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Items: 1 to 20 of 28


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

Rudnick PA, Markey SP, Roth J, Mirokhin Y, Yan X, Tchekhovskoi DV, Edwards NJ, Thangudu RR, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Stein SE.

J Proteome Res. 2016 Mar 4;15(3):1023-32. doi: 10.1021/acs.jproteome.5b01091. Epub 2016 Feb 25.


MRM as a discovery tool?

Rudnick PA.

Proteomics. 2015 Apr;15(7):1194-5. doi: 10.1002/pmic.201500090.


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

Dong Q, Yan X, Kilpatrick LE, Liang Y, Mirokhin YA, Roth JS, Rudnick PA, Stein SE.

Mol Cell Proteomics. 2014 Sep;13(9):2435-49. doi: 10.1074/mcp.O113.037135. Epub 2014 Jun 2.


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

Rudnick PA, Wang X, Yan X, Sedransk N, Stein SE.

Mol Cell Proteomics. 2014 May;13(5):1341-51. doi: 10.1074/mcp.M113.030593. Epub 2014 Feb 21.


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 Y, Lowenthal MS, Kilpatrick LE, Sampson ML, Telu KH, Rudnick PA, Mallard WG, Bearden DW, Schock TB, Tchekhovskoi DV, Blonder N, Yan X, Liang Y, Zheng Y, Wallace WE, Neta P, Phinney KW, Remaley AT, Stein SE.

Anal Chem. 2013 Dec 17;85(24):11725-31. doi: 10.1021/ac402503m. Epub 2013 Dec 3.


Refining spectral library searching.

Rudnick PA.

Proteomics. 2013 Nov;13(22):3247-50. doi: 10.1002/pmic.201300426.


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

Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.

J Proteome Res. 2013 Dec 6;12(12):5666-80. doi: 10.1021/pr400611h. Epub 2013 Nov 14.


Interlaboratory studies and initiatives developing standards for proteomics.

Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST.

Proteomics. 2013 Mar;13(6):904-9. doi: 10.1002/pmic.201200532. Epub 2013 Feb 19.


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

Lowenthal MS, Phillips MM, Rimmer CA, Rudnick PA, Simón-Manso Y, Stein SE, Tchekhovskoi D, Phinney KW.

Anal Bioanal Chem. 2013 May;405(13):4451-65. doi: 10.1007/s00216-012-6346-3. Epub 2012 Sep 2.


Depletion of abundant plasma proteins and limitations of plasma proteomics.

Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJ, Liebler DC.

J Proteome Res. 2010 Oct 1;9(10):4982-91. doi: 10.1021/pr100646w.


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

Johann DJ Jr, Wei BR, Prieto DA, Chan KC, Ye X, Valera VA, Simpson RM, Rudnick PA, Xiao Z, Issaq HJ, Linehan WM, Stein SE, Veenstra TD, Blonder J.

Anal Chem. 2010 Mar 1;82(5):1584-8. doi: 10.1021/ac902204k.


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.

J Proteome Res. 2010 Feb 5;9(2):761-76. doi: 10.1021/pr9006365.


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.

Mol Cell Proteomics. 2010 Feb;9(2):242-54. doi: 10.1074/mcp.M900222-MCP200. Epub 2009 Oct 26.


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.

Mol Cell Proteomics. 2010 Feb;9(2):225-41. doi: 10.1074/mcp.M900223-MCP200. Epub 2009 Oct 16.


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.

Nat Biotechnol. 2009 Jul;27(7):633-41. doi: 10.1038/nbt.1546. Epub 2009 Jun 28. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.


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

Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, Weil RJ, DeVoe DL, Lee CS, Balgley BM.

J Histochem Cytochem. 2007 Jul;55(7):763-72. Epub 2007 Apr 4.


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

Wang W, Guo T, Rudnick PA, Song T, Li J, Zhuang Z, Zheng W, Devoe DL, Lee CS, Balgley BM.

Anal Chem. 2007 Feb 1;79(3):1002-9.


Proteome analysis of microdissected tumor tissue using a capillary isoelectric focusing-based multidimensional separation platform coupled with ESI-tandem MS.

Wang Y, Rudnick PA, Evans EL, Li J, Zhuang Z, Devoe DL, Lee CS, Balgley BM.

Anal Chem. 2005 Oct 15;77(20):6549-56.


Large scale analysis of MASCOT results using a Mass Accuracy-based THreshold (MATH) effectively improves data interpretation.

Rudnick PA, Wang Y, Evans E, Lee CS, Balgley BM.

J Proteome Res. 2005 Jul-Aug;4(4):1353-60.


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