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LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers.

Gao Y, Wang H, Nicora CD, Shi T, Smith RD, Sigdel TK, Sarwal MM, Camp DG 2nd, Qian WJ.

Methods Mol Biol. 2018;1788:145-156. doi: 10.1007/7651_2017_93.


Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics.

Wang H, Barbieri CE, He J, Gao Y, Shi T, Wu C, Schepmoes AA, Fillmore TL, Chae SS, Huang D, Mosquera JM, Qian WJ, Smith RD, Srivastava S, Kagan J, Camp DG 2nd, Rodland KD, Rubin MA, Liu T.

J Transl Med. 2017 Aug 15;15(1):175. doi: 10.1186/s12967-017-1276-7.


Mining the human urine proteome for monitoring renal transplant injury.

Sigdel TK, Gao Y, He J, Wang A, Nicora CD, Fillmore TL, Shi T, Webb-Robertson BJ, Smith RD, Qian WJ, Salvatierra O, Camp DG 2nd, Sarwal MM.

Kidney Int. 2016 Jun;89(6):1244-52. doi: 10.1016/j.kint.2015.12.049. Epub 2016 Mar 4.


Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function during Nanoparticle-Induced Oxidative Stress.

Duan J, Kodali VK, Gaffrey MJ, Guo J, Chu RK, Camp DG, Smith RD, Thrall BD, Qian WJ.

ACS Nano. 2016 Jan 26;10(1):524-38. doi: 10.1021/acsnano.5b05524. Epub 2015 Dec 29.


The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification.

Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG 2nd.

Expert Rev Proteomics. 2016;13(1):99-114. doi: 10.1586/14789450.2016.1122529. Epub 2015 Dec 19. Review.


Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics.

El Ouaamari A, Zhou JY, Liew CW, Shirakawa J, Dirice E, Gedeon N, Kahraman S, De Jesus DF, Bhatt S, Kim JS, Clauss TR, Camp DG 2nd, Smith RD, Qian WJ, Kulkarni RN.

J Proteome Res. 2015 Aug 7;14(8):3111-3122. doi: 10.1021/acs.jproteome.5b00587. Epub 2015 Jul 30.


Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods.

He J, Schepmoes AA, Shi T, Wu C, Fillmore TL, Gao Y, Smith RD, Qian WJ, Rodland KD, Liu T, Camp DG 2nd, Rastogi A, Tan SH, Yan W, Mohamed AA, Huang W, Banerjee S, Kagan J, Srivastava S, McLeod DG, Srivastava S, Petrovics G, Dobi A, Srinivasan A.

J Transl Med. 2015 Feb 12;13:54. doi: 10.1186/s12967-015-0418-z.


Perturbations in the urinary exosome in transplant rejection.

Sigdel TK, Ng YW, Lee S, Nicora CD, Qian WJ, Smith RD, Camp DG 2nd, Sarwal MM.

Front Med (Lausanne). 2015 Jan 5;1:57. doi: 10.3389/fmed.2014.00057. eCollection 2014.


Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment.

Shi T, Gao Y, Gaffrey MJ, Nicora CD, Fillmore TL, Chrisler WB, Gritsenko MA, Wu C, He J, Bloodsworth KJ, Zhao R, Camp DG 2nd, Liu T, Rodland KD, Smith RD, Wiley HS, Qian WJ.

Anal Chem. 2015 Jan 20;87(2):1103-10. doi: 10.1021/ac503797x. Epub 2014 Dec 31.


HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa.

Jonkers W, Leeder AC, Ansong C, Wang Y, Yang F, Starr TL, Camp DG 2nd, Smith RD, Glass NL.

PLoS Genet. 2014 Nov 20;10(11):e1004783. doi: 10.1371/journal.pgen.1004783. eCollection 2014 Nov.


Proteomic approaches for site-specific O-GlcNAcylation analysis.

Wang S, Yang F, Camp DG 2nd, Rodland K, Qian WJ, Liu T, Smith RD.

Bioanalysis. 2014;6(19):2571-80. doi: 10.4155/bio.14.239. Review.


Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer.

He J, Sun X, Shi T, Schepmoes AA, Fillmore TL, Petyuk VA, Xie F, Zhao R, Gritsenko MA, Yang F, Kitabayashi N, Chae SS, Rubin MA, Siddiqui J, Wei JT, Chinnaiyan AM, Qian WJ, Smith RD, Kagan J, Srivastava S, Rodland KD, Liu T, Camp DG 2nd.

Mol Oncol. 2014 Oct;8(7):1169-80. doi: 10.1016/j.molonc.2014.02.004. Epub 2014 Feb 21.


Expediting SRM assay development for large-scale targeted proteomics experiments.

