Support for the publications involves either instrument access, computational analysis, consultation with lab or computational staff, etc. It is our policy that key collaborator(s) within the UWPR share in co-authorship of any manuscripts that are the result of work performed at the Resource. Minimally, the Proteomics Resource should always be acknowledged as follows in publications:

This work is supported in part by the University of Washington’s Proteomics Resource (UWPR95794).

2025

  • The E3 ubiquitin ligase MGRN1 targets melanocortin receptors MC1R and MC4R via interactions with transmembrane adapters. Parashara P, Gao L, Riglos A, Lartey D, Sidhu SB, Marks T, Williams C, Siauw G, Lee KJ, Ostrem AIL, Siebold C, Riffle M, Kinnebrew M, Gunn TM, Kong JH. J Cell Sci. 2025 Dec 1. PMID: 41178558
  • Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface. Hoopmann MR, McGann CD, Canterbury JD, von Haller PD, Schweppe DK. J Proteome Res. 2025 Oct 3. PMID: 40939636
  • Association of protein arginine deiminase 4 with the myosin-9 motor complex. Wang X, Moadab F, Shaikh F, An J, Mustelin C, Le E, Van der Bogaerde S, Najjar R, Mustelin T. J Biol Chem. 2025 Sep;301(9). PMID: 40707001
  • Nova: A Library for Rapid Development of Mass Spectrometry Software Applications. Hoopmann MR, McGann CD, Rose CM, Schweppe DK. J Am Soc Mass Spectrom. 2025 Aug 6. PMID: 40690708
  • Extensive citrullination of human serum albumin is physiological and not inherently immunogenic in rheumatoid arthritis. Mustelin C, Einstein A, Wang X, Shaikh F, Mustelin T. J Biol Chem. Aug;301(8). PMID: 40609794
  • Elevated apolipoprotein C3 heightens atherosclerosis risk by mediating arterial accumulation of free cholesterol and local inflammation in diabetes. Bornfeldt K, Kanter J, Hsu CC, Kramer F, Shao B, Vaisar T, den Hartigh L, Reed A, Luo J, Tran A, Tang J, Mangalapalli H, Cervantes J, Shimizu-Albergine M, Reaven P, Koska J, Jensen M, Davies B, Fisher E, Davidson N, Stitziel N, Mullick A, Goldberg I. Res Sq. 2025 Jul 16. PMID: 40709279
  • Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing McGann CD,. Bergstrom EJ, Sharma V, Yu Q, Eng JK, Schweppe DK. J Proteome Res. 2025 Jul 4. PMID: 40526826
  • Effect of complete, lifelong ANGPTL3 deficiency on triglyceride-rich lipoprotein kinetics. Fappi A, Patterson BW, Burks KH, Davidson NO, Vaisar T, Kanter JE, Bornfeldt KE, Fisher EA, Goldberg IJ, Stitziel NO, Mittendorfer B. Cell Rep Med. 2025 Jun 17. PMID: 40446802
  • Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. Wen B, Freestone J, Riffle M, MacCoss MJ, Noble WS, Keich U. Nat Methods. 2025 Jun 16. PMID: 40524023
  • Defining the Features of Complement-Active IgM. Watson MJ, Cundorff CC, Lynch EM, Kollman JM, Kearney JF, Guttman M. J Mol Biol. 2025 Jun 15. PMID: 40154915
  • Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants. Woods CN, Janowska MK, Ulmer LD, Kaur Sidhu J, Stone NL, James EI, Guttman M, Bush MF, Klevit RE. Proc Natl Acad Sci U S A. 2025 May 20. PMID: 40377988
  • Open-Source and FAIR Research Software for Proteomics. Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Gröning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE. J Proteome Res. 2025 May 2. PMID: 40267229
  • Lecithin:cholesterol acyltransferase binds a discontinuous binding site on adjacent apolipoprotein A-I belts in HDL. Coleman B, Bedi S, Hill JH, Morris J, Manthei KA, Hart RC, He Y, Shah AS, Jerome WG, Vaisar T, Bornfeldt KE, Song H, Segrest JP, Heinecke JW, Aller SG, Tesmer JJG, Davidson WS. J Lipid Res. 2025 May;66(5). PMID: 40147634
  • Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome. Mudge MC, Riffle M, Chebli G, Plubell DL, Rynearson TA, Noble WS, Timmins-Schiffman E, Kubanek J, Nunn BL. Nat Commun. 2025 Apr 29. PMID: 40295559
  • Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines. Riffle M, Zelter A, Jaschob D, Hoopmann MR, Faivre DA, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N. J Proteome Res. 2025 Apr 4. PMID: 40036265
  • Inclusion of AVβ3 integrin into extracellular vesicles in a caveolin-1 tyrosine-14- phosphorylation dependent manner and subsequent transfer to recipient melanoma cells promotes migration, invasion and metastasis. Huilcaman R, Campos A, Contreras P, Simón L, Varas-Godoy M, Grönenwald F, Shao B, Heinecke J, Lobos-Gonzalez L, Leyton L, Quest AFG. Cell Commun Signal. 2025 Mar 17. PMID: 40098186
  • Protein signatures predict coral resilience and survival to thermal bleaching events. Nunn BL, Brown T, Timmins-Schiffman EB, Mudge MC, Riffle M, Axworthy JB, Dilworth J, Kenkel CD, Zaneveld J, Rodrigues LJ, Padilla-Gamiño JL. Communications Earth & Environment 2025 Mar 08. PMID: Nature
  • Proteomic Plasticity in the Coral Montipora capitata Gamete Bundles after Parent Thermal Bleaching. Timmins-Schiffman EB, Khanna R, Brown T, Dilworth J, MacLean BX, Mudge MC, White SJ, Kenkel CD, Rodrigues LJ, Nunn BL, Padilla-Gamiño JL. J Proteome Res 2025 Mar 7. PMID: 39996506
  • Proteomic Insights into Psychrophile Growth in Perchlorate-Amended Subzero Conditions: Implications for Martian Life Detection. Gentilhomme AS, Dhakar K, Timmins-Schiffman E, Chaw M, Firth E, Junge K, Nunn BL. Astrobiology. 2025 Mar;25(3). PMID: 39960803
  • An In-Depth Coho Salmon (Oncorhynchus kisutch) Ovarian Follicle Proteome Reveals Coordinated Changes Across Diverse Cellular Processes during the Transition From Primary to Secondary Growth. Timmins-Schiffman E, Telish J, Field C, Monson C, Guzmán JM, Nunn BL, Young G, Forsgren K. Proteomics. 2025 Mar;25(5-6). PMID: 39648474
  • Elevated levels of serum alpha-2-macroglobulin associate with diabetes status and incident CVD in type 1 diabetes. Shao B, Snell-Bergeon JK, de Boer IH, Davidson WS, Bornfeldt KE, Heinecke JW. J Lipid Res. Feb;66(2). PMID: 39761918
  • High-Density Lipoprotein Lipid and Protein Cargo and Cholesterol Efflux Capacity Before and After Bariatric Surgery. Zahid S, Schlamp F, Gildea MA, Lin BX, Chaloemtoem A, Falis M, Parikh M, Fisher EA, Hornemann T, Vaisar T, Heffron SP. Arterioscler Thromb Vasc Biol. 2025 Feb;45(2). PMID: 39744840