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Items: 1 to 50 of 96

1.

Proteomics Standards Initiative Extended FASTA Format.

Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW.

J Proteome Res. 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.

PMID:
31081335
2.

In Vivo Proteome of Pseudomonas aeruginosa in Airways of Cystic Fibrosis Patients.

Wu X, Siehnel RJ, Garudathri J, Staudinger BJ, Hisert KB, Ozer EA, Hauser AR, Eng JK, Manoil C, Singh PK, Bruce JE.

J Proteome Res. 2019 Jun 7;18(6):2601-2612. doi: 10.1021/acs.jproteome.9b00122. Epub 2019 May 22.

PMID:
31060355
3.

A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry.

Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather DN, Deutsch EW, Kappe SHI, Moritz RL.

J Proteome Res. 2019 Feb 1;18(2):652-663. doi: 10.1021/acs.jproteome.8b00638. Epub 2018 Dec 21.

PMID:
30523691
4.

Tools for 3D Interactome Visualization.

Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE.

J Proteome Res. 2019 Feb 1;18(2):753-758. doi: 10.1021/acs.jproteome.8b00703. Epub 2018 Dec 18.

PMID:
30520642
5.

Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins.

Ting SY, Bosch DE, Mangiameli SM, Radey MC, Huang S, Park YJ, Kelly KA, Filip SK, Goo YA, Eng JK, Allaire M, Veesler D, Wiggins PA, Peterson SB, Mougous JD.

Cell. 2018 Nov 15;175(5):1380-1392.e14. doi: 10.1016/j.cell.2018.09.037. Epub 2018 Oct 18.

PMID:
30343895
6.

Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.

Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE.

Anal Chem. 2018 May 15;90(10):6028-6034. doi: 10.1021/acs.analchem.7b04991. Epub 2018 Apr 27.

7.

Sipros Ensemble improves database searching and filtering for complex metaproteomics.

Guo X, Li Z, Yao Q, Mueller RS, Eng JK, Tabb DL, Hervey WJ 4th, Pan C.

Bioinformatics. 2018 Mar 1;34(5):795-802. doi: 10.1093/bioinformatics/btx601.

8.

Extracellular Matrix Proteins Mediate HIV-1 gp120 Interactions with α4β7.

Plotnik D, Guo W, Cleveland B, von Haller P, Eng JK, Guttman M, Lee KK, Arthos J, Hu SL.

J Virol. 2017 Oct 13;91(21). pii: e01005-17. doi: 10.1128/JVI.01005-17. Print 2017 Nov 1.

9.

Large-Scale and Targeted Quantitative Cross-Linking MS Using Isotope-Labeled Protein Interaction Reporter (PIR) Cross-Linkers.

Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE.

J Proteome Res. 2017 Feb 3;16(2):720-727. doi: 10.1021/acs.jproteome.6b00752. Epub 2016 Nov 30.

10.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

Chavez JD, Eng JK, Schweppe DK, Cilia M, Rivera K, Zhong X, Wu X, Allen T, Khurgel M, Kumar A, Lampropoulos A, Larsson M, Maity S, Morozov Y, Pathmasiri W, Perez-Neut M, Pineyro-Ruiz C, Polina E, Post S, Rider M, Tokmina-Roszyk D, Tyson K, Vieira Parrine Sant'Ana D, Bruce JE.

PLoS One. 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547. eCollection 2016.

11.

Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis.

Nigjeh EN, Chen R, Brand RE, Petersen GM, Chari ST, von Haller PD, Eng JK, Feng Z, Yan Q, Brentnall TA, Pan S.

J Proteome Res. 2017 Feb 3;16(2):665-676. doi: 10.1021/acs.jproteome.6b00727. Epub 2017 Jan 3.

12.

In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.

Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE.

Nat Commun. 2016 Nov 11;7:13414. doi: 10.1038/ncomms13414.

13.

In Vivo Conformational Dynamics of Hsp90 and Its Interactors.

Chavez JD, Schweppe DK, Eng JK, Bruce JE.

Cell Chem Biol. 2016 Jun 23;23(6):716-26. doi: 10.1016/j.chembiol.2016.05.012.