Wu C, Shi T, Brown JN, He J, Gao Y, Fillmore TL, Shukla AK, Moore RJ, Camp DG 2nd, Rodland KD, Qian WJ, Liu T, Smith RD.

J Proteome Res. 2014 Oct 3;13(10):4479-87. doi: 10.1021/pr500500d. Epub 2014 Sep 4.


Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry.

Kronewitter SR, Marginean I, Cox JT, Zhao R, Hagler CD, Shukla AK, Carlson TS, Adkins JN, Camp DG 2nd, Moore RJ, Rodland KD, Smith RD.

Anal Chem. 2014 Sep 2;86(17):8700-10. doi: 10.1021/ac501839b. Epub 2014 Aug 21.


Detecting differential protein expression in large-scale population proteomics.

Ryu SY, Qian WJ, Camp DG, Smith RD, Tompkins RG, Davis RW, Xiao W.

Bioinformatics. 2014 Oct;30(19):2741-6. doi: 10.1093/bioinformatics/btu341. Epub 2014 Jun 12.


GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization.

Kronewitter SR, Slysz GW, Marginean I, Hagler CD, LaMarche BL, Zhao R, Harris MY, Monroe ME, Polyukh CA, Crowell KL, Fillmore TL, Carlson TS, Camp DG 2nd, Moore RJ, Payne SH, Anderson GA, Smith RD.

Anal Chem. 2014 Jul 1;86(13):6268-76. doi: 10.1021/ac501492f. Epub 2014 Jun 13.


Cytomegalovirus pp65 limits dissemination but is dispensable for persistence.

Malouli D, Hansen SG, Nakayasu ES, Marshall EE, Hughes CM, Ventura AB, Gilbride RM, Lewis MS, Xu G, Kreklywich C, Whizin N, Fischer M, Legasse AW, Viswanathan K, Siess D, Camp DG 2nd, Axthelm MK, Kahl C, DeFilippis VR, Smith RD, Streblow DN, Picker LJ, Früh K.

J Clin Invest. 2014 May;124(5):1928-44. Epub 2014 Apr 1.


Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani.

Martin JL, Yates PA, Soysa R, Alfaro JF, Yang F, Burnum-Johnson KE, Petyuk VA, Weitz KK, Camp DG 2nd, Smith RD, Wilmarth PA, David LL, Ramasamy G, Myler PJ, Carter NS.

PLoS Pathog. 2014 Feb 27;10(2):e1003938. doi: 10.1371/journal.ppat.1003938. eCollection 2014 Feb.


Optimization for peptide sample preparation for urine peptidomics.

Sigdel TK, Nicora CD, Hsieh SC, Dai H, Qian WJ, Camp DG 2nd, Sarwal MM.

Clin Proteomics. 2014 Feb 25;11(1):7. doi: 10.1186/1559-0275-11-7.


LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism.

Depuydt G, Xie F, Petyuk VA, Smolders A, Brewer HM, Camp DG 2nd, Smith RD, Braeckman BP.

J Proteome Res. 2014 Apr 4;13(4):1938-56. doi: 10.1021/pr401081b. Epub 2014 Mar 3.


Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications.

Guo J, Gaffrey MJ, Su D, Liu T, Camp DG 2nd, Smith RD, Qian WJ.

Nat Protoc. 2014 Jan;9(1):64-75. doi: 10.1038/nprot.2013.161. Epub 2013 Dec 12.


The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics.

Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton DJ, Moore RJ, Hsieh SC, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian WJ, Camp DG 2nd, Sarwal MM.

Mol Cell Proteomics. 2014 Feb;13(2):621-31. doi: 10.1074/mcp.M113.030577. Epub 2013 Dec 12.


Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling.

Su D, Gaffrey MJ, Guo J, Hatchell KE, Chu RK, Clauss TR, Aldrich JT, Wu S, Purvine S, Camp DG, Smith RD, Thrall BD, Qian WJ.

Free Radic Biol Med. 2014 Feb;67:460-70. doi: 10.1016/j.freeradbiomed.2013.12.004. Epub 2013 Dec 11.


Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens.

Zaborin A, Defazio JR, Kade M, Kaiser BL, Belogortseva N, Camp DG 2nd, Smith RD, Adkins JN, Kim SM, Alverdy A, Goldfeld D, Firestone MA, Collier JH, Jabri B, Tirrell M, Zaborina O, Alverdy JC.

Antimicrob Agents Chemother. 2014;58(2):966-77. doi: 10.1128/AAC.02183-13. Epub 2013 Nov 25.


A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum.

Shi T, Gao Y, Quek SI, Fillmore TL, Nicora CD, Su D, Zhao R, Kagan J, Srivastava S, Rodland KD, Liu T, Smith RD, Chan DW, Camp DG 2nd, Liu AY, Qian WJ.

