/Nmeth.2139 |
0.393 |
|
| 2012 |
Peng L, Dasari S, Tabb DL, Turesky RJ. 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. 25: 2179-93. PMID 22827630 DOI: 10.1021/Tx300253J |
0.32 |
|
| 2012 |
Ma ZQ, Polzin KO, Dasari S, Chambers MC, Schilling B, Gibson BW, Tran BQ, Vega-Montoto L, Liebler DC, Tabb DL. QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation. Analytical Chemistry. 84: 5845-50. PMID 22697456 DOI: 10.1021/Ac300629P |
0.435 |
|
| 2012 |
Chen YY, Dasari S, Ma ZQ, Vega-Montoto LJ, Li M, Tabb DL. Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines. Analytical and Bioanalytical Chemistry. 404: 1115-25. PMID 22552787 DOI: 10.1007/S00216-012-6011-X |
0.475 |
|
| 2012 |
Holman JD, Ma ZQ, Tabb DL. Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit13.17. PMID 22389012 DOI: 10.1002/0471250953.Bi1317S37 |
0.488 |
|
| 2012 |
Dasari S, Chambers MC, Martinez MA, Carpenter KL, Ham AJ, Vega-Montoto LJ, Tabb DL. Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. Journal of Proteome Research. 11: 1686-95. PMID 22217208 DOI: 10.1021/Pr200874E |
0.505 |
|
| 2012 |
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. Journal of Proteome Research. 11: 1009-17. PMID 22103967 DOI: 10.1021/Pr200766Z |
0.428 |
|
| 2012 |
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, ... ... Tabb DL, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Proteomics. 12: 11-20. PMID 22069307 DOI: 10.1002/Pmic.201100562 |
0.383 |
|
| 2012 |
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, ... ... Tabb DL, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Journal of Proteome Research. 11: 1412-9. PMID 22053864 DOI: 10.1021/Pr201071T |
0.384 |
|
| 2012 |
Wang X, Slebos RJC, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B. Correction to Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data Journal of Proteome Research. 11: 4764-4764. DOI: 10.1021/Pr300713G |
0.385 |
|
| 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, ... ... Tabb DL, et al. Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). Molecular & Cellular Proteomics : McP. 10: O111.015446. PMID 22052993 DOI: 10.1074/Mcp.O111.015446 |
0.384 |
|
| 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 (Oxford, England). 27: 3214-5. PMID 21965817 DOI: 10.1093/Bioinformatics/Btr544 |
0.383 |
|
| 2011 |
Eng JK, Searle BC, Clauser KR, Tabb DL. A face in the crowd: recognizing peptides through database search. Molecular & Cellular Proteomics : McP. 10: R111.009522. PMID 21876205 DOI: 10.1074/Mcp.R111.009522 |
0.486 |
|
| 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. Journal of Proteome Research. 10: 2896-904. PMID 21520941 DOI: 10.1021/Pr200118R |
0.485 |
|
| 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. Molecular & Cellular Proteomics : McP. 10: M110.006536. PMID 21389108 DOI: 10.1074/Mcp.M110.006536 |
0.452 |
|
| 2011 |
McConnell RE, Benesh AE, Mao S, Tabb DL, Tyska MJ. Proteomic analysis of the enterocyte brush border. American Journal of Physiology. Gastrointestinal and Liver Physiology. 300: G914-26. PMID 21330445 DOI: 10.1152/Ajpgi.00005.2011 |
0.347 |
|
| 2011 |
Dasari S, Chambers MC, Codreanu SG, Liebler DC, Collins BC, Pennington SR, Gallagher WM, Tabb DL. Sequence tagging reveals unexpected modifications in toxicoproteomics. Chemical Research in Toxicology. 24: 204-16. PMID 21214251 DOI: 10.1021/Tx100275T |
0.463 |
|
| 2011 |
Tabb DL, Liebler DC. Bioinformatic challenges for proteomic biomarkers of cancer Bmc Bioinformatics. 12: 1-1. DOI: 10.1186/1471-2105-12-S7-A17 |
0.437 |
|
| 2010 |
MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (Oxford, England). 26: 966-8. PMID 20147306 DOI: 10.1093/Bioinformatics/Btq054 |
0.43 |
|
| 2010 |
Dasari S, Chambers MC, Slebos RJ, Zimmerman LJ, Ham AJ, Tabb DL. TagRecon: high-throughput mutation identification through sequence tagging. Journal of Proteome Research. 9: 1716-26. PMID 20131910 DOI: 10.1021/Pr900850M |
0.418 |
|
| 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. Molecular & Cellular Proteomics : McP. 9: 1243-59. PMID 20124353 DOI: 10.1074/Mcp.M900387-Mcp200 |
0.39 |
|
| 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, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. Journal of Proteome Research. 9: 761-76. PMID 19921851 DOI: 10.1021/Pr9006365 |
0.512 |
|
| 2010 |
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, et al. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Molecular & Cellular Proteomics : McP. 9: 242-54. PMID 19858499 DOI: 10.1074/Mcp.M900222-Mcp200 |
0.46 |
|
| 2010 |
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, ... ... Tabb DL, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Molecular & Cellular Proteomics : McP. 9: 225-41. PMID 19837981 DOI: 10.1074/Mcp.M900223-Mcp200 |
0.426 |
|
| 2010 |
Li J, Ma Z, Slebos RJC, Tabb DL, Liebler DC, Zhang B. Enabling proteomics-based identification of human cancer variations Bmc Bioinformatics. 11: 29. DOI: 10.1186/1471-2105-11-S4-P29 |
0.435 |
|
| 2009 |
Li J, Zimmerman LJ, Park BH, Tabb DL, Liebler DC, Zhang B. Network-assisted protein identification and data interpretation in shotgun proteomics. Molecular Systems Biology. 5: 303. PMID 19690572 DOI: 10.1038/Msb.2009.54 |
