publications.php

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                        <h1>Publications</h1>
                        <span class="byline">UWPR supported publications</span>
                     </header>

               <p>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:
               <span style="color:blue; font-style:italic;">This work is supported in part by the University of Washington's Proteomics Resource (UWPR95794).</span></p>


<ol class="default" reversed>

<p><h3>2026</h3>

<li>Plasma-driven disassembly of amyloid-&#x3b2; aggregates by the interplay of physicochemical stimuli.
Jo Y, Bae JH, Jang J, Lee H, Heo Y, Lee YH, Park CB, Park S.
<li>Cell Reports Physical Science</i> Vol 7, Issue 2103090, 2026/02/18. doi: 10.1016/j.xcrp.2025.103090
<a target="new" href="https://doi.org/10.1016/j.xcrp.2025.103090/">ScienceDirect</a>

<li>The ProteomeXchange consortium in 2026: making proteomics data FAIR.
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Bandla C, Kamatchinathan S, Hewapathirana S, Sun Z, Kawano S, Okuda S, Connolly B, MacLean B, MacCoss MJ, Chen T, Zhu Y, Ishihama Y, Vizcaíno JA.
<i>Nucleic Acids Res.</i> 2026 Jan 6;54(D1):D459-D469. doi: 10.1093/nar/gkaf1146.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/41206473/">PubMed</a>

<p><h3>2025</h3>

<li>Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface.
Hoopmann MR, McGann CD, Canterbury JD, von Haller PD, Schweppe DK.
<i>J Proteome Res.</i> 2025 Oct 3;24(10):5277-5281. doi: 10.1021/acs.jproteome.5c00269. Epub 2025 Sep 12.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40939636/">PubMed</a>

<li>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.
<i>J Biol Chem.</i> Sep;301(9):110513. doi: 10.1016/j.jbc.2025.110513. Epub 2025 Jul 22.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40707001/">PubMed</a>

<li>Nova: A Library for Rapid Development of Mass Spectrometry Software Applications
Hoopmann MR, McGann CD, Rose CM, Schweppe DK.
<i>J Am Soc Mass Spectrom.</i> 2025 Aug 6;36(8):1836-1839. doi: 10.1021/jasms.5c00141. Epub 2025 Jul 21.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40690708/">PubMed</a>

<li>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.
<i>Res Sq.</i> 2025 Jul 16:rs.3.rs-6979508. doi: 10.21203/rs.3.rs-6979508/v1.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40709279/">PubMed</a>

<li>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.
<i>J Biol Chem.</i> 2025 Aug;301(8):110438. doi: 10.1016/j.jbc.2025.110438. Epub 2025 Jul 1.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40609794/">PubMed</a>

<li>Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing
McGann CD, Bergstrom EJ, Sharma V, Yu Q, Eng JK, Schweppe DK.
<i>J Proteome Res.</i> 2025 Jul 4;24(7):3715-3721. doi: 10.1021/acs.jproteome.4c01094. Epub 2025 Jun 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40526826/">PubMed</a>

<li>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.
<i>Nat Methods.</i> 2025 Jun 16. doi: 10.1038/s41592-025-02719-x. Online ahead of print.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40524023/">PubMed</a>

<li>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.
<i>Cell Rep Med.</i> 2025 Jun 17;6(6):102152. doi: 10.1016/j.xcrm.2025.102152. Epub 2025 May 29.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40446802/">PubMed</a>

<li>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.
<i>Proc Natl Acad Sci U S A.</i> 2025 May 20;122(20):e2425061122. doi: 10.1073/pnas.2425061122. Epub 2025 May 16.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40377988/">PubMed</a>

<li>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.
<i>Nat Commun.</i> 2025 Apr 29;16(1):3986. doi: 10.1038/s41467-025-59250-y.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40295559/">PubMed</a>

<li>Open-Source and FAIR Research Software for Proteomics.
Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning 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.
<i>J Proteome Res.</i> 2025 May 2;24(5):2222-2234. doi: 10.1021/acs.jproteome.4c01079. Epub 2025 Apr 23.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40267229/">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2025 Apr 4;24(4):1895-1906. doi: 10.1021/acs.jproteome.4c00968. Epub 2025 Mar 4.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40036265/">PubMed</a>

<li>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.
<i>J Lipid Res. 2025.</i> May;66(5):100786. doi: 10.1016/j.jlr.2025.100786. Epub 2025 Mar 25.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40147634/">PubMed</a>

<li>Inclusion of ΑVβ3 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, Grünenwald F, Shao B, Heinecke J, Lobos-Gonzalez L, Leyton L, Quest AFG.
<i>Cell Commun Signal.</i>. 2025 Mar 17;23(1):139. doi: 10.1186/s12964-025-02131-0.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/40098186/">PubMed</a>

<li>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.
<i>J Proteome Res</i>. 2025 Mar 7;24(3):1317-1328. doi: 10.1021/acs.jproteome.4c00946. Epub 2025 Feb 25.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39996506/">PubMed</a>

<li>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.
<i>Astrobiology.</i> Mar;25(3):177-188. doi: 10.1089/ast.2024.0065. Epub 2025 Feb 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39960803/">PubMed</a>

<li>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.
<i>J Lipid Res.</i> 2025 Feb;66(2):100741. doi: 10.1016/j.jlr.2025.100741. Epub 2025 Jan 4.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39761918/">PubMed</a>

<li>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.
<i>Arterioscler Thromb Vasc Biol.</i> 2025 Feb;45(2):e48-e62. doi: 10.1161/ATVBAHA.124.321686. Epub 2025
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39744840/">PubMed</a>

<li>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.
<i>Communications Earth &amp; Environment</i> 2025, 6, Article number: 191 (2025)
<a target="new" href="https://doi.org/10.1038/s43247-025-02167-7">publication</a>

<li>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.
<i>Proteomics.</i> 2025 Mar;25(5-6):e202400311. doi: 10.1002/pmic.202400311. Epub 2024 Dec 8.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39648474/">PubMed</a>

<p><h3>2024</h3>

<li>Reproductive resilience: pathways to gametogenic success in Montipora capitata after bleaching.
Timmins-Schiffman E, Duselis E, Brown T, Axworthy JB, Backstrom CH, Riffle M, Dilworth J, Kenkel CD, Rodrigues LJ, Nunn BL, Padilla-Gamiño JL.
<i>Sci Rep.</i> 2024 Nov 13;14(1):27765. doi: 10.1038/s41598-024-78768-7.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39532979/">PubMed</a>

<li>Detection and Quantification of Drug-Protein Adducts in Human Liver.
Zelter A, Riffle M, Shteynberg DD, Zhong G, Riddle EB, Hoopmann MR, Jaschob D, Moritz RL, Davis TN, MacCoss MJ, Isoherranen N.
<i>J Proteome Res.</i> 2024 Nov 1;23(11):5143-5152. doi: 10.1021/acs.jproteome.4c00663. Epub 2024 Oct 23.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39442081/">PubMed</a>

<li>APOA2 increases cholesterol efflux capacity to plasma HDL by displacing the C-terminus of resident APOA1.
Sarkar S, Morris J, You Y, Sexmith H, Street SE, Thibert SM, Attah IK, Hutchinson Bunch CM, Novikova IV, Evans JE, Shah AS, Gordon SM, Segrest JP, Bornfeldt KE, Vaisar T, Heinecke JW, Davidson WS, Melchior JT.
<i>J Lipid Res.</i> 2024 Dec;65(12):100686. doi: 10.1016/j.jlr.2024.100686. Epub 2024 Oct 28.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39490930/">PubMed</a>

<li>RNA structures within Venezuelan equine encephalitis virus E1 alter macrophage replication fitness and contribute to viral emergence.
Hickson SE, Hyde JL.
<i>PLoS Pathog.</i> 2024 Sep 27;20(9):e1012179. doi: 10.1371/journal.ppat.1012179. eCollection 2024 Sep.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39331659/">PubMed</a>

<li>Relationships between HDL subpopulation proteome and HDL function in overweight/obese people with and without coronary heart disease.
Vaisar T, Babenko I, Horvath KV, Niisuke K, Asztalos BF.
<i>Atherosclerosis.</i> 2024 Oct;397:118565. doi: 10.1016/j.atherosclerosis.2024.118565. Epub 2024 Aug 13.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39260003/">PubMed</a>

<li>A Framework for Quality Control in Quantitative Proteomics.
Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ.
<i>J Proteome Res.</i> 2024 Oct 4;23(10):4392-4408. doi: 10.1021/acs.jproteome.4c00363. Epub 2024 Sep 9. PMID: 39248652
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/39248652/">PubMed</a>

<li>A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.
Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A.
<i>Anal Chem.</i> 2024 May 14;96(19):7373-7379. doi: 10.1021/acs.analchem.4c00829. Epub 2024 May 2.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38696819/">PubMed</a>

<li>High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.
Ulmer LD, Canzani D, Woods CN, Stone NL, Janowska MK, Klevit RE, Bush MF.
<i>J Proteome Res.</i> 2024 Aug 2;23(8):3560-3570. doi: 10.1021/acs.jproteome.4c00194. Epub 2024 Jul 5.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38968604/">PubMed</a>

<li>Comparative Analysis of Protein Quantification by the SomaScan Assay versus Orthogonal Methods in Urine from People with Diabetic Kidney Disease.
Lopez LN, Durbin-Johnson B, Vargas CR, Ruzinski J, Goodling A, Mehrotra R, Vaisar T, Rocke DM, Afkarian M.
<i>J Proteome Res.</i> 2024 Jul 5;23(7):2598-2607. doi: 10.1021/acs.jproteome.4c00322. Epub 2024 Jun 18.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38965919/">PubMed</a>

<li>A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.
Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A.
<i>Anal Chem.</i> 2024 May 14;96(19):7373-7379. doi: 10.1021/acs.analchem.4c00829. Epub 2024 May 2.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38696819/">PubMed</a>

<li>Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod.
Timmins-Schiffman E, Maas AE, Khanna R, Blanco-Bercial L, Huang E, Nunn BL.
<i>J Proteome Res.</i> 2024 Jun 7;23(6):2112-2123. doi: 10.1021/acs.jproteome.4c00086. Epub 2024 May 1.PMID: 38690632
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38690632/">PubMed</a>

<li>A targeted proteomics method for quantifying plasma apolipoprotein kinetics in individual mice using stable isotope labeling.
Shao B, Shimizu-Albergine M, Kramer F, Kanter JE, Heinecke JW, Vaisar T, Mittendorfer B, Patterson BW, Bornfeldt KE.
<i>J Lipid Res.</i> 2024 Apr;65(4):100531. doi: 10.1016/j.jlr.2024.100531. Epub 2024 Mar 13.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38490635/">PubMed</a>

<li>Diel metabolic patterns revealed by in situ transcriptome and proteome in a vertically migratory copepod.
Maas AE, Timmins-Schiffman E, Tarrant AM, Nunn BL, Park J, Blanco-Bercial L.
<i>Mol Ecol.</i> 2024 Mar;33(6):e17284. doi: 10.1111/mec.17284. Epub 2024 Jan 22
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38258354/">PubMed</a>

<li>Flipped C-Terminal Ends of APOA1 Promote ABCA1-Dependent Cholesterol Efflux by Small HDLs.
He Y, Pavanello C, Hutchins PM, Tang C, Pourmousa M, Vaisar T, Song HD, Pastor RW, Remaley AT, Goldberg IJ, Costacou T, Sean Davidson W, Bornfeldt KE, Calabresi L, Segrest JP, Heinecke JW.
<i>Circulation.</i> 2024 Mar 5;149(10):774-787. doi: 10.1161/CIRCULATIONAHA.123.065959. Epub 2023 Nov 29.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/37961344/">PubMed</a>

<li>Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure to Mycobacterium tuberculosis.
Dill-McFarland KA, Simmons JD, Peterson GJ, Nguyen FK, Campo M, Benchek P, Stein CM, Vaisar T, Mayanja-Kizza H, Boom WH, Hawn TR.
<i>bioRxiv [Preprint].</i> 2024 Mar 4:2024.02.27.582348. doi: 10.1101/2024.02.27.582348.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38464296/">PubMed</a>

<li>Sex differences in the associations of HDL particle concentration and cholesterol efflux capacity with incident coronary artery disease in type 1 diabetes: The RETRO HDLc cohort study.
Costacou T, Miller RG, Bornfeldt KE, Heinecke JW, Orchard TJ, Vaisar T.
<i>J Clin Lipidol.</i> 2024 Mar-Apr;18(2):e218-e229. doi: 10.1016/j.jacl.2024.01.004. Epub 2024 Jan 29.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38320926/">PubMed</a>

