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1.

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V.

Zhang, Xu; Nguyen, Khoa Dang; Rudnick, Paul A; Roper, Nitin; Kawaler, Emily; Maity, Tapan K; Awasthi, Shivangi; Gao, Shaojian; Biswas, Romi; Venugopalan, Abhilash; Cultraro, Constance M; Fenyö, David; Guha, Udayan.

Mol Cell Proteomics ; 18(4): 622-641, 2019 04.

Artículo en Inglés | MEDLINE | ID: mdl-30617155

2.

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

Rudnick, Paul A; Markey, Sanford P; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V; Edwards, Nathan J; Thangudu, Ratna R; Ketchum, Karen A; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E.

J Proteome Res ; 15(3): 1023-32, 2016 Mar 04.

Artículo en Inglés | MEDLINE | ID: mdl-26860878

3.

Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data.

Rudnick, Paul A; Wang, Xia; Yan, Xinjian; Sedransk, Nell; Stein, Stephen E.

Mol Cell Proteomics ; 13(5): 1341-51, 2014 May.

Artículo en Inglés | MEDLINE | ID: mdl-24563535

4.

Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA).

Dong, Qian; Yan, Xinjian; Kilpatrick, Lisa E; Liang, Yuxue; Mirokhin, Yuri A; Roth, Jeri S; Rudnick, Paul A; Stein, Stephen E.

Mol Cell Proteomics ; 13(9): 2435-49, 2014 Sep.

Artículo en Inglés | MEDLINE | ID: mdl-24889059

5.

MRM as a discovery tool?

Rudnick, Paul A.

Proteomics ; 15(7): 1194-5, 2015 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-25762020

6.

Refining spectral library searching.

Rudnick, Paul A.

Proteomics ; 13(22): 3247-50, 2013 Nov.

Artículo en Inglés | MEDLINE | ID: mdl-24123856

7.

Interlaboratory studies and initiatives developing standards for proteomics.

Ivanov, Alexander R; Colangelo, Christopher M; Dufresne, Craig P; Friedman, David B; Lilley, Kathryn S; Mechtler, Karl; Phinney, Brett S; Rose, Kristie L; Rudnick, Paul A; Searle, Brian C; Shaffer, Scott A; Weintraub, Susan T.

Proteomics ; 13(6): 904-9, 2013 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-23319436

8.

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

Walmsley, Scott J; Rudnick, Paul A; Liang, Yuxue; Dong, Qian; Stein, Stephen E; Nesvizhskii, Alexey I.

J Proteome Res ; 12(12): 5666-80, 2013 Dec 06.

Artículo en Inglés | MEDLINE | ID: mdl-24116745

9.

Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources.

Simón-Manso, Yamil; Lowenthal, Mark S; Kilpatrick, Lisa E; Sampson, Maureen L; Telu, Kelly H; Rudnick, Paul A; Mallard, W Gary; Bearden, Daniel W; Schock, Tracey B; Tchekhovskoi, Dmitrii V; Blonder, Niksa; Yan, Xinjian; Liang, Yuxue; Zheng, Yufang; Wallace, William E; Neta, Pedatsur; Phinney, Karen W; Remaley, Alan T; Stein, Stephen E.

Anal Chem ; 85(24): 11725-31, 2013 Dec 17.

Artículo en Inglés | MEDLINE | ID: mdl-24147600

10.

Developing qualitative LC-MS methods for characterization of Vaccinium berry Standard Reference Materials.

Lowenthal, Mark S; Phillips, Melissa M; Rimmer, Catherine A; Rudnick, Paul A; Simón-Manso, Yamil; Stein, Stephen E; Tchekhovskoi, Dmitrii; Phinney, Karen W.

Anal Bioanal Chem ; 405(13): 4451-65, 2013 May.

Artículo en Inglés | MEDLINE | ID: mdl-22941178

11.

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

Paulovich, Amanda G; Billheimer, Dean; Ham, Amy-Joan L; Vega-Montoto, Lorenzo; Rudnick, Paul A; Tabb, David L; Wang, Pei; Blackman, Ronald K; Bunk, David M; Cardasis, Helene L; Clauser, Karl R; Kinsinger, Christopher R; Schilling, Birgit; Tegeler, Tony J; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Fenyo, David; Carr, Steven A; Fisher, Susan J; Gibson, Bradford W; Mesri, Mehdi; Neubert, Thomas A; Regnier, Fred E; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E; Tempst, Paul; Liebler, Daniel C.

Mol Cell Proteomics ; 9(2): 242-54, 2010 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-19858499

12.

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

Rudnick, Paul A; Clauser, Karl R; Kilpatrick, Lisa E; Tchekhovskoi, Dmitrii V; Neta, Pedatsur; Blonder, Niksa; Billheimer, Dean D; Blackman, Ronald K; Bunk, David M; Cardasis, Helene L; Ham, Amy-Joan L; Jaffe, Jacob D; Kinsinger, Christopher R; Mesri, Mehdi; Neubert, Thomas A; Schilling, Birgit; Tabb, David L; Tegeler, Tony J; Vega-Montoto, Lorenzo; Variyath, Asokan Mulayath; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Carr, Steven A; Fisher, Susan J; Gibson, Bradford W; Paulovich, Amanda G; Regnier, Fred E; Rodriguez, Henry; Spiegelman, Cliff; Tempst, Paul; Liebler, Daniel C; Stein, Stephen E.