0.402 |
|
| 2009 |
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, ... ... Tabb DL, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nature Biotechnology. 27: 633-41. PMID 19561596 DOI: 10.1038/Nbt.1546 |
0.375 |
|
| 2009 |
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. Journal of Proteome Research. 8: 3872-81. PMID 19522537 DOI: 10.1021/Pr900360J |
0.476 |
|
| 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. Clinical Applications. 2: 1223. PMID 20107526 DOI: 10.1002/Prca.200780073 |
0.335 |
|
| 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. Journal of Proteome Research. 7: 5286-94. PMID 18939861 DOI: 10.1021/Pr8004666 |
0.479 |
|
| 2008 |
Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC. DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. Journal of Proteome Research. 7: 3838-46. PMID 18630943 DOI: 10.1021/Pr800154P |
0.449 |
|
| 2008 |
Arnett DR, Jennings JL, Tabb DL, Link AJ, Weil PA. A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Molecular & Cellular Proteomics : McP. 7: 2090-106. PMID 18596064 DOI: 10.1074/Mcp.M800221-Mcp200 |
0.371 |
|
| 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. Molecular & Cellular Proteomics : McP. 7: 1651-67. PMID 18504258 DOI: 10.1074/Mcp.M700155-Mcp200 |
0.327 |
|
| 2008 |
Tabb DL. What's driving false discovery rates? Journal of Proteome Research. 7: 45-6. PMID 18081243 DOI: 10.1021/Pr700728T |
0.336 |
|
| 2007 |
Padliya ND, Garrett WM, Campbell KB, Tabb DL, Cooper B. Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences. Proteomics. 7: 3932-42. PMID 17922518 DOI: 10.1002/Pmic.200700419 |
0.472 |
|
| 2007 |
Zhang B, Chambers MC, Tabb DL. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Journal of Proteome Research. 6: 3549-57. PMID 17676885 DOI: 10.1021/Pr070230D |
0.487 |
|
| 2007 |
Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Journal of Proteome Research. 6: 654-61. PMID 17269722 DOI: 10.1021/Pr0604054 |
0.44 |
|
| 2006 |
Tabb DL, Friedman DB, Ham AJ. Verification of automated peptide identifications from proteomic tandem mass spectra. Nature Protocols. 1: 2213-22. PMID 17406459 DOI: 10.1038/Nprot.2006.330 |
0.451 |
|
| 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. Analytical Chemistry. 78: 125-34. PMID 16383319 DOI: 10.1021/Ac051348L |
0.432 |
|
| 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. Analytical Chemistry. 77: 7581-93. PMID 16316165 DOI: 10.1021/ac0501745 |
0.382 |
|
| 2005 |
Tabb DL, Thompson MR, Khalsa-Moyers G, VerBerkmoes NC, McDonald WH. MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. Journal of the American Society For Mass Spectrometry. 16: 1250-61. PMID 15979332 DOI: 10.1016/j.jasms.2005.04.010 |
0.35 |
|
| 2005 |
Tabb DL, Narasimhan C, Strader MB, Hettich RL. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Analytical Chemistry. 77: 2464-74. PMID 15828782 DOI: 10.1021/Ac0487000 |
0.397 |
|
| 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. Journal of Proteome Research. 3: 965-78. PMID 15473684 DOI: 10.1021/Pr049940Z |
0.47 |
|
| 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 Communications in Mass Spectrometry : Rcm. 18: 2162-8. PMID 15317041 DOI: 10.1002/Rcm.1603 |
0.427 |
|
| 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. Analytical Chemistry. 76: 1243-8. PMID 14987077 DOI: 10.1021/Ac0351163 |
0.364 |
|
| 2003 |
Tabb DL, Saraf A, Yates JR. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Analytical Chemistry. 75: 6415-21. PMID 14640709 DOI: 10.1021/Ac0347462 |
0.474 |
|
| 2003 |
Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR. Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Analytical Chemistry. 75: 2470-7. PMID 12918992 DOI: 10.1021/Ac026424O |
0.386 |
|
| 2003 |
Breci LA, Tabb DL, Yates JR, Wysocki VH. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Analytical Chemistry. 75: 1963-71. PMID 12720328 DOI: 10.1021/Ac026359I |
0.391 |
|
| 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. Analytical Chemistry. 75: 1155-63. PMID 12641236 DOI: 10.1021/Ac026122M |
0.359 |
|
| 2003 |
Lin D, Tabb DL, Yates JR. Large-scale protein identification using mass spectrometry. Biochimica Et Biophysica Acta. 1646: 1-10. PMID 12637006 DOI: 10.1016/S1570-9639(02)00546-0 |
0.436 |
|
| 2002 |
Tabb DL, McDonald WH, Yates JR. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. Journal of Proteome Research. 1: 21-6. PMID 12643522 |
0.401 |
|
| 2002 |
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, et al. A proteomic view of the Plasmodium falciparum life cycle. Nature. 419: 520-6. PMID 12368866 DOI: 10.1038/Nature01107 |
0.351 |
|
| 2002 |
Huang Y, Wysocki VH, Tabb DL, Yates JR. The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides International Journal of Mass Spectrometry. 219: 233-244. DOI: 10.1016/S1387-3806(02)00660-7 |
0.351 |
|
| 2000 |
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. Analytical Chemistry. 72: 4033-40. PMID 10994962 DOI: 10.1021/Ac000142B |
0.354 |
|
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