<li>A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.
Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K.
<i>Lab Invest.</i> 2024 Jan;104(1):100282. doi: 10.1016/j.labinv.2023.100282. Epub 2023 Nov 3.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/37924947/">PubMed</a>

<p><h3>2023</h3>

<li>An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting.
Hodge EA, Chatterjee A, Chen C, Naika GS, Laohajaratsang M, Mangala Prasad V, Lee KK.
<i>Npj Viruses.</i> 2023;1(1):2. doi: 10.1038/s44298-023-00002-4. Epub 2023 Oct 5.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/38665238/">PubMed</a>

<li>Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta).
Gomes KM, Nunn BL, Chappell PD, Jenkins BD.
<i>J Phycol.</i> 2023 Oct;59(5):1085-1099. doi: 10.1111/jpy.13379. Epub 2023 Aug 24.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/37615442/">PubMed</a>

<li>BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation.
Witus SR, Tuttle LM, Li W, Zelter A, Wang M, Kermoade KE, Wilburn DB, Davis TN, Brzovic PS, Zhao W, Klevit RE.
<i>EMBO J. </i> 2023 Aug 1;42(15):e113565. doi: 10.15252/embj.2023113565. Epub 2023 Jun 12.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/37305927/">PubMed</a>

<li>hACE2-Induced Allosteric Activation in SARS-CoV versus SARS-CoV-2 Spike Assemblies Revealed by Structural Dynamics.
Chen C, Zhu R, Hodge EA, Díaz-Salinas MA, Nguyen A, Munro JB, Lee KK.
<i>ACS Infect Dis. </i> 2023 Jun 9;9(6):1180-1189. doi: 10.1021/acsinfecdis.3c00010. Epub 2023 May 11.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/37166130/">PubMed</a>

<li>Apolipoprotein C3 induces inflammasome activation only in its delipidated form.
Hsu CC, Shao B, Kanter JE, He Y, Vaisar T, Witztum JL, Snell-Bergeon J, McInnes G, Bruse S, Gottesman O, Mullick AE, Bornfeldt KE.
<i>Nat Immunol.</i> 2023 Mar;24(3):408-411. doi: 10.1038/s41590-023-01423-2. Epub 2023 Feb 13.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36781985/">PubMed</a>

<li>MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes.
Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K.
<i>bioRxiv [Preprint]. </i> 2023 Mar 20:2023.03.16.533031. doi: 10.1101/2023.03.16.533031.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36993219/">PubMed</a>

<li>Disordered region encodes α-crystallin chaperone activity toward lens client γD-crystallin.
Woods CN, Ulmer LD, Guttman M, Bush MF, Klevit RE.
<i>Proc Natl Acad Sci U S A.</i> 2023 Feb 7;120(6):e2213765120. doi: 10.1073/pnas.2213765120. Epub 2023 Jan 31.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36719917/">PubMed</a>

<li>Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.
Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL.
<i>J Proteome Res.</i> 2023 Feb 3;22(2):615-624. doi: 10.1021/acs.jproteome.2c00624. Epub 2023 Jan 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36648445/">PubMed</a>

<li>Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.
Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL.
<i>J Proteome Res.</i> 2023 Feb 3;22(2):615-624. doi: 10.1021/acs.jproteome.2c00624. Epub 2023 Jan 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36648445/">PubMed</a>

<li>The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.
Kertesz-Farkas A, Nii Adoquaye Acquaye FL, Bhimani K, Eng JK, Fondrie WE, Grant C, Hoopmann MR, Lin A, Lu YY, Moritz RL, MacCoss MJ, Noble WS.
<i>J Proteome Res.</i> 2023 Feb 3;22(2):561-569. doi: 10.1021/acs.jproteome.2c00615. Epub 2023 Jan 4.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36598107/">PubMed</a>

<p><h3>2022</h3>

<li>Conditional Fragment Ion Probabilities Improve Database Searching for Nonmonoisotopic Precursors.
O'Brien JJ, Gadzuk-Shea M, Seitzer PM, Rad R, McAllister FE, Schweppe DK.
<i>J Proteome Res.</i> 2022 Nov 22. doi: 10.1021/acs.jproteome.2c00247.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36414539/">PubMed</a>

<li>Protein kinase R dependent phosphorylation of α-synuclein regulates its membrane binding and aggregation.
Reimer L, Gram H, Jensen NM, Betzer C, Yang L, Jin L, Shi M, Boudeffa D, Fusco G, De Simone A, Kirik D, Lashuel HA, Zhang J, Jensen PH.
<i>PNAS Nexus.</i> 2022 Nov 16;1(5):pgac259. doi: 10.1093/pnasnexus/pgac259. eCollection 2022 Nov.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36712380/">PubMed</a>

<li>The ProteomeXchange consortium at 10 years: 2023 update.
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.
<i>Nucleic Acids Res.</i> 2022 Nov 12:gkac1040. doi: 10.1093/nar/gkac1040.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36370099/">PubMed</a>

<li>Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification.
Smith IR, Eng JK, Barente AS, Hogrebe A, Llovet A, Rodriguez-Mias RA, Villén J.
<i>Anal Chem.</i> 2022 Nov 8;94(44):15198-15206. doi: 10.1021/acs.analchem.2c01711. Epub 2022 Oct 28.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36306373/">PubMed</a>

<li>Extracellular vesicles from gastric epithelial GES-1 cells infected with Helicobacter pylori promote changes in recipient cells associated with malignancy.
González MF, Burgos-Ravanal R, Shao B, Heinecke J, Valenzuela-Valderrama M, Corvalán AH, Quest AFG
<i>Front Oncol.</i> 2022 Oct 12;12:962920. doi: 10.3389/fonc.2022.962920. eCollection 2022.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/36313672/">PubMed</a>

<li>Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature.
Crandall G, Thompson RE, Eudeline B, Vadopalas B, Timmins-Schiffman E, Roberts E.
<i>PeerJ</i> 2022 Oct 4. doi: 10.7717/peerj.14158
<a target="new" href="https://peerj.com/articles/14158">publication</a>

<li>Effect of Selective Androgen Receptor Modulator on Cholesterol Efflux Capacity, Size, and Subspecies of HDL Particles
Guo W, Pencina KM, Furtado JD, Sacks FM, Vaisar T, Cheng M, Sniderman AD, Page ST, Bhasin S.
<i>J Endocr Soc. </i> 2022 Jun 28;6(8):bvac099. doi: 10.1210/jendso/bvac099. eCollection 2022 Aug 1.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35822201/">PubMed</a>

<li>Transitioning global change experiments on Southern Ocean phytoplankton from lab to field settings: Insights and challenges.
Boyd PW, Doney SC, EgginsS, Ellwood MH, Fourquez M, Nunn BL, Strzepek R, Timmins-Schiffman E.
<i>Limnology and Oceanography</i> 25 June 2022. doi.org/10.1002/lno.12175
<a target="new" href="https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lno.12175">publication</a>

<li>Osmotic Processor for Enabling Sensitive and Rapid Biomarker Detection via Lateral Flow Assays.
Chen SY, Wu AY, Lunde R, Lai JJ.
<i>Front Bioeng Biotechnol.</i> 2022 Jun 1;10:884271. doi: 10.3389/fbioe.2022.884271. eCollection 2022.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35721843/">PubMed</a>

<li>10,12-Conjugated linoleic acid supplementation improves HDL composition and function in mice.
Vaisar T, Wang S, Omer M, Irwin AD, Storey C, Tang C, den Hartigh LJ.
<i>J Lipid Res.</i> 2022 Jun 15;63(8):100241. doi: 10.1016/j.jlr.2022.100241.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35714730/">PubMed</a>

<li>Structural dynamics reveal isolate-specific differences at neutralization epitopes on HIV Env.
Hodge EA, Naika GS, Kephart SM, Nguyen A, Zhu R, Benhaim MA, Guo W, Moore JP, Hu SL, Sanders RW, Lee KK.
<i>iScience.</i> 2022 May 23;25(6):104449. doi: 10.1016/j.isci.2022.104449. eCollection 2022 Jun 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35677643/">PubMed</a>

<li>Conformational flexibility of apolipoprotein A-I amino- and carboxy-termini is necessary for lipid binding but not cholesterol efflux.
Bedi S, Morris J, Shah A, Hart RC, Jerome WG, Aller SG, Tang C, Vaisar T, Bornfeldt KE, Segrest JP, Heinecke JW, Davidson WS.
<i>J Lipid Res.</i> 2022 Mar;63(3):100168. doi: 10.1016/j.jlr.2022.100168. Epub 2022 Jan 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35051413/">PubMed</a>

<li>Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality.
Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE.
<i>mSphere</i> 2021 May 12;6(3):e00009-21. doi: 10.1128/mSphere.00009-21.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33980670/">PubMed</a>

<li>Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load.
Flores RL, Peterson ZE, Zelter A, Riffle M, Asbury CL, Davis TN.
<i>J Cell Biol. </i> 2022 May 2;221(5):e202107016. doi: 10.1083/jcb.202107016. Epub 2022 Mar 30.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35353161/">PubMed</a>

<li>Pulmonary surfactant protein B carried by HDL predicts incident CVD in patients with type 1 diabetes.
Shao B, Snell-Bergeon JK, Pyle LL, Thomas KE, de Boer IH, Kothari V, Segrest J, Davidson WS, Bornfeldt KE, Heinecke JW.
<i>J Lipid Res</i> 2022 Apr;63(4):100196. doi: 10.1016/j.jlr.2022.100196. Epub 2022 Mar 14.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35300983/">PubMed</a>

<li>Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies.
Sahoo A, Hodge EA, LaBranche CC, Styles TM, Shen X, Cheedarla N, Shiferaw A, Ozorowski G, Lee WH, Ward AB, Tomaras GD, Montefiori DC, Irvine DJ, Lee KK, Amara RR.
<i>Cell Rep. </i> 2022 Mar 1;38(9):110436. doi: 10.1016/j.celrep.2022.110436.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35235790/">PubMed</a>

<li>Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry.
Riffle M, Hoopmann MR, Jaschob D, Zhong G, Moritz RL, MacCoss MJ, Davis TN, Isoherranen N, Zelter A.
<i>Anal Chem.</i> 2022 Mar 1;94(8):3501-3509. doi: 10.1021/acs.analchem.1c04101. Epub 2022 Feb 20.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35184559/">PubMed</a>

<li>Shotgun Proteomics Identifies Active Metabolic Pathways in Bleached Coral Tissue and Intraskeletal Compartments
Axworthy, Jeremy B; Timmins-Schiffman, Emma; Brown, Tanya; Rodrigues, Lisa J; Nunn, Brook L.
<i>Frontiers in Marine Science.</i> Lausanne (Feb 14, 2022). doi:10.3389/fmars.2022.797517.
<a target="new" href="https://www.frontiersin.org/articles/10.3389/fmars.2022.797517/full">publication</a>

<li>Cryo-ET of Env on intact HIV virions reveals structural variation and positioning on the Gag lattice.
Prasad VM, Leaman DP, Lovendahl KN, Croft JT, Benhaim MA, Hodge EA, Zwick MB, Lee KK.
<i>Cell</i> 2022 Feb 4;185(4):641-653. dOI:https://doi.org/10.1016/j.cell.2022.01.013.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35123651/">PubMed</a>

<p><h3>2021</h3>

<li>A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours
Cui C, Chakraborty K, Tang XA, Schoenfelt KQ, Hoffman A, Blank A, McBeth B, Pulliam N, Reardon CA, Kulkarni SA, Vaisar T, Ballabio A, Krishnan Y, Becker L.
<i>Nat Nanotechnol. </i> 2021 Dec;16(12):1394-1402. doi: 10.1038/s41565-021-00988-z. Epub 2021 Nov 11.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34764452/">PubMed</a>

<li>Amino acid primed mTOR activity is essential for heart regeneration.
Miklas JW, Levy S, Hofsteen P, Mex DI, Clark E, Muster J, Robitaille AM, Sivaram G, Abell L, Goodson JM, Pranoto I, Madan A, Chin MT, Tian R, Murry CE, Moon RT, Wang Y, Ruohola-Baker H.
<i>iScience.</i> 2021 Dec 6;25(1):103574. doi: 10.1016/j.isci.2021.103574. eCollection 2022 Jan 21.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34988408/">PubMed</a>