Mol Cell Proteomics ; 9(2): 225-41, 2010 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-19837981

13.

Depletion of abundant plasma proteins and limitations of plasma proteomics.

Tu, Chengjian; Rudnick, Paul A; Martinez, Misti Y; Cheek, Kristin L; Stein, Stephen E; Slebos, Robbert J C; Liebler, Daniel C.

J Proteome Res ; 9(10): 4982-91, 2010 Oct 01.

Artículo en Inglés | MEDLINE | ID: mdl-20677825

14.

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.

Tabb, David L; Vega-Montoto, Lorenzo; Rudnick, Paul A; Variyath, Asokan Mulayath; Ham, Amy-Joan L; Bunk, David M; Kilpatrick, Lisa E; Billheimer, Dean D; Blackman, Ronald K; Cardasis, Helene L; Carr, Steven A; Clauser, Karl R; Jaffe, Jacob D; Kowalski, Kevin A; Neubert, Thomas A; Regnier, Fred E; Schilling, Birgit; Tegeler, Tony J; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R; Zimmerman, Lisa J; Fisher, Susan J; Gibson, Bradford W; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E; Tempst, Paul; Paulovich, Amanda G; Liebler, Daniel C; Spiegelman, Cliff.

J Proteome Res ; 9(2): 761-76, 2010 Feb 05.

Artículo en Inglés | MEDLINE | ID: mdl-19921851

15.

Combined blood/tissue analysis for cancer biomarker discovery: application to renal cell carcinoma.

Johann, Donald J; Wei, Bih-Rong; Prieto, DaRue A; Chan, King C; Ye, Xiaying; Valera, Vladimir A; Simpson, R Mark; Rudnick, Paul A; Xiao, Zhen; Issaq, Haleem J; Linehan, W Marston; Stein, Stephen E; Veenstra, Timothy D; Blonder, Josip.

Anal Chem ; 82(5): 1584-8, 2010 Mar 01.

Artículo en Inglés | MEDLINE | ID: mdl-20121140

16.

Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens.

Guo, Tong; Wang, Weijie; Rudnick, Paul A; Song, Tao; Li, Jie; Zhuang, Zhengping; Weil, Robert J; DeVoe, Don L; Lee, Cheng S; Balgley, Brian M.

J Histochem Cytochem ; 55(7): 763-72, 2007 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-17409379

17.

Effects of chromatography conditions on intact protein separations for top-down proteomics.

Wang, Yueju; Balgley, Brian M; Rudnick, Paul A; Lee, Cheng S.

J Chromatogr A ; 1073(1-2): 35-41, 2005 May 06.

Artículo en Inglés | MEDLINE | ID: mdl-15909503

18.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Addona, Terri A; Abbatiello, Susan E; Schilling, Birgit; Skates, Steven J; Mani, D R; Bunk, David M; Spiegelman, Clifford H; Zimmerman, Lisa J; Ham, Amy-Joan L; Keshishian, Hasmik; Hall, Steven C; Allen, Simon; Blackman, Ronald K; Borchers, Christoph H; Buck, Charles; Cardasis, Helene L; Cusack, Michael P; Dodder, Nathan G; Gibson, Bradford W; Held, Jason M; Hiltke, Tara; Jackson, Angela; Johansen, Eric B; Kinsinger, Christopher R; Li, Jing; Mesri, Mehdi; Neubert, Thomas A; Niles, Richard K; Pulsipher, Trenton C; Ransohoff, David; Rodriguez, Henry; Rudnick, Paul A; Smith, Derek; Tabb, David L; Tegeler, Tony J; Variyath, Asokan M; Vega-Montoto, Lorenzo J; Wahlander, Asa; Waldemarson, Sofia; Wang, Mu; Whiteaker, Jeffrey R; Zhao, Lei; Anderson, N Leigh; Fisher, Susan J; Liebler, Daniel C; Paulovich, Amanda G; Regnier, Fred E; Tempst, Paul; Carr, Steven A.

Nat Biotechnol ; 27(7): 633-41, 2009 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-19561596

19.

Membrane proteome analysis of microdissected ovarian tumor tissues using capillary isoelectric focusing/reversed-phase liquid chromatography-tandem MS.

Wang, Weijie; Guo, Tong; Rudnick, Paul A; Song, Tao; Li, Jie; Zhuang, Zhengping; Zheng, Wenxin; Devoe, Don L; Lee, Cheng S; Balgley, Brian M.

Anal Chem ; 79(3): 1002-9, 2007 Feb 01.

Artículo en Inglés | MEDLINE | ID: mdl-17263328

20.

Characterization of the human salivary proteome by capillary isoelectric focusing/nanoreversed-phase liquid chromatography coupled with ESI-tandem MS.

Guo, Tong; Rudnick, Paul A; Wang, Weijie; Lee, Cheng S; Devoe, Don L; Balgley, Brian M.

J Proteome Res ; 5(6): 1469-78, 2006 Jun.

Artículo en Inglés | MEDLINE | ID: mdl-16739998

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