faculty
Devin Schweppe
dkschwep@uw.edu
Assistant Professor
University of Washington
Cancer Biology
Cell Signaling & Cell/Environment Interactions
Microbiology, Infection & Immunity
Systems proteomics and intelligent mass spectrometry
Faculty Contact Information
Building: Foege Building
Room: S-041
Box: Box 355065
Phone: 206-616-6031
http://www.schweppelab.org/
Research Summary
Modern proteomics enables quantitation of up to 10,000 proteins from complex cellular matrices. At the interface of cell biology, biochemistry and proteomics, we are attempting to understand how proteins govern key cellular pathways involved in normal cellular function and disease. We are building adaptive strategies to harness spectral data on the millisecond time scale to determine quantitative disparities between cellular states. Intelligent data acquisition in mass spectrometry driven proteomics can enhance the accuracy and efficiency of proteomics data collection.
DEI Statement
The lab is dedicated to providing a harassment-free workplace for everyone, regardless of gender, gender identity/expression, age, sexual orientation, disability, socioeconomics, physical appearance, body size, race, national origin, or religion. We do not tolerate harassment of lab members in any form. All lab members/visitors are expected to agree to the lab’s code of conduct (lab handbook). We do not tolerate the perpetuation of stereotypes; we do not tolerate other acts of microaggression. We are a team. We stand up for one another. We learn from each other. We hold each other accountable.
Training Summary
As a member of the Genome Science faculty, I have engaged in DEI training with both the Lavender Rights Project and Greg Taylor. These trainings were focused in part on addressing the effects of racism, implicit biases, and micro/macroaggressions. As a mentor, I participated in the New Faculty Transition Program to learn how to build upon skills to run a successful research program. This program included mentoring from leaders in the Seattle research community.
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Publications
The following publications were retrieved from PubMed:
Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning.
Dincer AB, Lu Y, Schweppe DK, Oh S, Noble WS.
J Proteome Res. 2022 Jul 1; 7(21)1771-1782
Skeens E, Gadzuk-Shea M, Shah D, Bhandari V, Schweppe DK, Berlow RB, Lisi GP.
Structure. 2022 Jun 2; 6(30)840-850.e6
Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.
Liu X, Fields R, Schweppe DK, Paulo JA.
Expert Rev Proteomics. 2021 Sep; 9(18)795-807
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP.
Cell. 2021 May 27; 11(184)3022-3040.e28
Advances in quantitative high-throughput phosphoproteomics with sample multiplexing.
Paulo JA, Schweppe DK.
Proteomics. 2021 May; 9(21)e2000140
Kuljanin M, Mitchell DC, Schweppe DK, Gikandi AS, Nusinow DP, Bulloch NJ, Vinogradova EV, Wilson DL, Kool ET, Mancias JD, Cravatt BF, Gygi SP.
Nat Biotechnol. 2021 May; 5(39)630-641
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage.
Rad R, Li J, Mintseris J, O'Connell J, Gygi SP, Schweppe DK.
J Proteome Res. 2021 Jan 1; 1(20)591-598
Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, Wu H, Gygi SP, Engen JR, Walensky LD.
Mol Cell. 2020 Jul 2; 1(79)68-83.e7
Jedrychowski MP, Lu GZ, Szpyt J, Mariotti M, Garrity R, Paulo JA, Schweppe DK, Laznik-Bogoslavski D, Kazak L, Murphy MP, Gladyshev VN, Gygi SP, Chouchani ET, Spiegelman BM.
Proc Natl Acad Sci U S A. 2020 May 19; 20(117)10789-10796
Sample multiplexing for targeted pathway proteomics in aging mice.
Yu Q, Xiao H, Jedrychowski MP, Schweppe DK, Navarrete-Perea J, Knott J, Rogers J, Chouchani ET, Gygi SP.
Proc Natl Acad Sci U S A. 2020 May 5; 18(117)9723-9732
Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics.
Yu Q, Paulo JA, Naverrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK.
Anal Chem. 2020 May 5; 9(92)6478-6485
Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA.
Nat Methods. 2020 Apr; 4(17)399-404
Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Wouters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP.
Anal Chem. 2020 Mar 17; 6(92)4690
Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP.
J Proteome Res. 2020 May 1; 5(19)2026-2034
A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging.
Xiao H, Jedrychowski MP, Schweppe DK, Huttlin EL, Yu Q, Heppner DE, Li J, Long J, Mills EL, Szpyt J, He Z, Du G, Garrity R, Reddy A, Vaites LP, Paulo JA, Zhang T, Gray NS, Gygi SP, Chouchani ET.
Cell. 2020 Mar 5; 5(180)968-983.e24
Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE.
J Am Soc Mass Spectrom. 2020 Feb 5; 2(31)190-195
Erickson BK, Schweppe DK, Yu Q, Rad R, Haas W, McAlister GC, Gygi SP.
J Proteome Res. 2020 Jul 2; 7(19)2750-2757
Quantitative Proteomics of the Cancer Cell Line Encyclopedia.
Nusinow DP, Szpyt J, Ghandi M, Rose CM, McDonald ER 3rd, Kalocsay M, Jané-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, Stegmeier F, Erickson BK, Garraway LA, Sellers WR, Gygi SP.
Cell. 2020 Jan 23; 2(180)387-402.e16
Schweppe DK, Rusin SF, Gygi SP, Paulo JA.
J Proteome Res. 2020 Jan 3; 1(19)554-560
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; 6(91)4010-4016
Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP.
J Proteome Res. 2019 Mar 1; 3(18)1299-1306
Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS.
J Proteome Res. 2019 Feb 1; 2(18)594-605
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; 12(430)1814-1828
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; 1(145)
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; 1(17)722-726
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)
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; 7655(545)505-509
Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE.
J Proteome Res. 2017 Feb 3; 2(16)720-727
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; 7(114)1732-1737
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; 12(11)e0167547
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
In Vivo Conformational Dynamics of Hsp90 and Its Interactors.
Chavez JD, Schweppe DK, Eng JK, Bruce JE.
Cell Chem Biol. 2016 Jun 23; 6(23)716-26
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; 17(32)2716-8
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; 5(15)1725-31
Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis.
Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML.
Arthritis Res Ther. 2016 Jan 22; (18)27
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; 11(22)1521-1530
Schweppe DK, Chavez JD, Bruce JE.
Bioinformatics. 2016 Jan 15; 2(32)306-8
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
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
Kettenbach AN, Schweppe DK, Faherty BK, Pechenick D, Pletnev AA, Gerber SA.
Sci Signal. 2011 Jun 28; 179(4)rs5
A nondesensitizing kainate receptor point mutant.
Nayeem N, Zhang Y, Schweppe DK, Madden DR, Green T.
Mol Pharmacol. 2009 Sep; 3(76)534-42
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Lab Information
Location: University of Washington
Building: Foege Building
Room: S-041
Box: Box 355065
Phone: 206-616-6031
https://www.schweppelab.org/
Building: Foege Building
Room: S-041
Box: Box 355065
Phone: 206-616-6031
https://www.schweppelab.org/