J Proteome Res. 2014 Feb 7;13(2):875-82. doi: 10.1021/pr400912c. Epub 2013 Dec 3.


Gray matter is targeted in first-attack multiple sclerosis.

Schutzer SE, Angel TE, Liu T, Schepmoes AA, Xie F, Bergquist J, Vécsei L, Zadori D, Camp DG 2nd, Holland BK, Smith RD, Coyle PK.

PLoS One. 2013 Sep 10;8(9):e66117. doi: 10.1371/journal.pone.0066117. eCollection 2013.


Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis.

Shi T, Fillmore TL, Gao Y, Zhao R, He J, Schepmoes AA, Nicora CD, Wu C, Chambers JL, Moore RJ, Kagan J, Srivastava S, Liu AY, Rodland KD, Liu T, Camp DG 2nd, Smith RD, Qian WJ.

Anal Chem. 2013 Oct 1;85(19):9196-203. doi: 10.1021/ac402105s. Epub 2013 Sep 19.


Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans.

Depuydt G, Xie F, Petyuk VA, Shanmugam N, Smolders A, Dhondt I, Brewer HM, Camp DG 2nd, Smith RD, Braeckman BP.

Mol Cell Proteomics. 2013 Dec;12(12):3624-39. doi: 10.1074/mcp.M113.027383. Epub 2013 Sep 3.


Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing.

Kim JS, Dai Z, Aryal UK, Moore RJ, Camp DG 2nd, Baker SE, Smith RD, Qian WJ.

Anal Chem. 2013 Jul 16;85(14):6826-32. doi: 10.1021/ac401000q. Epub 2013 Jun 27.


Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion.

Shi T, Sun X, Gao Y, Fillmore TL, Schepmoes AA, Zhao R, He J, Moore RJ, Kagan J, Rodland KD, Liu T, Liu AY, Smith RD, Tang K, Camp DG 2nd, Qian WJ.

J Proteome Res. 2013 Jul 5;12(7):3353-61. doi: 10.1021/pr400178v. Epub 2013 Jun 13.


Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling.

Zhou JY, Krovvidi RK, Gao Y, Gao H, Petritis BO, De AK, Miller-Graziano CL, Bankey PE, Petyuk VA, Nicora CD, Clauss TR, Moore RJ, Shi T, Brown JN, Kaushal A, Xiao W, Davis RW, Maier RV, Tompkins RG, Qian WJ, Camp DG 2nd, Smith RD; Inflammation and the Host Response to Injury Large Scale Collaborative Research Program.

Proteomics Clin Appl. 2013 Aug;7(7-8):571-83. doi: 10.1002/prca.201200109. Epub 2013 May 22.


Determination of burn patient outcome by large-scale quantitative discovery proteomics.

Finnerty CC, Jeschke MG, Qian WJ, Kaushal A, Xiao W, Liu T, Gritsenko MA, Moore RJ, Camp DG 2nd, Moldawer LL, Elson C, Schoenfeld D, Gamelli R, Gibran N, Klein M, Arnoldo B, Remick D, Smith RD, Davis R, Tompkins RG, Herndon DN; Investigators of the Inflammation and the Host Response Glue Grant.

Crit Care Med. 2013 Jun;41(6):1421-34. doi: 10.1097/CCM.0b013e31827c072e.


Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis.

Piehowski PD, Petyuk VA, Orton DJ, Xie F, Moore RJ, Ramirez-Restrepo M, Engel A, Lieberman AP, Albin RL, Camp DG, Smith RD, Myers AJ.

J Proteome Res. 2013 May 3;12(5):2128-37. doi: 10.1021/pr301146m. Epub 2013 Apr 10.


STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

Piehowski PD, Petyuk VA, Sandoval JD, Burnum KE, Kiebel GR, Monroe ME, Anderson GA, Camp DG 2nd, Smith RD.

Proteomics. 2013 Mar;13(5):766-70. doi: 10.1002/pmic.201200096. Epub 2013 Feb 4.


Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry.

Su D, Shukla AK, Chen B, Kim JS, Nakayasu E, Qu Y, Aryal U, Weitz K, Clauss TR, Monroe ME, Camp DG 2nd, Bigelow DJ, Smith RD, Kulkarni RN, Qian WJ.

Free Radic Biol Med. 2013 Apr;57:68-78. doi: 10.1016/j.freeradbiomed.2012.12.010. Epub 2012 Dec 28.


In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics.

Kim JS, Monroe ME, Camp DG 2nd, Smith RD, Qian WJ.

J Proteome Res. 2013 Feb 1;12(2):910-6. doi: 10.1021/pr300955f. Epub 2013 Jan 16.


A systematic analysis of a deep mouse epididymal sperm proteome.