<li>Tandem Mass Spectrometry–Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing.
Phipps WS, D Smith KD, Yang HY, Henderson CM, Pflaum H, Lerch ML, Fondrie WE, Emrick MA, Wu CC, MacCoss MJ, Noble WS, Hoofnagle AN.
<i>Am J of Clin Pathol.</i> 2021 Nov 22; https://doi.org/10.1093/ajcp/aqab185.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/35512256/">PubMed</a>

<li>CREBH normalizes dyslipidemia and halts atherosclerosis in diabetes by decreasing circulating remnant lipoproteins
Shimizu-Albergine M, Basu D, Kanter JE, Kramer F, Kothari V, Barnhart S, Thornock C, Mullick AE, Clouet-Foraison N, Vaisar T, Heinecke JW, Hegele RA, Goldberg IJ, Bornfeldt KE.
<i>J Clin Invest. </i> 2021 Nov 15;131(22):e153285. doi: 10.1172/JCI153285.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34491909/">PubMed</a>

<li>Altered HDL proteome predicts incident CVD in chronic kidney disease patients.
Shao B, Mathew AV, Thornock C, Pennathur S; Michigan Kidney Translational Core CPROBE Investigator Group.
<i>J Lipid Res.</i> 2021;62:100135. doi: 10.1016/j.jlr.2021.100135. Epub 2021 Oct 9.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34634315/">PubMed</a>

<li>Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora.
Petrou K, Nunn BL, Padula MP, Miller DJ, Nielsen DA.
<i>Sci Rep. </i> 2021 Sep 24;11(1):19061. doi: 10.1038/s41598-021-98548-x.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34561509/">PubMed</a>

<li>Decoding Post-Translational Modification Crosstalk With Proteomics.
Leutert M, Entwisle SW, Villén J.
<i>Mol Cell Proteomics. </i> 2021;20:100129. doi: 10.1016/j.mcpro.2021.100129. Epub 2021 Jul 30.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34339852/">PubMed</a>

<li>Apolipoprotein A-I modulates HDL particle size in the absence of apolipoprotein A-II
Melchior JT, Street SE, Vaisar T, Hart R, Jerome J, Kuklenyik Z, Clouet-Foraison N, Thornock C, Bedi S, Shah AS, Segrest JP, Heinecke JW, Davidson WS.
<i>J Lipid Res. </i> 2021;62:100099. doi: 10.1016/j.jlr.2021.100099. Epub 2021 Jul 27.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34324889/">PubMed</a>

<li>Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.
Lin A, Plubell DL, Keich U, Noble WS.
<i>J Proteome Res.</i> 2021 Aug 6;20(8):4153-4164. doi: 10.1021/acs.jproteome.1c00483. Epub 2021 Jul 8.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34236864/">PubMed</a>

<li>Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments.
Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ.
<i>Environ Microbiol.</i> 2021 Aug;23(8):4646-4660. doi: 10.1111/1462-2920.15656. Epub 2021 Jul 13.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34190392/">PubMed</a>

<li>Niacin Increases Atherogenic Proteins in High-Density Lipoprotein of Statin-Treated Subjects
Ronsein GE, Vaisar T, Davidson WS, Bornfeldt KE, Probstfield JL, O'Brien KD, Zhao XQ, Heinecke JW.
<i>Arterioscler Thromb Vasc Biol. </i> 2021 Aug;41(8):2330-2341. doi: 10.1161/ATVBAHA.121.316278. Epub 2021
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34134520/">PubMed</a>

<li>Identification of phosphosites that alter protein thermal stability.
Smith IR, Hess KN, Bakhtina AA, Valente AS, Rodríguez-Mias RA, Villén J.
<i>Nat Methods.</i> 2021 Jul;18(7):760-762. doi: 10.1038/s41592-021-01178-4. Epub 2021 Jun 17.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/34140699/">PubMed</a>

<li>Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis.
Cui C, Chakraborty K, Tang XA, Zhou G, Schoenfelt KQ, Becker KM, Hoffman A, Chang YF, Blank A, Reardon CA, Kenny HA, Vaisar T, Lengyel E, Greene G, Becker L.
<i>Cell.</i> 2021 Jun 10;184(12):3163-3177.e21. doi: 10.1016/j.cell.2021.04.016. Epub 2021 May 7.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33964209/">PubMed</a>

<li>Bacterial quorum-sensing signal arrests phytoplankton cell division and impacts virus-induced mortality.
Pollara SB, Becker JW, Nunn BL, Boiteau R, Repeta D, Mudge MC, Downing G, Chase D, Harvey EL, Whalen KE.
<i>mSphere.</i> 2021 May 12;6(3):e00009-21. doi: 10.1128/mSphere.00009-21.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33980670/">PubMed</a>

<li>Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery.
Timmins-Schiffman E, White SJ, Thompson RE, Vadopalas B, Eudeline B, Nunn BL, Roberts SB.
<i>Environ Microbiome.</i> 2021 Mar 31;16(1):7. doi: 10.1186/s40793-021-00376-z.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33902744/">PubMed</a>

<li>Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments.
Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA.
<i>Environ Microbiol.</i> 2021 Mar 24. doi: 10.1111/1462-2920.15485.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33760340/">PubMed</a>

<li>HCN Channel Phosphorylation Sites Mapped by Mass Spectrometry in Human Epilepsy Patients and in an Animal Model of Temporal Lobe Epilepsy.
Concepcion FA, Khan MN, Ju Wang JD, Wei AD, Ojemann JG, Ko AL, Shi Y, Eng JK, Ramirez JM, Poolos NP.
<i>Neuroscience.</i> 2021 Feb 9:S0306-4522(21)00063-4. doi: 10.1016/j.neuroscience.2021.01.038.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33571596/">PubMed</a>

<li>Physiological and molecular responses of lobe coral indicate nearshore adaptations to anthropogenic stressors.
Tisthammer KH, Timmins-Schiffman E, Seneca FO, Nunn BL, Richmond RH.
<i>Sci Rep.</i> 2021 Feb 9;11(1):3423. doi: 10.1038/s41598-021-82569-7.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33564085/">PubMed</a>

<p><h3>2020</h3>


<li>Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2.
Alexandra C Walls, Brooke Fiala, Alexandra Schäfer, Samuel Wrenn, Minh N Pham, Michael Murphy, Longping V Tse, Laila Shehata, Megan A O'Connor, Chengbo Chen, Mary Jane Navarro, Marcos C Miranda, Deleah Pettie, Rashmi Ravichandran, John C Kraft, Cassandra Ogohara, Anne Palser, Sara Chalk, E-Chiang Lee, Elizabeth Kepl, Cameron M Chow, Claire Sydeman, Edgar A Hodge, Brieann Brown, Jim T Fuller, Kenneth H Dinnon, Lisa E Gralinski, Sarah R Leist, Kendra L Gully, Thomas B Lewis, Miklos Guttman, Helen Y Chu, Kelly K Lee, Deborah H Fuller, Ralph S Baric, Paul Kellam, Lauren Carter, Marion Pepper, Timothy P Sheahan, David Veesler, Neil P King
<i> Cell </i>  2020 Nov 25;183(5):1367-1382.e17. doi: 10.1016/j.cell.2020.10.043. Epub 2020 Oct 31.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/33160446/">PubMed</a>

<li>Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc.
Trigg SA, Mitchell KR, Thompson RE, Eudeline B, Vadopalas B, Timmins-Schiffman EB, Roberts SB.
<i> BMC Genomics </i>  2020 Oct 19;21(1):723. doi: 10.1186/s12864-020-07127-3.
<a target="new" href=https://pubmed.ncbi.nlm.nih.gov/33076839/">PubMed</a>

<li>Diabetes Impairs Cellular Cholesterol Efflux from ABCA1 to Small HDL Particles.
He Y, Ronsein GE, Tang C, Jarvik GP, Davidson WS, Kothari V, Song HD, Segrest J, Bornfeldt KE, Heinecke JW.
<i>Circ Res.</i> 2020 Oct 9;127(9):1198-1210. doi: 10.1161/CIRCRESAHA.120.317178. Epub 2020 Aug 21.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32819213/">PubMed</a>

<li>Parallel Murine and Human Plaque Proteomics Reveals Pathways of Plaque Rupture.
Vaisar T, Hu JH, Airhart N, Fox KA, Heinecke JW, Nicosia RF, Kohler TR, Potter ZE, Simon GM, Dix M, Cravatt B, Gharib SA, Dichek D.
<i>Circ Res.</i> 2020 Sep 25;127(8):997-1022. doi: 10.1161/CIRCRESAHA.120.317295. Epub 2020 Jul 30.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32762496/">PubMed</a>

<li>Proteome and Phosphoproteome Analysis of Brown Adipocytes Reveals That RICTOR Loss Dampens Global Insulin/AKT Signaling.
Entwisle SW, Martinez Calejman C, Valente AS, Lawrence RT, Hung CM, Guertin DA, Villén J.
<i>Mol Cell Proteomics. </i> 2020 Jul;19(7):1104-1119. doi: 10.1074/mcp.RA120.001946. Epub 2020 Mar 31.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32234964/">PubMed</a>

<li>How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture.
Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ.
<i>ACS Chem Biol. </i> 2020 Jul 17;15(7):2005-2016. doi: 10.1021/acschembio.0c00429. Epub 2020 Jun 23.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32479050/">PubMed</a>

<li>Presence of serum amyloid A3 in mouse plasma is dependent on the nature and extent of the inflammatory stimulus.
Chait A, den Hartigh LJ, Wang S, Goodspeed L, Babenko I, Altemeier WA, Vaisar T.
<i>Sci Rep</i> 2020 Jun 25;10(1):10397. doi: 10.1038/s41598-020-66898-7.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32587356/">PubMed</a>

<li>Systemic Proteome Alterations Linked to Early Stage Pancreatic Cancer in Diabetic Patients.
Peng H, Pan S, Yan Y, Brand RE, Petersen GM, Chari ST, Lai LA, Eng JK, Brentnall TA, Chen R.
<i>Cancers (Basel).</i> 2020 Jun 11;12(6):1534. doi: 10.3390/cancers12061534.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32545216/">PubMed</a>

<li>Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics.
Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP.
<i>J Proteome Res.</i> 2020 May 1;19(5):2026-2034. doi: 10.1021/acs.jproteome.9b00860. Epub 2020 Apr 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/32126768">PubMed</a>

<li>Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.
Eng JK, Deutsch EW.
<i>Proteomics.</i> 2020 Nov;20(21-22):e1900362. doi: 10.1002/pmic.201900362. Epub 2020 Apr 2.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/32106352">PubMed</a>

<li>Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates.
Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB.
<i>Sci Rep.</i> Apr 8;10(1):6042. doi: 10.1038/s41598-020-63218-x.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/32269285/">PubMed</a>

<li>Increased Drp1 Acetylation by Lipid Overload Induces Cardiomyocyte Death and Heart Dysfunction.
Hu Q, Zhang H, Gutiérrez Cortés N, Wu D, Wang P, Zhang J, Mattison JA, Smith E, Bettcher LF, Wang M, Lakatta EG, Sheu SS, Wang W.
<i>Circ Res.</i> 2020 Feb 14;126(4):456-470. doi: 10.1161/CIRCRESAHA.119.315252. Epub 2020 Jan 3.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31896304">PubMed</a>

<li>In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes.
Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE.
<i>J Am Soc Mass Spectrom.</i> 2020 Feb 5;31(2):190-195. doi: 10.1021/jasms.9b00021. Epub 2019 Nov 21.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/32031408">PubMed</a>

<li>A proteomic atlas of senescence-associated secretomes for aging biomarker development.
Basisty N, Kale A, Jeon OH, Kuehnemann C, Payne T, Rao C, Holtz A, Shah S, Sharma V, Ferrucci L, Campisi J, Schilling B.
<i>PLoS Biol. </i> 2020 Jan 16;18(1):e3000599. doi: 10.1371/journal.pbio.3000599. eCollection 2020 Jan.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31945054">PubMed</a>

<li>The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S,
Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA.
<i>Nucleic Acids Res. </i> 2020 Jan 8;48(D1):D1145-D1152. doi: 10.1093/nar/gkz984.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31686107">PubMed</a>

<li>High Concentration of Medium-Sized HDL Particles and Enrichment in HDL Paraoxonase 1 Associate With Protection From Vascular Complications in People With Long-standing Type 1 Diabetes.
Vaisar T, Kanter JE, Wimberger J, Irwin AD, Gauthier J, Wolfson E, Bahnam V, Wu IH, Shah H, Keenan HA, Greenbaum CJ, King GL, Heinecke JW, Bornfeldt KE.
<i>Diabetes Care </i> 2020 Jan;43(1):178-186. doi: 10.2337/dc19-0772. Epub 2019 Oct 9.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/31597668/">PubMed</a>

