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Items: 36

1.

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities.

Vasaikar S, Huang C, Wang X, Petyuk VA, Savage SR, Wen B, Dou Y, Zhang Y, Shi Z, Arshad OA, Gritsenko MA, Zimmerman LJ, McDermott JE, Clauss TR, Moore RJ, Zhao R, Monroe ME, Wang YT, Chambers MC, Slebos RJC, Lau KS, Mo Q, Ding L, Ellis M, Thiagarajan M, Kinsinger CR, Rodriguez H, Smith RD, Rodland KD, Liebler DC, Liu T, Zhang B; Clinical Proteomic Tumor Analysis Consortium.

Cell. 2019 May 2;177(4):1035-1049.e19. doi: 10.1016/j.cell.2019.03.030. Epub 2019 Apr 25.

2.

Mineral Surfaces as Agents of Environmental Proteolysis: Mechanisms and Controls.

Chacon SS, Reardon PN, Burgess CJ, Purvine S, Chu RK, Clauss TR, Walter E, Myrold DD, Washton N, Kleber M.

Environ Sci Technol. 2019 Mar 19;53(6):3018-3026. doi: 10.1021/acs.est.8b05583. Epub 2019 Feb 28.

PMID:
30767514
3.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.

Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, Carr SA.

Nat Protoc. 2018 Jul;13(7):1632-1661. doi: 10.1038/s41596-018-0006-9.

4.

High-Fat Diets Alter the Modulatory Effects of Xenobiotics on Cytochrome P450 Activities.

Sadler NC, Webb-Robertson BM, Clauss TR, Pounds JG, Corley R, Wright AT.

Chem Res Toxicol. 2018 May 21;31(5):308-318. doi: 10.1021/acs.chemrestox.8b00008. Epub 2018 May 4.

PMID:
29688711
5.

Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data.

Stanfill BA, Nakayasu ES, Bramer LM, Thompson AM, Ansong CK, Clauss TR, Gritsenko MA, Monroe ME, Moore RJ, Orton DJ, Piehowski PD, Schepmoes AA, Smith RD, Webb-Robertson BM, Metz TO; TEDDY Study Group.

Mol Cell Proteomics. 2018 Sep;17(9):1824-1836. doi: 10.1074/mcp.RA118.000648. Epub 2018 Apr 17.

6.

Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study.

Bryant AE, Aldape MJ, Bayer CR, Katahira EJ, Bond L, Nicora CD, Fillmore TL, Clauss TR, Metz TO, Webb-Robertson BJ, Stevens DL.

PLoS One. 2017 Feb 28;12(2):e0172486. doi: 10.1371/journal.pone.0172486. eCollection 2017.

7.

Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism.

Romine MF, Rodionov DA, Maezato Y, Anderson LN, Nandhikonda P, Rodionova IA, Carre A, Li X, Xu C, Clauss TR, Kim YM, Metz TO, Wright AT.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1205-E1214. doi: 10.1073/pnas.1612360114. Epub 2017 Jan 30.

8.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry.

Burnum-Johnson KE, Nie S, Casey CP, Monroe ME, Orton DJ, Ibrahim YM, Gritsenko MA, Clauss TR, Shukla AK, Moore RJ, Purvine SO, Shi T, Qian W, Liu T, Baker ES, Smith RD.

Mol Cell Proteomics. 2016 Dec;15(12):3694-3705. Epub 2016 Sep 25.

9.

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.

10.

Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes.

Bhatt S, Gupta MK, Khamaisi M, Martinez R, Gritsenko MA, Wagner BK, Guye P, Busskamp V, Shirakawa J, Wu G, Liew CW, Clauss TR, Valdez I, El Ouaamari A, Dirice E, Takatani T, Keenan HA, Smith RD, Church G, Weiss R, Wagers AJ, Qian WJ, King GL, Kulkarni RN.

Cell Metab. 2015 Aug 4;22(2):239-52. doi: 10.1016/j.cmet.2015.07.015.

11.

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.

12.

Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid.

Hyung SW, Piehowski PD, Moore RJ, Orton DJ, Schepmoes AA, Clauss TR, Chu RK, Fillmore TL, Brewer H, Liu T, Zhao R, Smith RD.

Anal Bioanal Chem. 2014 Nov;406(28):7117-25. doi: 10.1007/s00216-014-8058-3. Epub 2014 Sep 6.

13.

Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva.

Mudenda L, Pierlé SA, Turse JE, Scoles GA, Purvine SO, Nicora CD, Clauss TR, Ueti MW, Brown WC, Brayton KA.

Int J Parasitol. 2014 Nov;44(13):1029-37. doi: 10.1016/j.ijpara.2014.07.003. Epub 2014 Aug 7.

PMID:
25110293
14.

Automated data extraction from in situ protein-stable isotope probing studies.

Slysz GW, Steinke L, Ward DM, Klatt CG, Clauss TR, Purvine SO, Payne SH, Anderson GA, Smith RD, Lipton MS.

J Proteome Res. 2014 Mar 7;13(3):1200-10. doi: 10.1021/pr400633j. Epub 2014 Feb 21.

PMID:
24467184
15.

A comprehensive collection of systems biology data characterizing the host response to viral infection.

Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A 3rd, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH.

Sci Data. 2014 Oct 14;1:140033. doi: 10.1038/sdata.2014.33. eCollection 2014.

16.

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.

17.

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.

18.

Automated immobilized metal affinity chromatography system for enrichment of Escherichia coli phosphoproteome.