14.

XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data.

Schweppe DK, Zheng C, Chavez JD, Navare AT, Wu X, Eng JK, Bruce JE.

Bioinformatics. 2016 Sep 1;32(17):2716-8. doi: 10.1093/bioinformatics/btw232. Epub 2016 Apr 29.

15.

Spectral Library Searching To Identify Cross-Linked Peptides.

Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE.

J Proteome Res. 2016 May 6;15(5):1725-31. doi: 10.1021/acs.jproteome.6b00014. Epub 2016 Apr 28.

16.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

DeBlasio SL, Chavez JD, Alexander MM, Ramsey J, Eng JK, Mahoney J, Gray SM, Bruce JE, Cilia M.

J Virol. 2015 Dec 9;90(4):1973-87. doi: 10.1128/JVI.01706-15. Print 2016 Feb 15.

17.

Quantitative interactome analysis reveals a chemoresistant edgotype.

Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE.

Nat Commun. 2015 Aug 3;6:7928. doi: 10.1038/ncomms8928.

18.

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME.

Mol Endocrinol. 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16.

19.

A deeper look into Comet--implementation and features.

Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1865-74. doi: 10.1007/s13361-015-1179-x. Epub 2015 Jun 27.

20.

Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment.

Wu X, Held K, Zheng C, Staudinger BJ, Chavez JD, Weisbrod CR, Eng JK, Singh PK, Manoil C, Bruce JE.

Mol Cell Proteomics. 2015 Aug;14(8):2126-37. doi: 10.1074/mcp.M115.050161. Epub 2015 May 27.

21.

Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.

Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE.

Structure. 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19.

22.

Crux: rapid open source protein tandem mass spectrometry analysis.

McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS.

J Proteome Res. 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y. Epub 2014 Sep 9.

23.

Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells.

James RG, Bosch KA, Kulikauskas RM, Yang PT, Robin NC, Toroni RA, Biechele TL, Berndt JD, von Haller PD, Eng JK, Wolf-Yadlin A, Chien AJ, Moon RT.

J Biol Chem. 2013 Nov 29;288(48):34658-70. doi: 10.1074/jbc.M113.500314. Epub 2013 Oct 10.

24.

In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy.

Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1569-79. doi: 10.1021/pr3011638. Epub 2013 Feb 28.

25.

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Zheng C, Weisbrod CR, Chavez JD, Eng JK, Sharma V, Wu X, Bruce JE.

J Proteome Res. 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5.

26.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3645-50. doi: 10.1073/pnas.1216918110. Epub 2013 Feb 6.

27.

Protein interactions, post-translational modifications and topologies in human cells.

Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE.

Mol Cell Proteomics. 2013 May;12(5):1451-67. doi: 10.1074/mcp.M112.024497. Epub 2013 Jan 25.

28.

Comet: an open-source MS/MS sequence database search tool.

Eng JK, Jahan TA, Hoopmann MR.

Proteomics. 2013 Jan;13(1):22-4. doi: 10.1002/pmic.201200439. Epub 2012 Dec 4.

PMID:
23148064
29.

De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics.

Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ.

J Am Soc Mass Spectrom. 2012 Dec;23(12):2075-82. doi: 10.1007/s13361-012-0482-z. Epub 2012 Sep 25.

30.

Androgen-sensitive microsomal signaling networks coupled to the proliferation and differentiation of human prostate cancer cells.

Martinez HD, Hsiao JJ, Jasavala RJ, Hinkson IV, Eng JK, Wright ME.

Genes Cancer. 2011 Oct;2(10):956-78. doi: 10.1177/1947601912436422.

31.

A mass spectrometry proteomics data management platform.

Sharma V, Eng JK, Maccoss MJ, Riffle M.

Mol Cell Proteomics. 2012 Sep;11(9):824-31. doi: 10.1074/mcp.O111.015149. Epub 2012 May 18.

32.

Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.

Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE.

J Proteome Res. 2012 May 4;11(5):2968-81. doi: 10.1021/pr300041t. Epub 2012 Mar 30.

33.

Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification.

Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.

J Proteome Res. 2012 Mar 2;11(3):1621-32. doi: 10.1021/pr2008175. Epub 2012 Feb 21.

34.

In vivo application of photocleavable protein interaction reporter technology.

Yang L, Zheng C, Weisbrod CR, Tang X, Munske GR, Hoopmann MR, Eng JK, Bruce JE.

J Proteome Res. 2012 Feb 3;11(2):1027-41. doi: 10.1021/pr200775j. Epub 2012 Jan 9.

35.

Installation and use of LabKey Server for proteomics.

Eckels J, Hussey P, Nelson EK, Myers T, Rauch A, Bellew M, Connolly B, Law W, Eng JK, Katz J, McIntosh M, Mallick P, Igra M.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.5.. doi: 10.1002/0471250953.bi1305s36.

PMID:
22161569
36.

Sites of ubiquitin attachment in Saccharomyces cerevisiae.

Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.

Proteomics. 2012 Jan;12(2):236-40. doi: 10.1002/pmic.201100166. Epub 2011 Dec 20.

37.

A face in the crowd: recognizing peptides through database search.

Eng JK, Searle BC, Clauser KR, Tabb DL.

Mol Cell Proteomics. 2011 Nov;10(11):R111.009522. doi: 10.1074/mcp.R111.009522. Epub 2011 Aug 29. Review.

38.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

39.

The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching.

Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE.

J Proteome Res. 2011 Sep 2;10(9):4134-49. doi: 10.1021/pr200313x. Epub 2011 Aug 16.

40.

Cross-linking measurements of in vivo protein complex topologies.

Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE.

Mol Cell Proteomics. 2011 Oct;10(10):M110.006841. doi: 10.1074/mcp.M110.006841. Epub 2011 Jun 22.

41.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB.

J Proteome Res. 2011 Jun 3;10(6):2882-8. doi: 10.1021/pr200074h. Epub 2011 May 5.

42.

Precursor charge state prediction for electron transfer dissociation tandem mass spectra.

Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS.

J Proteome Res. 2010 Oct 1;9(10):5438-44. doi: 10.1021/pr1006685.

43.

ChromEval: a software application for the rapid evaluation of HPLC system performance in proteomic applications.

Sigmon I, Lee LW, Chang DK, Krusberski N, Cohen D, Eng JK, Martin DB.

Anal Chem. 2010 Jun 15;82(12):5060-8. doi: 10.1021/ac100043x.

PMID:
20503988
44.

A photocleavable and mass spectrometry identifiable cross-linker for protein interaction studies.

Yang L, Tang X, Weisbrod CR, Munske GR, Eng JK, von Haller PD, Kaiser NK, Bruce JE.

Anal Chem. 2010 May 1;82(9):3556-66. doi: 10.1021/ac902615g.

45.

Differential protein expression profiles in estrogen receptor-positive and -negative breast cancer tissues using label-free quantitative proteomics.

Rezaul K, Thumar JK, Lundgren DH, Eng JK, Claffey KP, Wilson L, Han DK.

Genes Cancer. 2010 Mar;1(3):251-71. doi: 10.1177/1947601910365896.

46.

A guided tour of the Trans-Proteomic Pipeline.

Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R.

Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375. Review.

47.

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.

Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R.

Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567.

48.

Derivation and characterization of human fetal MSCs: an alternative cell source for large-scale production of cardioprotective microparticles.

Lai RC, Arslan F, Tan SS, Tan B, Choo A, Lee MM, Chen TS, Teh BJ, Eng JK, Sidik H, Tanavde V, Hwang WS, Lee CN, El Oakley RM, Pasterkamp G, de Kleijn DP, Tan KH, Lim SK.

J Mol Cell Cardiol. 2010 Jun;48(6):1215-24. doi: 10.1016/j.yjmcc.2009.12.021. Epub 2010 Jan 11.

PMID:
20064522
49.

Proteomics data repositories.

Riffle M, Eng JK.

Proteomics. 2009 Oct;9(20):4653-63. doi: 10.1002/pmic.200900216. Review.

50.

Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK.

Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007.

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