<p><h3>2019</h3>

<li>RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions.
Schwerk J, Soveg FW, Ryan AP, Thomas KR, Hatfield LD, Ozarkar S, Forero A, Kell AM, Roby JA, So L, Hyde JL, Gale M Jr, Daugherty MD, Savan R.
<i>Nat Immunol. </i> 2019 Dec;20(12):1610-1620. doi: 10.1038/s41590-019-0527-6. Epub 2019 Nov 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31740798">PubMed</a>

<li>R2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies.
Leutert M, Rodríguez-Mias RA, Fukuda NK, Villén J.
<i>Mol Syst Biol. </i> 2019 Dec;15(12):e9021. doi: 10.15252/msb.20199021.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31885202">PubMed</a>

<li>Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2.
Timmins-Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts S2.
<i>Ecol Evol. </i> 2019 Dec 6;10(1):185-197. doi: 10.1002/ece3.5885. eCollection 2020 Jan.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31988722">PubMed</a>

<li>Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi.
Krayushkina D, Timmins-Schiffman E, Faux J, May DH, Riffle M, Harvey HR, Nunn BL.
<i>Sci Data. </i> 2019 Dec 3;6(1):303. doi: 10.1038/s41597-019-0308-y.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31796751">PubMed</a>

<li>Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization.
Parks KR, MacCamy AJ, Trichka J, Gray M, Weidle C, Borst AJ, Khechaduri A, Takushi B, Agrawal P, Guenaga J, Wyatt RT, Coler R,
Seaman M, LaBranche C, Montefiori DC, Veesler D, Pancera M, McGuire A, Stamatatos L.
<i>Cell Rep. </i> 2019 Dec 3;29(10):3060-3072.e7. doi: 10.1016/j.celrep.2019.10.071.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31801073">PubMed</a>

<li>Postprandial remodeling of high-density lipoprotein following high saturated fat and high carbohydrate meals.
Averill M, Rubinow KB, Cain K, Wimberger J, Babenko I, Becker JO, Foster-Schubert KE, Cummings DE, Hoofnagle AN, Vaisar T.
<i>J Clin Lipidol.</i>  2020 Jan-Feb;14(1):66-76.e11. doi: 10.1016/j.jacl.2019.11.002. Epub 2019 Nov 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31859127">PubMed</a>

<li>Cellular Interactome Dynamics during Paclitaxel Treatment.
Chavez JD, Keller A, Zhou B, Tian R, Bruce JE.
<i>Cell Rep.</i> 2019 Nov 19;29(8):2371-2383.e5. doi: 10.1016/j.celrep.2019.10.063.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31747606">PubMed</a>

<li>An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections.
Dang HV, Chan YP, Park YJ, Snijder J, Da Silva SC, Vu B, Yan L, Feng YR, Rockx B, Geisbert TW, Mire CE, Broder CC, Veesler D.
<i>Nat Struct Mol Biol.</i> 2019 Oct;26(10):980-987. doi: 10.1038/s41594-019-0308-9. Epub 2019 Sep 30.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31570878">PubMed</a>

<li>Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry Strategy
Canzani D, Rusnac DV, Zheng N, Bush MF.
<i>Anal Chem.</i> 2019 Oct 15;91(20):12775-12783. doi: 10.1021/acs.analchem.9b02331. Epub 2019 Sep 26.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/31525912/">PubMed</a>

<li>Development of a Chemical Toolset for Studying the Paralog-Specific Function of IRE1.
Feldman HC, Vidadala VN, Potter ZE, Papa FR, Backes BJ, Maly DJ.
<i>ACS Chem Biol. </i> 2019 Dec 20;14(12):2595-2605. doi: 10.1021/acschembio.9b00482. Epub 2019 Oct 14.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31609569">PubMed</a>

<li>Increased apolipoprotein C3 drives cardiovascular risk in type 1 diabetes.
Kanter JE, Shao B, Kramer F, Barnhart S, Shimizu-Albergine M, Vaisar T, Graham MJ, Crooke RM, Manuel CR, Haeusler RA,
Mar D, Bomsztyk K, Hokanson JE, Kinney GL, Snell-Bergeon JK, Heinecke JW, Bornfeldt KE.
<i>J Clin Invest.</i> 2019 Jul 11;129(10):4165-4179. doi: 10.1172/JCI127308.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31295146">PubMed</a>

<li>Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes.
Mikan MP, Harvey HR, Timmins-Schiffman E, Riffle M, May DH, Salter I, Noble WS, Nunn BL.
<i>ISME J.</i> 2020 Jan;14(1):39-52. doi: 10.1038/s41396-019-0503-z. Epub 2019 Sep 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31492961">PubMed</a>

<li>Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy.
Peng H, Chen R, Brentnall TA, Eng JK, Picozzi VJ, Pan S.
<i>Clin Proteomics.</i> 2019 Jul 17;16:31. doi: 10.1186/s12014-019-9251-3. eCollection 2019.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31346328">PubMed</a>

<li>Chemoproteomic Method for Profiling Inhibitor-Bound Kinase Complexes.
Fang L, Chakraborty S, Dieter EM, Potter ZE, Lombard CK, Maly DJ.
<i>J Am Chem Soc.</i> 2019 Jul 31;141(30):11912-11922. doi: 10.1021/jacs.9b02963. Epub 2019 Jul 5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31274292">PubMed</a>

<li>Pacific geoduck (Panopea generosa) resilience to natural pH variation.
Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB.
<i>Comp Biochem Physiol Part D Genomics Proteomics. </i> 2019 Jun;30:91-101. doi: 10.1016/j.cbd.2019.01.010. Epub 2019 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30818101">PubMed</a>

<li>Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone.
Fuchsman CA, Palevsky HI, Widner B, Duffy M, Carlson MCG, Neibauer JA, Mulholland MR, Keil RG, Devol AH, Rocap G.
<i>ISME J.</i> 2019 Nov;13(11):2714-2726. doi: 10.1038/s41396-019-0452-6. Epub 2019 Jun 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31249393">PubMed</a>

<li>Structural basis for human coronavirus attachment to sialic acid receptors.
Tortorici MA, Walls AC, Lang Y, Wang C, Li Z, Koerhuis D, Boons GJ, Bosch BJ, Rey FA, de Groot RJ, Veesler D.
<i>Nat Struct Mol Biol.</i> 2019 Jun;26(6):481-489. doi: 10.1038/s41594-019-0233-y. Epub 2019 Jun 3.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31160783">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2019 Jun 7;18(6):2686-2692. doi: 10.1021/acs.jproteome.9b00064. Epub 2019 May 23.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31081335">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2019 Jun 7;18(6):2601-2612. doi: 10.1021/acs.jproteome.9b00122. Epub 2019 May 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31060355">PubMed</a>

<li>Apolipoprotein A1 Forms 5/5 and 5/4 Antiparallel Dimers in Human High-density Lipoprotein.
He Y, Song HD, Anantharamaiah GM, Palgunachari MN, Bornfeldt KE, Segrest JP, Heinecke JW.
<i>Mol Cell Proteomics.</i> 2019 May;18(5):854-864. doi: 10.1074/mcp.RA118.000878. Epub 2019 Jan 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30659061">PubMed</a>

<li>Albuminuria, the High-Density Lipoprotein Proteome, and Coronary Artery Calcification in Type 1 Diabetes Mellitus.
Shao B, Zelnick LR, Wimberger J, Himmelfarb J, Brunzell J, Davidson WS, Snell-Bergeon JK, Bornfeldt KE, de Boer IH, Heinecke JW.   
<i>Arterioscler Thromb Vasc Biol.</i> 2019 Jul;39(7):1483-1491. doi: 10.1161/ATVBAHA.119.312556. Epub 2019 May 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/31092010">PubMed</a>

<li>The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.
Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW.
<i>Science.</i> 2019 Apr 12;364(6436). pii: eaau8650. doi: 10.1126/science.aau8650.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30975860">PubMed</a>

<li>Proteome-wide Analysis of Cellular Response to Ultraviolet Light for Biomaterial Synthesis and Modification.
Ruskowitz ER, DeForest CA.
<i>ACS Biomater Sci Eng.</i> 2019 May 13;5(5):2111-2116. doi: 10.1021/acsbiomaterials.9b00177. Epub 2019 Apr 5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/33405713">PubMed</a>

<li>Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective.
Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ.
<i>Autophagy.</i> 2019 Sep;15(9):1592-1605. doi: 10.1080/15548627.2019.1586258. Epub 2019 Mar 21.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30865561">PubMed</a>

<li>Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
Walls AC, Xiong X, Park YJ, Tortorici MA, Snijder J, Quispe J, Cameroni E, Gopal R, Dai M, Lanzavecchia A, Zambon M, Rey FA, Corti D, Veesler D.
<i>Cell.</i> 2019 Feb 21;176(5):1026-1039.e15. doi: 10.1016/j.cell.2018.12.028. Epub 2019 Jan 31.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30712865">PubMed</a>

<li>Metabolism as an early predictor of DPSCs aging.
Macrin D, Alghadeer A, Zhao YT, Miklas JW, Hussein AM, Detraux D, Robitaille AM, Madan A, Moon RT, Wang Y, Devi A, Mathieu J, Ruohola-Baker H.
<i>Sci Rep.</i> 2019 Feb 18;9(1):2195. doi: 10.1038/s41598-018-37489-4.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30778087">PubMed</a>

<li>Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency.
Mathieu J, Detraux D, Kuppers D, Wang Y, Cavanaugh C, Sidhu S, Levy S, Robitaille AM, Ferreccio A, Bottorff T, McAlister A, Somasundaram L, Artoni F, Battle S, Hawkins RD, Moon RT, Ware CB, Paddison PJ, Ruohola-Baker H.
<i>Nat Commun.</i> 2019 Feb 7;10(1):632. doi: 10.1038/s41467-018-08020-0.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30733432">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2019 Feb 1;18(2):652-663. doi: 10.1021/acs.jproteome.8b00638. Epub 2018 Dec 21. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30523691">PubMed</a>

<li>Sestd1 Encodes a Developmentally Dynamic Synapse Protein That Complexes With BCR Rac1-GAP to Regulate Forebrain Dendrite, Spine and Synapse Formation.
Yang XY, Stanley RE, Ross AP, Robitaille AM, Gray JA, Cheyette BNR.
<i>Cereb Cortex. </i> 2019 Feb 1;29(2):505-516. doi: 10.1093/cercor/bhx333. Erratum in: Cereb Cortex. 2019 Mar 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29293918">PubMed</a>

<li>Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences.
Venkataraman, Y.R., Timmins-Schiffman, E., Horwith, M.J., Lowe, A.T., Nunn, B., Vadopalas, B., Spencer, L.H., and Roberts, S.B.
<i>Mar Ecol Prog Ser 610, 65-81. </i> 2019 Feb 1.
<a target="new" href="https://www.int-res.com/abstracts/meps/v610/meps12858">publication</a>

<li>Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.
Riffle M, Jaschob D, Zelter A, Davis TN.
<i>J Proteome Res.</i> 2019 Feb 1;18(2):759-764. doi: 10.1021/acs.jproteome.8b00726. Epub 2018 Dec 19.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/30525651/">PubMed</a>

<p><h3>2018</h3>

<li>Tools for 3D Interactome Visualization.
Keller A, Chavez JD, Eng JK, Thornton Z, Bruce JE.
<i>J Proteome Res.</i> 2019 Feb 1;18(2):753-758. doi: 10.1021/acs.jproteome.8b00703. Epub 2018 Dec 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30520642">PubMed</a>

<li>Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.
Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS, Stewart-Jones GB, Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M, Veesler D.
<i>Elife.</i> 2018 Nov 7;7:e37688. doi: 10.7554/eLife.37688.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30403372">PubMed</a>

<li>Urine Complement Proteins and the Risk of Kidney Disease Progression and Mortality in Type 2 Diabetes.
Vaisar T, Durbin-Johnson B, Whitlock K, Babenko I, Mehrotra R, Rocke DM, Afkarian M.
<i>Diabetes Care.</i> 2018 Nov;41(11):2361-2369. doi: 10.2337/dc18-0699. Epub 2018 Aug 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30150236">PubMed</a>

<li>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.
<i>Cell.</i> 2018 Nov 15;175(5):1380-1392.e14. doi: 10.1016/j.cell.2018.09.037. Epub 2018 Oct 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30343895">PubMed</a>