Chauvin T, Xie F, Liu T, Nicora CD, Yang F, Camp DG 2nd, Smith RD, Roberts KP.

Biol Reprod. 2012 Dec 21;87(6):141. doi: 10.1095/biolreprod.112.104208. Print 2012 Jun.


Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum.

Shi T, Fillmore TL, Sun X, Zhao R, Schepmoes AA, Hossain M, Xie F, Wu S, Kim JS, Jones N, Moore RJ, Pasa-Tolić L, Kagan J, Rodland KD, Liu T, Tang K, Camp DG 2nd, Smith RD, Qian WJ.

Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15395-400. Epub 2012 Sep 4.


Cerebrospinal fluid proteome of patients with acute Lyme disease.

Angel TE, Jacobs JM, Smith RP, Pasternack MS, Elias S, Gritsenko MA, Shukla A, Gilmore EC, McCarthy C, Camp DG 2nd, Smith RD, Warren HS.

J Proteome Res. 2012 Oct 5;11(10):4814-22. doi: 10.1021/pr300577p. Epub 2012 Aug 31.


Analysis of serum total and free PSA using immunoaffinity depletion coupled to SRM: correlation with clinical immunoassay tests.

Liu T, Hossain M, Schepmoes AA, Fillmore TL, Sokoll LJ, Kronewitter SR, Izmirlian G, Shi T, Qian WJ, Leach RJ, Thompson IM, Chan DW, Smith RD, Kagan J, Srivastava S, Rodland KD, Camp DG 2nd.

J Proteomics. 2012 Aug 3;75(15):4747-57. doi: 10.1016/j.jprot.2012.01.035. Epub 2012 Feb 13.


Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1.

Malouli D, Nakayasu ES, Viswanathan K, Camp DG 2nd, Chang WL, Barry PA, Smith RD, Früh K.

J Virol. 2012 Sep;86(17):8959-73. doi: 10.1128/JVI.01132-12. Epub 2012 Jun 20.


Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics.

Shi T, Su D, Liu T, Tang K, Camp DG 2nd, Qian WJ, Smith RD.

Proteomics. 2012 Apr;12(8):1074-92. doi: 10.1002/pmic.201100436. Review.


Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets.

Alfaro JF, Gong CX, Monroe ME, Aldrich JT, Clauss TR, Purvine SO, Wang Z, Camp DG 2nd, Shabanowitz J, Stanley P, Hart GW, Hunt DF, Yang F, Smith RD.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):7280-5. doi: 10.1073/pnas.1200425109. Epub 2012 Apr 19.


Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model.

Yang F, Waters KM, Webb-Robertson BJ, Sowa MB, von Neubeck C, Aldrich JT, Markillie LM, Wirgau RM, Gritsenko MA, Zhao R, Camp DG 2nd, Smith RD, Stenoien DL.

Exp Dermatol. 2012 May;21(5):352-7. doi: 10.1111/j.1600-0625.2012.01470.x.


High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis.

Yang F, Shen Y, Camp DG 2nd, Smith RD.

Expert Rev Proteomics. 2012 Apr;9(2):129-34. doi: 10.1586/epr.12.15.


The cerebrospinal fluid proteome in HIV infection: change associated with disease severity.

Angel TE, Jacobs JM, Spudich SS, Gritsenko MA, Fuchs D, Liegler T, Zetterberg H, Camp DG 2nd, Price RW, Smith RD.

Clin Proteomics. 2012 Mar 20;9(1):3. doi: 10.1186/1559-0275-9-3.


Simple sodium dodecyl sulfate-assisted sample preparation method for LC-MS-based proteomics applications.

Zhou JY, Dann GP, Shi T, Wang L, Gao X, Su D, Nicora CD, Shukla AK, Moore RJ, Liu T, Camp DG 2nd, Smith RD, Qian WJ.

Anal Chem. 2012 Mar 20;84(6):2862-7. doi: 10.1021/ac203394r. Epub 2012 Mar 2.


Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation.

Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JF, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL Jr, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG.

Hepatology. 2012 Jul;56(1):28-38. doi: 10.1002/hep.25649. Epub 2012 Apr 24.


Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.

Dresang LR, Teuton JR, Feng H, Jacobs JM, Camp DG 2nd, Purvine SO, Gritsenko MA, Li Z, Smith RD, Sugden B, Moore PS, Chang Y.

BMC Genomics. 2011 Dec 20;12:625. doi: 10.1186/1471-2164-12-625.


Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry.

Wang L, Aryal UK, Dai Z, Mason AC, Monroe ME, Tian ZX, Zhou JY, Su D, Weitz KK, Liu T, Camp DG 2nd, Smith RD, Baker SE, Qian WJ.

J Proteome Res. 2012 Jan 1;11(1):143-56. doi: 10.1021/pr200916k. Epub 2011 Dec 2.

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