Qu Y, Wu S, Zhao R, Zink E, Orton DJ, Moore RJ, Meng D, Clauss TR, Aldrich JT, Lipton MS, Paša-Tolić L.

Electrophoresis. 2013 Jun;34(11):1619-26. doi: 10.1002/elps.201200628. Epub 2013 May 8.

PMID:
23494780
19.

Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes.

Zhang Q, Fillmore TL, Schepmoes AA, Clauss TR, Gritsenko MA, Mueller PW, Rewers M, Atkinson MA, Smith RD, Metz TO.

J Exp Med. 2013 Jan 14;210(1):191-203. doi: 10.1084/jem.20111843. Epub 2012 Dec 31.

20.

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.

21.

Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum.

Nguyen TH, Brechenmacher L, Aldrich JT, Clauss TR, Gritsenko MA, Hixson KK, Libault M, Tanaka K, Yang F, Yao Q, Pasa-Tolić L, Xu D, Nguyen HT, Stacey G.

Mol Cell Proteomics. 2012 Nov;11(11):1140-55. doi: 10.1074/mcp.M112.018028. Epub 2012 Jul 25.

22.

Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels.

Brown JN, Ortiz GM, Angel TE, Jacobs JM, Gritsenko M, Chan EY, Purdy DE, Murnane RD, Larsen K, Palermo RE, Shukla AK, Clauss TR, Katze MG, McCune JM, Smith RD.

Mol Cell Proteomics. 2012 Sep;11(9):605-18. doi: 10.1074/mcp.M111.016121. Epub 2012 May 11.

23.

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.

24.

Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects.

Zhang Q, Monroe ME, Schepmoes AA, Clauss TR, Gritsenko MA, Meng D, Petyuk VA, Smith RD, Metz TO.

J Proteome Res. 2011 Jul 1;10(7):3076-88. doi: 10.1021/pr200040j. Epub 2011 Jun 10.

25.

Formation of iron complexes from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis.

Shukla A, Zhang R, Orton DJ, Zhao R, Clauss TR, Moore R, Smith RD.

Rapid Commun Mass Spectrom. 2011 May 30;25(10):1452-6. doi: 10.1002/rcm.5017.

26.

Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome.

Schutzer SE, Angel TE, Liu T, Schepmoes AA, Clauss TR, Adkins JN, Camp DG, Holland BK, Bergquist J, Coyle PK, Smith RD, Fallon BA, Natelson BH.

PLoS One. 2011 Feb 23;6(2):e17287. doi: 10.1371/journal.pone.0017287.

27.

Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response.

Brown JN, Estep RD, Lopez-Ferrer D, Brewer HM, Clauss TR, Manes NP, O'Connor M, Li H, Adkins JN, Wong SW, Smith RD.

Mol Cell Proteomics. 2010 Dec;9(12):2760-71. doi: 10.1074/mcp.M110.001875. Epub 2010 Aug 24.

28.

Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique.

Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ.

PLoS One. 2010 May 5;5(5):e10487. doi: 10.1371/journal.pone.0010487.

29.

Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica.

Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TR, Heffron F, Smith RD, Adkins JN.

Infect Immun. 2009 Aug;77(8):3227-33. doi: 10.1128/IAI.00063-09. Epub 2009 Jun 15.

30.

Spatial mapping of the neurite and soma proteomes reveals a functional Cdc42/Rac regulatory network.

Pertz OC, Wang Y, Yang F, Wang W, Gay LJ, Gristenko MA, Clauss TR, Anderson DJ, Liu T, Auberry KJ, Camp DG 2nd, Smith RD, Klemke RL.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1931-6. doi: 10.1073/pnas.0706545105. Epub 2008 Feb 1.

31.

Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions.

Manes NP, Estep RD, Mottaz HM, Moore RJ, Clauss TR, Monroe ME, Du X, Adkins JN, Wong SW, Smith RD.

J Proteome Res. 2008 Mar;7(3):960-8. doi: 10.1021/pr070432+. Epub 2008 Jan 19. Erratum in: J Proteome Res. 2013 Jan 4;12(1):546.

32.

Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus.

Yang F, Camp DG 2nd, Gritsenko MA, Luo Q, Kelly RT, Clauss TR, Brinkley WR, Smith RD, Stenoien DL.

J Cell Sci. 2007 Nov 15;120(Pt 22):4060-70. Epub 2007 Oct 30.

33.

A method for selective enrichment and analysis of nitrotyrosine-containing peptides in complex proteome samples.

Zhang Q, Qian WJ, Knyushko TV, Clauss TR, Purvine SO, Moore RJ, Sacksteder CA, Chin MH, Smith DJ, Camp DG 2nd, Bigelow DJ, Smith RD.

J Proteome Res. 2007 Jun;6(6):2257-68. Epub 2007 May 12.

PMID:
17497906
34.

Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline.

Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD.

Anal Chem. 2006 Nov 1;78(21):7397-409.

PMID:
17073405
35.

Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions.

Adkins JN, Mottaz HM, Norbeck AD, Gustin JK, Rue J, Clauss TR, Purvine SO, Rodland KD, Heffron F, Smith RD.

Mol Cell Proteomics. 2006 Aug;5(8):1450-61. Epub 2006 May 8.

36.

Development and evaluation of a micro- and nanoscale proteomic sample preparation method.

Wang H, Qian WJ, Mottaz HM, Clauss TR, Anderson DJ, Moore RJ, Camp DG 2nd, Khan AH, Sforza DM, Pallavicini M, Smith DJ, Smith RD.

J Proteome Res. 2005 Nov-Dec;4(6):2397-403.

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