<li>Variations in Copepod Proteome and Respiration Rate in Association with Diel Vertical Migration and Circadian Cycle.
Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E.
<i>Biol Bull.</i> 2018 Aug;235(1):30-42. doi: 10.1086/699219. Epub 2018 Aug 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/30160998">PubMed</a>

<li>Sex steroids mediate discrete effects on HDL cholesterol efflux capacity and particle concentration in healthy men.
Rubinow KB, Vaisar T, Chao JH, Heinecke JW, Page ST.
<i>J Clin Lipidol. </i>. 2018 Jul - Aug;12(4):1072-1082. doi: 10.1016/j.jacl.2018.04.013. Epub 2018 Apr 30.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29793828">PubMed</a>

<li>MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides.
Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL.
<i>Sci Rep.</i>. 2018 Jun 18;8(1):9276. doi: 10.1038/s41598-018-27650-4.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29915279">PubMed</a>

<li>Obesity and Insulin Resistance Promote Atherosclerosis through an IFNγ-Regulated Macrophage Protein Network.
Reardon CA, Lingaraju A, Schoenfelt KQ, Zhou G, Cui C, Jacobs-El H, Babenko I, Hoofnagle A, Czyz D, Shuman H, Vaisar T, Becker L.
<i>Cell Rep.</i>. 2018 Jun 5;23(10):3021-3030. doi: 10.1016/j.celrep.2018.05.010.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29874587">PubMed</a>

<li>Mango: A general tool for CID-cleavable cross-linked peptide identification.
Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE.
<i>Anal Chem</i>.  2018 May 15;90(10):6028-6034. doi: 10.1021/acs.analchem.7b04991. Epub 2018 Apr 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29676898">PubMed</a>

<li>An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus.
Snijder J, Ortego MS, Weidle C, Stuart AB, Gray MD, McElrath MJ, Pancera M, Veesler D, McGuire AT.
<i>Immunity</i>. 2018 Apr 17;48(4):799-811.e9. doi: 10.1016/j.immuni.2018.03.026.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29669253">PubMed</a>

<li>ALPK2 Promotes Cardiogenesis in Zebrafish and Human Pluripotent Stem Cells
Hofsteen P, Robitaille AM, Strash N, Palpant N, Moon RT, Pabon L, Murray Ce.
<i>iScience</i> 2018 Apr 27;(2)88-100. doi: 10.1016/j.isci.2018.03.010.

<li>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.
<i>Bioinformatics.</i> 2018 Mar 1;34(5):795-802. doi: 10.1093/bioinformatics/btx601.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29028897">PubMed</a>

<li>Panorama Public: A public repository for quantitative data sets processed in Skyline.
Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B.
<i>Mol Cell Proteomics.</i> 2018 Feb 27. pii: mcp.RA117.000543. doi: 10.1074/mcp.RA117.000543.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29487113">PubMed</a>

<li>Type 2 diabetes is associated with loss of HDL endothelium protective functions.
Vaisar T, Couzens E, Hwang A, Russell M, Barlow CE, DeFina LF, Hoofnagle AN, Kim F.
<i>PLoS One</i>. 2018 Mar 15;13(3):e0192616. doi: 10.1371.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29543843">PubMed</a>

<li>Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome.
Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S.
<i>J Proteomics </i>. 2018 Feb 20;173:89-98. doi: 10.1016/j.jprot.2017.11.025. Epub 2017 Dec 5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29208510">PubMed</a>

<li>Sestd1 Encodes a Developmentally Dynamic Synapse Protein That Complexes With BCR Rac1-GAP to Regulate Forebrain Dendrite, Spine and Synapse Formation.
Yang XY, Stanley RE, Ross AP, Robitaille AM, Gray JA, Cheyette BNR.
<i>Cereb Cortex.</i> 2018 Feb 21. doi: 10.1093/cercor/bhy026. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29474518">PubMed</a>

<li>Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.
Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE.
<i>Cell Syst </i>. 2018 Jan 24;6(1):136-141.e5. doi: 10.1016/j.cels.2017.10.017. Epub 2017 Nov 29.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29199018">PubMed</a>

<li>Quantifying HDL proteins by mass spectrometry: how many proteins are there and what are their functions?
Shao B, Heinecke JW.
<i>Expert Rev Proteomics. </i>. 2018 Jan;15(1):31-40. doi: 10.1080/14789450.2018.1402680. Epub 2017 Nov 13.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29113513">PubMed</a>

<p><h3>2017</h3>

<li>MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.
Riffle M, May DH, Timmins-Schiffman E, Mikan MP, Jaschob D, Noble WS, Nunn BL.
<i>Proteomes. </i>. 2017 Dec 27;6(1). pii: E2. doi: 10.3390/proteomes6010002.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29280960">PubMed</a>

<li>Glycan shield and fusion activation of a deltacoronavirus spike glycoprotein fine-tuned for enteric infections.
Xiong X, Tortorici MA, Snijder J, Yoshioka C, Walls AC, Li W, McGuire AT, Rey FA, Bosch BJ, Veesler D.
<i>J Virol. </i>. 2017 Nov 1. pii: JVI.01628-17. doi: 10.1128/JVI.01628-17.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29093093">PubMed</a>

<li>Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion.
Walls AC, Tortorici MA, Snijder J, Xiong X, Bosch BJ, Rey FA, Veesler D.
<i>Proc Natl Acad Sci U S A</i>. 2017 Oct 17;114(42):11157-11162. doi: 10.1073/pnas.1708727114. Epub 2017 Oct 3.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/29073020">PubMed</a>

<li>ELISA reagent coverage evaluation by affinity purification tandem mass spectrometry.
Henry SM, Sutlief E, Salas-Solano O, Valliere-Douglass J.
<i>MAbs</i>. 2017 Oct;9(7):1065-1075. doi: 10.1080/19420862.2017.1349586. Epub 2017 Jul 14.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28708446">PubMed</a>

<li>First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.
Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H.
<i>Proc Natl Acad Sci U S A.</i> 2017 Sep 19;114(38):10125-10130. doi: 10.1073/pnas.1706907114. Epub 2017 Sep 1.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28864533">PubMed</a>

<li>Integrating Discovery-driven Proteomics and Selected Reaction Monitoring To Develop a Noninvasive Assay for Geoduck Reproductive Maturation.
Timmins-Schiffman EB, Crandall GA, Vadopalas B, Riffle ME, Nunn BL, Roberts SB.
<i>J Proteome Res.</i> 2017 Sep 1;16(9):3298-3309. doi: 10.1021/acs.jproteome.7b00288. Epub 2017 Aug 11.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28730805">PubMed</a>

<li>Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer.
Chen R, Lai LA, Sullivan Y, Wong M, Wang L, Riddell J, Jung L, Pillarisetty VG, Brentnall TA, Pan S.
<i>Sci Rep.</i> 2017 Aug 11;7(1):7950. doi: 10.1038/s41598-017-08436-6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28801576">PubMed</a>

<li>Extracellular Matrix Proteins Mediate HIV-1 gp120 Interactions with &#945;4&#946;7.
Plotnik D, Guo W, Cleveland B, von Haller P, Eng JK, Guttman M, Lee KK, Arthos J, Hu SL.
<i>J Virol.</i> 2017 Oct 13;91(21). pii: e01005-17. doi: 10.1128/JVI.01005-17. Print 2017 Nov 1.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28814519">PubMed</a>

<li>Ageing and hypoxia cause protein aggregation in mitochondria.
Kaufman DM, Wu X, Scott BA, Itani OA, Van Gilst MR, Bruce JE, Michael Crowder C.
<i>Cell Death Differ. </i> 2017 Oct;24(10):1730-1738. doi: 10.1038/cdd.2017.101. Epub 2017 Jun 23.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28644434">PubMed</a>

<li>Spectral library-based glycopeptide analysis - detection of circulating galectin-3 binding protein in pancreatic cancer.
Nigjeh EN, Chen R, Allen-Tamura Y, Brand RE, Brentnall TA, Pan S.
<i>Proteomics Clin Appl. </i> 2017 Sep;11(9-10). doi: 10.1002/prca.201700064. Epub 2017 Jul 10.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28627758">PubMed</a>
<li>WNT/β-catenin signaling regulates mitochondrial activity to alter the oncogenic potential of melanoma in a PTEN-dependent manner.
Brown K, Yang P, Salvador D, Kulikauskas R, Ruohola-Baker H, Robitaille AM, Chien AJ, Moon RT, Sherwood V.
<i>Oncogene. </i> 2017 Jun 1;36(22):3119-3136. doi: 10.1038/onc.2016.450. Epub 2017 Jan 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28092677">PubMed</a>

<li>Long-lived pancreatic ductal adenocarcinoma slice cultures enable precise study of the immune microenvironment.
Jiang X, Seo YD, Chang JH, Coveler A, Nigjeh EN, Pan S, Jalikis F, Yeung RS, Crispe IN, Pillarisetty VG.
<i>Oncoimmunology. </i> 2017 May 25;6(7):e1333210. doi: 10.1080/2162402X.2017.1333210. eCollection 2017.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28811976">PubMed</a>

<li>Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry.
Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC.
<i>Virus Res. </i> 2017 Sep 15;241:42-52. doi: 10.1016/j.virusres.2017.05.005. Epub 2017 May 11.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28502641">PubMed</a>

<li>An alpha-synuclein MRM assay with diagnostic potential for Parkinson's disease and monitoring disease progression.
Yang L, Stewart T, Shi M, Pottiez G, Dator R, Wu R, Aro P, Schuster RJ, Ginghina C, Pan C, Gao Y, Qian W, Zabetian CP, Hu SC, Quinn JF, Zhang J.
<i>Proteomics Clin Appl.</i> 2017 Jul;11(7-8). doi: 10.1002/prca.201700045. Epub 2017 Apr 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28319654">PubMed</a>

<li>Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism.
Sychev ZE, Hu A, DiMaio TA, Gitter A, Camp ND, Noble WS, Wolf-Yadlin A, Lagunoff M.
<i>PLoS Pathog. </i> 2017 Mar 3;16(3):1228-1238. doi: 10.1021/acs.jproteome.6b00829. Epub 2017 Feb 7.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28112948">PubMed</a>

<li>Mass-Spectrometry-Based Method To Quantify in Parallel Tau and Amyloid β 1-42 in CSF for the Diagnosis of Alzheimer's Disease.
Pottiez G, Yang L, Stewart T, Song N, Aro P, Galasko DR, Quinn JF, Peskind ER, Shi M, Zhang J.
<i>J Proteome Res. </i> 2017 Mar 3;13(3):e1006256. doi: 10.1371/journal.ppat.1006256. eCollection 2017 Mar.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28257516">PubMed</a>

<li>Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.
Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL.
<i>ISME J.</i> 2017 Feb;11(2):309-314. doi: 10.1038/ismej.2016.132.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27824341">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2017 Feb 3;16(2):720-727. doi: 10.1021/acs.jproteome.6b00752.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28152603">PubMed</a>

<li>Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.
Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT.
<i>Proc Natl Acad Sci U S A</i> 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/28096348">PubMed</a>

<li>Proteome analysis of mast cell releasates reveals a role for chymase in the regulation of coagulation factor XIIIA levels via proteolytic degradation.
Shubin NJ, Glukhova VA, Clauson M, Truong P, Abrink M, Pejler G, White NJ, Deutsch GH, Reeves SR, Vaisar T, James RG, Piliponsky AM.
<i>J Allergy Clin Immunol.</i> 2017 Jan;139(1):323-334. doi: 10.1016/j.jaci.2016.03.051. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27302551">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2017 Jan 3. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27995795">PubMed</a>

<li>Tartrate-Resistant Acid Phosphatase Deficiency in the Predisposition to Systemic Lupus Erythematosus.
An J, Briggs TA, Dumax-Vorzet A, Alarcón-Riquelme ME, Belot A, Beresford M, Bruce IN, Carvalho C, Chaperot L, Frostegård J, Plumas J, Rice GI, Vyse TJ, Wiedeman A, Crow YJ, Elkon KB.
<i>Arthritis Rheumatol.</i> 2017 Jan;69(1):131-142. doi: 10.1002/art.39810.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27390188">PubMed</a>

<p><h3>2016</h3>

<li>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.
<i>PLoS One.</i> 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27997545">PubMed</a>

