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Items: 21

1.

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.

Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP.

Anal Chem. 2019 Mar 19;91(6):4010-4016. doi: 10.1021/acs.analchem.8b05399. Epub 2019 Feb 26.

PMID:
30672687
2.

Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows.

Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP.

J Proteome Res. 2019 Mar 1;18(3):1299-1306. doi: 10.1021/acs.jproteome.8b00899. Epub 2019 Feb 4.

PMID:
30658528
3.

TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays.

Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS.

J Proteome Res. 2019 Feb 1;18(2):594-605. doi: 10.1021/acs.jproteome.8b00767. Epub 2018 Dec 12.

PMID:
30501201
4.

Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.

Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z.

J Mol Biol. 2018 Jun 8;430(12):1814-1828. doi: 10.1016/j.jmb.2018.04.010. Epub 2018 Apr 14.

5.

The skeletal phenotype of achondrogenesis type 1A is caused exclusively by cartilage defects.

Bird IM, Kim SH, Schweppe DK, Caetano-Lopes J, Robling AG, Charles JF, Gygi SP, Warman ML, Smits PJ.

Development. 2018 Jan 8;145(1). pii: dev156588. doi: 10.1242/dev.156588.

6.

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

Schweppe DK, Huttlin EL, Harper JW, Gygi SP.

J Proteome Res. 2018 Jan 5;17(1):722-726. doi: 10.1021/acs.jproteome.7b00572. Epub 2017 Oct 31.

PMID:
29054129
7.

Intrinsic disorder within AKAP79 fine-tunes anchored phosphatase activity toward substrates and drug sensitivity.

Nygren PJ, Mehta S, Schweppe DK, Langeberg LK, Whiting JL, Weisbrod CR, Bruce JE, Zhang J, Veesler D, Scott JD.

Elife. 2017 Oct 2;6. pii: e30872. doi: 10.7554/eLife.30872.

8.

Architecture of the human interactome defines protein communities and disease networks.

Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW.

Nature. 2017 May 25;545(7655):505-509. doi: 10.1038/nature22366. Epub 2017 May 17.

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.

Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.

Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):1732-1737. doi: 10.1073/pnas.1617220114. Epub 2017 Jan 27.

11.

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.

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.

Host-Microbe Protein Interactions during Bacterial Infection.

Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE.

Chem Biol. 2015 Nov 19;22(11):1521-1530. doi: 10.1016/j.chembiol.2015.09.015. Epub 2015 Nov 5.

17.

XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.

Schweppe DK, Chavez JD, Bruce JE.

Bioinformatics. 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519. Epub 2015 Sep 26.

18.

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.

19.

Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors.

Schweppe DK, Rigas JR, Gerber SA.

J Proteomics. 2013 Oct 8;91:286-96. doi: 10.1016/j.jprot.2013.07.023. Epub 2013 Aug 2.

20.

Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells.

Kettenbach AN, Schweppe DK, Faherty BK, Pechenick D, Pletnev AA, Gerber SA.

Sci Signal. 2011 Jun 28;4(179):rs5. doi: 10.1126/scisignal.2001497.

21.

A nondesensitizing kainate receptor point mutant.

Nayeem N, Zhang Y, Schweppe DK, Madden DR, Green T.

Mol Pharmacol. 2009 Sep;76(3):534-42. doi: 10.1124/mol.109.056598. Epub 2009 Jun 26.

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