<li>CNS tau efflux via exosomes is likely increased in Parkinson disease but not in Alzheimer disease.
Min Shi, Andrej Kovac, Ane Korff, Travis J. Cook, Carmen Ginghina, Kristin M. Bullock, Li Yang, Tessandra Stewart, Danfeng Zheng, Patrick Aro, Anzari Atik, Kathleen F. Kerr, Cyrus P. Zabetian, Elaine R. Peskind, Shu-Ching Hu, Joseph F. Quinn, Douglas R. Galasko, Thomas J. Montine, William A. Banks, Jing Zhang
<i>Alzheimers Dement.</i> 2016 Nov;12(11):1125-1131. doi: 10.1016/j.jalz.2016.04.003. Epub 2016 May 24.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27234211">PubMed</a>

<li>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.
<i>Nat Commun.</i> 2016 Nov 11. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27834373">PubMed</a>

<li>Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy.
Walls AC, Tortorici MA, Frenz B, Snijder J, Li W, Rey FA, DiMaio F, Bosch BJ, Veesler D.
<i>Nat Struct Mol Biol.</i> 2016 Oct;23(10):899-905. doi: 10.1038/nsmb.3293. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27617430">PubMed</a>

<li>Wnt/β-catenin signaling promotes self-renewal and inhibits the primed state transition in naïve human embryonic stem cells.
Xu Z, Robitaille AM, Berndt JD, Davidson KC, Fischer KA, Mathieu J, Potter JC, Ruohola-Baker H, Moon RT.
<i>Proc Natl Acad Sci U S A.</i> 2016 Oct 18;113(42):E6382-E6390. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27698112">PubMed</a>

<li>Identification of the nuclear localisation signal of O-GlcNAc transferase and its nuclear import regulation.
Seo HG, Kim HB, Kang MJ, Ryum JH, Yi EC, Cho JW.
<i>Sci Rep.</i> 2016 Oct 7. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27713473">PubMed</a>

<li>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.
<i>Bioinformatics.</i> 2016 Sep 1. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27153666">PubMed</a>

<li>ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.
Riffle M, Jaschob D, Zelter A, Davis TN.
<i>J Proteome Res.</i> 2016 Aug 5;15(8):2863-70. doi: 10.1021/acs.jproteome.6b00274. Epub 2016 Jun 24.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27302480">PubMed</a>

<li>In Vivo Conformational Dynamics of Hsp90 and Its Interactors.
Chavez JD, Schweppe DK, Eng JK, Bruce JE.
<i>Cell Chem Biol.</i> 2016 Jun 23. 
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27341434">PubMed</a>

<li>Spectral library searching to identify crosslinked peptides.
Schweppe DK, Chavez JD, Navare AT, Wu X, Ruiz B, Eng JK, Lam H, Bruce JE.
<i>J Proteome Res.</i> 2016 May 6;15(5):1725-31. doi: 10.1021/acs.jproteome.6b00014. Epub 2016 Apr 28.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/27089058">PubMed</a>

<li>Quantitative proteomics identify DAB2 as a cardiac developmental regulator that inhibits WNT/β-catenin signaling.
Hofsteen P, Robitaille AM, Chapman DP, Moon RT, Murry CE.
<i>Proc Natl Acad Sci U S A.</i> 2016 Jan 26;113(4):1002-7. doi: 10.1073/pnas.1523930113. Epub 2016 Jan 11.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26755607">PubMed</a>

<li>Proteomic analysis of HDL from inbred mice strains implicates APOE associated with HDL in reduced cholesterol efflux capacity via the ABCA1 pathway.
Pamir N, Hutchins P, Ronsein G, Vaisar T, Reardon CA, Getz GS, Lusis AJ, Heinecke JW.
<i>J Lipid Res.</i> 2016 Feb;57(2):246-57. doi: 10.1194/jlr.M063701. Epub 2015 Dec 15.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26673204">PubMed</a>

<li>Targeted Proteomics Identifies Paraoxonase/Arylesterase 1 (PON1) and Apolipoprotein Cs as Potential Risk Factors for Hypoalphalipoproteinemia in Diabetic Subjects Treated with Fenofibrate and Rosiglitazone.
Ronsein GE, Reyes-Soffer G, He Y, Oda M, Ginsberg H, Heinecke JW.
<i>Mol Cell Proteomics.</i> 2016 Mar;15(3):1083-93. doi: 10.1074/mcp.M115.054528. Epub 2015 Dec 14.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26667175">PubMed</a>

<li>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.
<i>J Virol.</i> 2015 Dec 9;90(4):1973-87. doi: 10.1128/JVI.01706-15.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26656710">PubMed</a>

<li>XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.
Schweppe DK, Chavez JD, Bruce JE.
<i>Bioinformatics. </i> 2016 Jan 15;32(2):306-8. doi: 10.1093/bioinformatics/btv519.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26411867">PubMed</a>

<li>Serum amyloid A impairs the antiinflammatory properties of HDL.
Han CY, Tang C, Guevara ME, Wei H, Wietecha T, Shao B, Subramanian S, Omer M, Wang S, O'Brien KD, Marcovina SM, Wight TN, Vaisar T, de Beer MC, de Beer FC, Osborne WR, Elkon KB, Chait A.
<i>J Clin Invest. </i> 2016 Jan 4;126(1):266-81. doi: 10.1172/JCI83475. Epub 2015 Dec 7.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26642365">PubMed</a>

<p><h3>2015</h3>

<li>The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition.
Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A, Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG, Margaretha L, Robitaille AM, Margineantu D, Fiehn O, Hockenbery D, Blau CA, Raftery D, Margolin AA, Hawkins RD, Moon RT, Ware CB, Ruohola-Baker H.
<i>Nat Cell Biol.</i> 2015 Dec;17(12):1523-35. doi: 10.1038/ncb3264. Epub 2015 Nov 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26571212">PubMed</a>

<li>Host-Microbe Protein Interactions during Bacterial Infection.
Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE.
<i>Chem Biol.</i> 2015 Nov 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26548613">PubMed</a>

<li>Filamentous Bacteriophage Promote Biofilm Assembly and Function.
Secor PR, Sweere JM, Michaels LA, Malkovskiy AV, Lazzareschi D, Katznelson E, Rajadas J, Birnbaum ME, Arrigoni A, Braun KR, Evanko SP, Stevens DA, Kaminsky W, Singh PK, Parks WC, Bollyky PL.
<i>Cell Host Microbe.</i> 2015 Nov 11;18(5):549-59. doi: 10.1016/j.chom.2015.10.013.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26567508">PubMed</a>

<li>A Quantitative Proteomic Analysis of Hemogenic Endothelium Reveals Differential Regulation of Hematopoiesis by SOX17.
Clarke RL, Robitaille AM, Moon RT, Keller G.
<i>Stem Cell Reports.</i> 2015 Aug 11;5(2):291-304. doi: 10.1016/j.stemcr.2015.07.008.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26267830">PubMed</a>

<li>Quantitative interactome analysis reveals a chemoresistant edgotype.
Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE.
<i>Nat Commun.</i> 2015 Aug 3;6:7928. doi: 10.1038/ncomms8928.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26235782">PubMed</a>

<li>Physiological responses of a Southern Ocean diatom to complex future ocean conditions.
Boyd PW, Dillingham PW, McGraw CM, Armstrong EA, Cornwall CE, Feng YY, Hurd CL, Gault-Ringold M, Roleda MY, Timmins-Schiffman E, Nunn BL.
<i>Nat Climate Change</i> 2015 Aug 27; doi:10.1038/nclimate2811.  Epub 2015 Oct 5.
<a target="new" href="https://www.nature.com/nclimate/journal/vaop/ncurrent/full/nclimate2811.html">publication</a>

<li>Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.
Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR.
<i>J Proteomics Bioinform</i> 2015; 8(10): 231–239. doi: 10.4172/jpb.1000374.
<a target="new" href="https://pubmed.ncbi.nlm.nih.gov/26962293/">PubMed</a>

<li>Site-specific activity of the acyltransferases HtrB1 and HtrB2 in Pseudomonas aeruginosa lipid A biosynthesis.
Hittle LE, Powell DA, Jones JW, Tofigh M, Goodlett DR, Moskowitz SM, Ernst RK.
<i>Pathog Dis.</i> 2015 Nov;73(8):ftv053. doi: 10.1093/femspd/ftv053. Epub 2015 Jul 29.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26223882">PubMed</a>

<li>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.
<i>Mol Endocrinol.</i> 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26181434">PubMed</a>

<li>Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.
Palpant NJ, Pabon L, Roberts M, Hadland B, Jones D, Jones C, Moon RT, Ruzzo WL, Bernstein I, Zheng Y, Murry CE.
<i>Development.</i> 2015 Sep 15;142(18):3198-209. doi: 10.1242/dev.117010. Epub 2015 Jul 7.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26153229">PubMed</a>

<li>Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development.
Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ.
<i>J Am Soc Mass Spectrom.</i> 2015 Nov;26(11):1827-36. doi: 10.1007/s13361-015-1193-z. Epub 2015 Jul 2.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26133526">PubMed</a>

<li>A Deeper Look into Comet-Implementation and Features.
Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ.
<i>J Am Soc Mass Spectrom.</i> 2015 Nov;26(11):1865-74. doi: 10.1007/s13361-015-1179-x. Epub 2015 Jun 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26115965">PubMed</a>

<li>The Tec Kinase-Regulated Phosphoproteome Reveals a Mechanism for the Regulation of Inhibitory Signals in Murine Macrophages.
Tampella G, Kerns HM, Niu D, Singh S, Khim S, Bosch KA, Garrett ME, Moguche A, Evans E, Browning B, Jahan TA, Nacht M, Wolf-Yadlin A, Plebani A, Hamerman JA, Rawlings DJ, James RG.
<i>J Immunol.</i> 2015 Jul 1;195(1):246-56. doi: 10.4049/jimmunol.1403238. Epub 2015 May 29.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26026062">PubMed</a>

<li>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.
<i>Mol Cell Proteomics.</i> 2015 Aug;14(8):2126-37. doi: 10.1074/mcp.M115.050161. Epub 2015 May 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26018413">PubMed</a>

<li>A Cluster of Proteins Implicated in Kidney Disease Is Increased in High-Density Lipoprotein Isolated from Hemodialysis Subjects.
Shao B, de Boer I, Tang C, Mayer PS, Zelnick L, Afkarian M, Heinecke JW, Himmelfarb J.
<i>J Proteome Res.</i> 2015 Jul 2;14(7):2792-806. doi: 10.1021/acs.jproteome.5b00060. Epub 2015 Jun 15.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/26011469">PubMed</a>

<li>Inflammatory remodeling of the HDL proteome impairs cholesterol efflux capacity.
Vaisar T, Tang C, Babenko I, Hutchins P, Wimberger J, Suffredini AF, Heinecke JW.
<i>J Lipid Res.</i> 2015 Aug;56(8):1519-30. doi: 10.1194/jlr.M059089. Epub 2015 May 20.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25995210">PubMed</a>

<li>Combining Near-UV Photodissociation with Electron Transfer. Reduction of the Diazirine Ring in a Photomethionine-Labeled Peptide Ion.
Shaffer CJ, Marek A, Nguyen HT, Tureček F.
<i>J Am Soc Mass Spectrom.</i> 2015 Aug;26(8):1367-81. doi: 10.1007/s13361-015-1139-5. Epub 2015 Apr 23.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25904063">PubMed</a>

<li>Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.
Jaschob D, Davis TN, Riffle M.
<i>BMC Res Notes.</i> 2015 Mar 7;8:70. doi: 10.1186/s13104-015-1009-z.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25884379">PubMed</a>

<li>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.
<i>Structure.</i> 2015 Apr 7;23(4):762-73. doi: 10.1016/j.str.2015.01.022. Epub 2015 Mar 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25800553">PubMed</a>

<li>Identification of synaptosomal proteins binding to monomeric and oligomeric α-synuclein.
Betzer C, Movius AJ, Shi M, Gai WP, Zhang J, Jensen PH.
<i>PLoS One</i> 2015 Feb 6;10(2):e0116473. doi: 10.1371/journal.pone.0116473. eCollection 2015.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25659148">PubMed</a>

<li>Proteomic profiling in MPTP monkey model for early Parkinson disease biomarker discovery.
Lin X, Shi M, Masilamoni JG, Dator R, Movius J, Aro P, Smith Y, Zhang J.
<i>Biochim Biophys Acta.</i> 2015 Jul;1854(7):779-87. doi: 10.1016/j.bbapap.2015.01.007. Epub 2015 Jan 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25617661">PubMed</a>

<li>Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation.
Shi M, Movius J, Dator R, Aro P, Zhao Y, Pan C, Lin X, Bammler TK, Stewart T, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Zhang J.
<i>Mol Cell Proteomics</i> 2015 Mar;14(3):544-55. doi: 10.1074/mcp.M114.040576. Epub 2015 Jan 2.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25556233">PubMed</a>

<li>Suspended marine particulate proteins in coastal and oligotrophic waters.
Bridoux MC, Neibauer J, Ingalls AE, Nunn BL, Keil RG.
<i>J Marine Systems</i> 2015 Mar;143:39-48. doi:10.1016/j.jmarsys.2014.10.014.
<a target="new" href="https://www.sciencedirect.com/science/article/pii/S0924796314002528">publication</a>

<li>Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics.
Ronsein GE, Pamir N, von Haller PD, Kim DS, Oda MN, Jarvik GP, Vaisar T, Heinecke JW.
<i>J Proteomics</i>  2015 Jan 15;113:388-99. doi: 10.1016/j.jprot.2014.10.017. Epub 2014 Oct 31.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25449833">PubMed</a>

<p><h3>2014</h3>

<li>An experimentally robust model of monomeric apolipoprotein A-I created from a chimera of two X-ray structures and molecular dynamics simulations.
Segrest JP, Jones MK, Shao B, Heinecke JW.
<i>Biochemistry.</i> 2014 Dec 9;53(48):7625-40. doi: 10.1021/bi501111j. Epub 2014 Nov 25.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25423138">PubMed</a>

<li>Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas.
Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH, Roberts SB.
<i>BMC Genomics.</i> 2014 Nov 3;15(1):951.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25362893">PubMed</a>

<li>Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.
Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA.
<i>J Am Soc Mass Spectrom.</i> 2014 Dec;25(12):2048-59. doi: 10.1007/s13361-014-0981-1. Epub 2014 Sep 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25261218">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2014 Oct 3;13(10):4488-91. doi: 10.1021/pr500741y. Epub 2014 Sep 9.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25182276">PubMed</a>

<li>Panorama: A Targeted Proteomics Knowledge Base.
Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B.
<i>J Proteome Res.</i> 2014 Sep 5;13(9):4205-10. doi: 10.1021/pr5006636. Epub 2014 Aug 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25102069">PubMed</a>

<li>SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences.
Jaschob D, Davis TN, Riffle M.
<i>BMC Res Notes.</i> 2014 Jul 23;7:468. doi: 10.1186/1756-0500-7-468.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/25056180">PubMed</a>

<li>Plasma exosomal α-synuclein is likely CNS-derived and increased in Parkinson's disease.
Shi M, Liu C, Cook TJ, Bullock KM, Zhao Y, Ginghina C, Li Y, Aro P, Dator R, He C, Hipp MJ, Zabetian CP, Peskind ER, Hu SC, Quinn JF, Galasko DR, Banks WA, Zhang J.
<i>Acta Neuropathol.</i> 2014 Nov;128(5):639-50. doi: 10.1007/s00401-014-1314-y. Epub 2014 Jul 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24997849">PubMed</a>

<li>Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton.
Poulson-Ellestad KL, Jones CM, Roy J, Viant MR, Fernández FM, Kubanek J, Nunn BL.
<i>Proc Natl Acad Sci U S A.</i> 2014 Jun 17;111(24):9009-14. doi: 10.1073/pnas.1402130111. Epub 2014 Jun 2.
Erratum in: Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12568.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24889616">PubMed</a>

<li>Targeted discovery and validation of plasma biomarkers of Parkinson's disease.
Pan C, Zhou Y, Dator R, Ginghina C, Zhao Y, Movius J, Peskind E, Zabetian CP, Quinn J, Galasko D, Stewart T, Shi M, Zhang J.
<i>J Proteome Res.</i> 2014 Nov 7;13(11):4535-45. Epub 2014 Jun 11.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24853996">PubMed</a>

<li>Humans with atherosclerosis have impaired ABCA1 cholesterol efflux and enhanced high-density lipoprotein oxidation by myeloperoxidase.
Shao B, Tang C, Sinha A, Mayer PS, Davenport GD, Brot N, Oda MN, Zhao XQ, Heinecke JW.
<i>Circ Res.</i> 2014 May 23;114(11):1733-42. doi: 10.1161/CIRCRESAHA.114.303454. Epub 2014 Mar 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24647144">PubMed</a>

<li>Collision-induced dissociation of diazirine-labeled peptide ions. Evidence for Brønsted-acid assisted elimination of nitrogen.
Marek A, Tureček F.
<i>J Am Soc Mass Spectrom.</i> 2014 May;25(5):778-89. doi: 10.1007/s13361-014-0832-0. Epub 2014 Feb 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24549894">PubMed</a>

<li>Quantitative glycoproteomics analysis reveals changes in N-glycosylation level associated with pancreatic ductal adenocarcinoma.
Pan S, Chen R, Tamura Y, Crispin DA, Lai LA, May DH, McIntosh MW, Goodlett DR, Brentnall TA.
<i>J Proteome Res.</i>  2014 Mar 7;13(3):1293-306. doi: 10.1021/pr4010184. Epub 2014 Jan 28.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24471499">PubMed</a>

<p><h3>2013</h3>

<li>Diatom proteomics reveals unique acclimation strategies to mitigate fe limitation.
Nunn BL, Faux JF, Hippmann AA, Maldonado MT, Harvey HR, Goodlett DR, Boyd PW, Strzepek RF.
<i>PLoS One.</i> 2013 Oct 16;8(10):e75653. doi: 10.1371/journal.pone.0075653.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24146769">PubMed</a>

<li>Protein Kinase PKN1 represses Wnt/beta-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.
<i>J Biol Chem.</i> 2013 Nov 29;288(48):34658-70. doi: 10.1074/jbc.M113.500314. Epub 2013 Oct 10.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/24114839">PubMed</a>

<li>Electron transfer dissociation of photolabeled peptides. Backbone cleavages compete with diazirine ring rearrangements.
Marek A, Pepin R, Peng B, Laszlo KJ, Bush MF, Turecek F.
<i>J Am Soc Mass Spectrom.</i>  2013 Nov;24(11):1641-53. doi: 10.1007/s13361-013-0630-0. Epub 2013 Apr 30.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23633016">PubMed</a>

<li>A disease-associated PTPN22 variant promotes systemic autoimmunity in murine models.
Dai X, James RG, Habib T, Singh S, Jackson S, Khim S, Moon RT, Liggitt D, Wolf-Yadlin A, Buckner JH, Rawlings DJ.
<i>J Clin Invest.</i> 2013 May 1;123(5):2024-36. doi: 10.1172/JCI66963. Epub 2013 Apr 24.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23619366">PubMed</a>

<li>Performance evaluation of a dual linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer for proteomics research.
Weisbrod CR, Hoopmann MR, Senko MW, Bruce JE.
<i>J Proteomics.</i> 2013 Aug 2;88:109-19. doi: 10.1016/j.jprot.2013.04.009. Epub 2013 Apr 13.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23590889">PubMed</a>

<li>Macrophage ADAM17 deficiency augments CD36-dependent apoptotic cell uptake and the linked anti-inflammatory phenotype.
Driscoll WS, Vaisar T, Tang J, Wilson CL, Raines EW.
<i>Circ Res.</i> 2013 Jun 21;113(1):52-61. doi: 10.1161/CIRCRESAHA.112.300683. Epub 2013 Apr 12.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23584255">PubMed</a>

<li>Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster.
Timmins-Schiffman EB Nunn BL, Goodlett DR and Roberts SB.
<i>Conservation Physiology.</i> 2013 Apr 11; 1: doi:10.1093/conphys/cot009f
<a target="new" href="https://conphys.oxfordjournals.org/content/1/1/cot009.abstract">publication</a>

<li>The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo.
Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ.
<i>Proc Natl Acad Sci U S A.</i> 2013 Apr 16;110(16):6400-5. doi: 10.1073/pnas.1221132110. Epub 2013 Mar 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23509287">PubMed</a>

<li>Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry.
Chapman JD, Gagné JP, Poirier GG, Goodlett DR.
<i>J Proteome Res.</i> 2013 Apr 5;12(4):1868-80. doi: 10.1021/pr301219h. Epub 2013 Mar 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23438649">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2013 Apr 5;12(4):1569-79. doi: 10.1021/pr3011638. Epub 2013 Feb 28.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23413883">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2013 Apr 5;12(4):1989-95. doi: 10.1021/pr301162j. Epub 2013 Mar 5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23413830">PubMed</a>

<li>Protein interactions, Posttranslational Modifications and Topologies in Human Cells.
Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE.
<i>Mol Cell Proteomics.</i> 2013 May;12(5):1451-67. doi: 10.1074/mcp.M112.024497. Epub 2013 Jan 25.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23354917">PubMed</a>

<li>Global analysis of condition-specific subcellular protein distribution and abundance.
Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.
<i>Mol Cell Proteomics.</i> 2013 May;12(5):1421-35. doi: 10.1074/mcp.O112.019166. Epub 2013 Jan 24.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23349476">PubMed</a>

<p><h3>2012</h3>

<li>Cross-linking mass spectrometry and mutagenesis confirm the functional importance of surface interactions between CYP3A4 and holo/apo cytochrome b(5).
Zhao C, Gao Q, Roberts AG, Shaffer SA, Doneanu CE, Xue S, Goodlett DR, Nelson SD, Atkins WM.
<i>Biochemistry.</i> 2012 Nov 27;51(47):9488-500. doi: 10.1021/bi301069r. Epub 2012 Nov 14.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23150942">PubMed</a>

<li>Comet: an open source tandem mass spectrometry sequence database search tool.
Eng JK, Jahan TA, Hoopmann MR.
<i>Proteomics.</i> 2013 Jan;13(1):22-4. doi: 10.1002/pmic.201200439. Epub 2012 Dec 4.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23148064">PubMed</a>

<li>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.
<i>J Am Soc Mass Spectrom.</i> 2012 Dec;23(12):2075-82. doi: 10.1007/s13361-012-0482-z. Epub 2012 Sep 25.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/23007965">PubMed</a>

<li>An expansive human regulatory lexicon encoded in transcription factor footprints.
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.
<i>Nature.</i> 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22955618">PubMed</a>

<li>Proteomic Classification of Acute Leukemias by Alignment-Based Quantitation of LC-MS/MS Data Sets.
Foss EJ, Radulovic D, Stirewalt DL, Radich J, Sala-Torra O, Pogosova-Agadjanyan EL, Hengel SM, Loeb KR, Deeg HJ, Meshinchi S, Goodlett DR, Bedalov A.
<i>J Proteome Res.</i> 2012 Oct 5;11(10):5005-10. doi: 10.1021/pr300567r. Epub 2012 Sep 11.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22900933">PubMed</a>

<li>Perturbing peptide cation-radical electronic states by thioxoamide groups: formation, dissociations, and energetics of thioxopeptide cation-radicals.
Zimnicka M1, Chung TW, Moss CL, Tureček F.
<i>J Phys Chem A.</i> 2013 Feb 14;117(6):1265-75. doi: 10.1021/jp305865q. Epub 2012 Jul 20.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22765351">PubMed</a>

<li>An Extraction Assay Analysis for Galanthamine in Guinea Pig Plasma and its Application to Nerve Agent Countermeasures
Steiner WE, Pikalov IA, Williams PT, English WA, Hilmas CJ.
<i>J Anal Bioanal Techniques</i> 2012, 3:5. doi: 10.4172/2155-9872.1000144.
<a target="new" href="https://www.omicsonline.org/2155-9872/2155-9872-3-144.php">publication</a>

<li>Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides.
Ledvina AR, Chung TW, Hui R, Coon JJ, Turecek F.
<i>J Am Soc Mass Spectrom.</i> 2012 Aug;23(8):1351-63. Epub 2012 Jun 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22669762">PubMed</a>

<li>Cascade dissociations of peptide cation-radicals. Part 1. Scope and effects of amino acid residues in penta-, nona-, and decapeptides.
Chung TW, Hui R, Ledvina A, Coon JJ, Turecek F.
<i>J Am Soc Mass Spectrom.</i> 2012 Aug;23(8):1336-50. Epub 2012 Jun 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22669761">PubMed</a>

<li>Surface acoustic wave nebulization facilitating lipid mass spectrometric analysis.
Yoon SH, Huang Y, Edgar JS, Ting YS, Heron SR, Kao Y, Li Y, Masselon CD, Ernst RK, Goodlett DR.
<i>Anal Chem.</i> 2012 Aug 7;84(15):6530-7.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22742654">PubMed</a>

<li>Chemical cross-linking, mass spectrometry and in silico modeling of proteasomal 20S core particles of the haloarchaeon Haloferax volcanii.
Karadzic I, Maupin-Furlow J, Humbard M, Prunetti L, Singh P, Goodlett DR.
<i>Proteomics.</i> 2012 Jun;12(11):1806-14. doi: 10.1002/pmic.201100260.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22623373">PubMed</a>

<li>Development of a Novel LC/MS/MS Extraction Assay for Galanthamine in Guinea Pig Plasma and its Application to Nerve Agent Countermeasures.
Steiner WE, Pikalov IA, Williams PT, English WA, Hilmas CJ.
<i>Open Access Scientific Reports</i>  2012. 1:149. doi:10.4172/scientificreports.149.
<a target="new" href="https://www.omicsonline.org/scientific-reports/srep149.php">publication</a>

<li>Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: protein synthesis, cell proliferation, and T-cell activation.
Navare AT, Sova P, Purdy DE, Weiss JM, Wolf-Yadlin A, Korth MJ, Chang ST, Proll SC, Jahan TA, Krasnoselsky AL, Palermo RE, Katze MG.
<i>Virology.</i> 2012 Jul 20;429(1):37-46. Epub 2012 Apr 26.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22542004">PubMed</a>

<li>Surface acoustic wave nebulization produces ions with lower internal energy than electrospray ionization.
Huang Y, Yoon SH, Heron SR, Masselon CD, Edgar JS, Turecek F, Goodlett DR.
<i>J Am Soc Mass Spectrom.</i> 2012 Jun;23(6):1062-70. Epub 2012 Apr 3.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22476889">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2012 May 4;11(5):2968-81. Epub 2012 Mar 30.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22390342">PubMed</a>

<li>Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study.
Pan S, Chen R, Brand RE, Hawley S, Tamura Y, Gafken PR, Milless BP, Goodlett DR, Rush J, Brentnall TA.
<i>J Proteome Res.</i> 2012 Mar 2;11(3):1937-48. Epub 2012 Feb 8.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22316387">PubMed</a>

<li>Multiple-Reaction Monitoring-Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures.
Hoofnagle AN, Becker JO, Oda MN, Cavigiolio G, Mayer P, Vaisar T.
<i>Clin Chem.</i> 2012 Apr;58(4):777-81. Epub 2012 Feb 3.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22307200">PubMed</a>

<li>Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification.
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.
<i>J Proteome Res.</i> 2012 Mar 2;11(3):1621-32. Epub 2012 Feb 21.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22288382">PubMed</a>

<li>Myeloperoxidase Targets Apolipoprotein A-I, the Major High Density Lipoprotein Protein, for Site-Specific Oxidation in Human Atherosclerotic Lesions.
Shao B, Pennathur S, Heinecke JW.
<i>J Biol Chem.</i> 2012 Feb 24.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22219194">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2012 Feb 3;11(2):1027-41. Epub 2012 Jan 9.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22168182">PubMed</a>

<li>MSDaPl (Mass Spectrometry Data Platform): A Proteomics Data Management Platform.
Sharma V, Eng JK, Maccoss MJ, Riffle M.
<i>Mol Cell Proteomics.</i> 2012 Sep;11(9):824-31. Epub 2012 May 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22611296">PubMed</a>

<li>Sites of ubiquitin attachment in Saccharomyces cerevisiae.
Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.
<i>Proteomics.</i> 2012 Jan;12(2):236-40. doi: 10.1002/pmic.201100166. Epub 2011 Dec 20.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22106047">PubMed</a>

<p><h3>2011</h3>

<li>Rapid empirical discovery of optimal peptides for targeted proteomics.
Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, Maccoss MJ.
<i>Nat Methods.</i> 2011 Nov 6;8(12):1041-3. doi: 10.1038/nmeth.1770.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22056677">PubMed</a>

<li>SILACtor: software to enable dynamic SILAC studies.
Hoopmann MR, Chavez JD, Bruce JE.
<i>Anal Chem.</i> 2011 Nov 15;83(22):8403-10. Epub 2011 Oct 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21954881">PubMed</a>

<li>Tunable charge tags for electron-based methods of peptide sequencing: design and applications.
Zimnicka M, Moss CL, Chung TW, Hui R, Tureček F.
<i>J Am Soc Mass Spectrom.</i> 2012 Apr;23(4):608-20. doi: 10.1007/s13361-011-0184-y. Epub 2011 Jun 23.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21952752">PubMed</a>

<li>Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistance.
Hengel SM, Murray E, Langdon S, Hayward L, O'Donoghue J, Panchaud A, Hupp T, Goodlett DR.
<i>J Proteome Res.</i> 2011 Oct 7;10(10):4567-78. Epub 2011 Sep 21.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21936522">PubMed</a>

<li>A face in the crowd: recognizing peptides through database search.
Eng JK, Searle BC, Clauser KR, Tabb DL.
<i>Mol Cell Proteomics.</i> 2011 Nov;10(11):R111.009522. Epub 2011 Aug 29.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21876205">PubMed</a>

<li>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.
<i>Mol Cell Proteomics.</i> 2011 Dec;10(12):M111.007690. Epub 2011 Aug 29.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21876204">PubMed</a>

<li>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.
<i>J Proteome Res.</i> 2011 Sep 2;10(9):4134-49. Epub 2011 Aug 16.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21728379">PubMed</a>

<li>Cross-linking measurements of in vivo protein complex topologies.
Zheng C, Yang L, Hoopmann MR, Eng JK, Tang X, Weisbrod CR, Bruce JE.
<i>Mol Cell Proteomics.</i> 2011 Oct;10(10):M110.006841. Epub 2011 Jun 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21697552">PubMed</a>

<li>Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex.
Helmlinger D, Marguerat S, Villen J, Swaney DL, Gygi SP, Bahler J, Winston F.
<i>EMBO J.</i> 2011 Jun 3;30(14):2843-52. doi: 10.1038/emboj.2011.181.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21642955">PubMed</a>

<li>Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.
Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE.
<i>PLoS One.</i> 2011;6(5):e19892. Epub 2011 May 26.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21637840">PubMed</a>

<li>Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses.
Chu LJ, Yang H, Shih P, Kao Y, Tsai YS, Chen J, Huang G, Weng RR, Ting YS, Fang X, von Haller PD, Goodlett DR, Ng WV.
<i>J Proteome Res.</i> 2011 Jul 1;10(7):3261-73. Epub 2011 Jun 14.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21598921">PubMed</a>

<li>Fast parallel tandem mass spectral library searching using GPU hardware acceleration.
Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB.
<i>J Proteome Res.</i> 2011 Jun 3;10(6):2882-8. Epub 2011 May 5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21545112">PubMed</a>

<li>Microdialysis combined with proteomics for protein identification in breast tumor microenvironment in vivo.
Xu BJ, Yan W, Jovanovic B, Shaw AK, An QA, Eng J, Chytil A, Link AJ, Moses HL.
<i>Cancer Microenviron.</i> 2011 Apr; 4(1): 61–71. Epub 2010 Apr 13.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21505562">PubMed</a>

<li>Impact of HDL oxidation by the myeloperoxidase system on sterol efflux by the ABCA1 pathway.
Shao B, Heinecke JW.
<i>J Proteomics.</i> 2011 Oct 19;74(11):2289-99. Epub 2011 Apr 9.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21501700">PubMed</a>

<li>Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides.
Moss CL, Chung TW, Wyer JA, Nielsen SB, Hvelplund P, Turecek F.
<i>J Am Soc Mass Spectrom.</i> 2011 Apr;22(4):731-51. Epub 2011 Feb 26.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21472611">PubMed</a>

<li>PAcIFIC goes faster, quantitative and accurate.
Alexandre Panchaud, Sunhee Jung, Scott A. Shaffer, John D. Aitchison, David R. Goodlett
<i>Anal Chem.</i> 2011 Mar 15;83(6):2250-7. doi: 10.1021/ac103079q. Epub 2011 Feb 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21341720">PubMed</a>

<li>Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics.
Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Turecek F.
<i>J Am Soc Mass Spectrom.</i> 2011 Jan;22(1):13-30. Epub 2011 Jan 20.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21472540">PubMed</a>

<li>Architecture and dynamics of an A-kinase anchoring protein 79 (AKAP79) signaling complex.
Gold MG, Stengel F, Nygren PJ, Weisbrod CR, Bruce JE, Robinson CV, Barford D, Scott JD.
<i>Proc Natl Acad Sci U S A.</i> 2011 Apr 19;108(16):6426-31. Epub 2011 Apr 4.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21464287">PubMed</a>

<li>Faster, quantitative, and accurate precursor acquisition independent from ion count.
Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.
<i>Anal Chem.</i> 2011 Mar 15;83(6):2250-7. Epub 2011 Feb 22.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21341720">PubMed</a>

<li>Proteomic analysis of acetaminophen-induced changes in mitochondrial protein expression using spectral counting.
Stamper BD, Mohar I, Kavanagh TJ, Nelson SD.
<i>Chem Res Toxicol.</i> 2011 Apr 18;24(4):549-58. Epub 2011 Feb 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21329376">PubMed</a>

<li>COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA.
Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ.
<i>Proteomics.</i> 2011 Mar;11(6):1064-74. doi: 10.1002/pmic.201000616. Epub 2011 Feb 7.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21298793">PubMed</a>

<li>New structural proteins of Halobacterium salinarum gas vesicle revealed by comparative proteomics analysis.
Chu LJ, Chen MC, Setter J, Tsai YS, Yang H, Fang X, Ting YS, Shaffer SA, Taylor GK, von Haller PD, Goodlett DR, Ng WV.
<i>J Proteome Res.</i> 2011 Mar 4;10(3):1170-8. Epub 2011 Jan 25.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21158390">PubMed</a>

<p><h3>2010</h3>

<li>Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.
Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ.
<i>Anal Chem.</i> 2010 Dec 15;82(24):10116-24. Epub 2010 Nov 19.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/21090646">PubMed</a>

<li>Improved strategies for rapid identification of chemically cross-linked peptides using protein interaction reporter technology.
Hoopmann MR, Weisbrod CR, Bruce JE.
<i>J Proteome Res.</i> 2010 Dec 3;9(12):6323-33. Epub 2010 Nov 10.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20886857">PubMed</a>

<li>Urinary proteomics evaluation in interstitial cystitis/painful bladder syndrome: a pilot study.
Goo YA, Tsai YS, Liu AY, Goodlett DR, Yang CC.
<i>Int Braz J Urol. </i> 2010 Jul-Aug;36(4):464-78; discussion 478-9, 479.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20815953">PubMed</a>

<li>Precursor charge state prediction for electron transfer dissociation tandem mass spectra.
Sharma V, Eng JK, Feldman S, von Haller PD, Maccoss MJ, Noble WS.
<i>J Proteome Res.</i> 2010 Oct 1;9(10):5438-44.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20731383">PubMed</a>

<li>The histidine effect. Electron transfer and capture cause different dissociations and rearrangements of histidine peptide cation-radicals.
Turecek F, Chung TW, Moss CL, Wyer JA, Ehlerding A, Holm AI, Zettergren H, Nielsen SB, Hvelplund P, Chamot-Rooke J, Bythell B, Paizs B.
<i>J Am Chem Soc.</i> 2010 Aug 11;132(31):10728-40.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20681705">PubMed</a>

<li>Sequence assignment of ADP-ribosylated peptides is facilitated as peptide length increases.
Hengel SM, Icenogle L, Collins C, Goodlett DR.
<i>Commun Mass Spectrom.</i> 2010 Aug 15;24(15):2312-6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20623715">PubMed</a>

<li>CD90/THY1 is overexpressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker.
True LD, Zhang H, Ye M, Huang CY, Nelson PS, von Haller PD, Tjoelker LW, Kim JS, Qian WJ, Smith RD, Ellis WJ, Liebeskind ES, Liu AY.
<i>Mod Pathol.</i> 2010 Oct;23(10):1346-56. Epub 2010 Jun 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20562849">PubMed</a>

<li>A review of tandem mass spectrometry characterization of adenosine diphosphate-ribosylated peptides.
Hengel SM, Goodlett DR.
<i>Int J Mass Spectrome.</i> 2012 Feb 15;312:114-121. doi: 10.1016/j.ijms.2011.06.003. Epub 2011 Jun 12.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/22563295">PubMed</a>

<li>Estimating false discovery rates for peptide and protein identification using randomized databases.
Hather G, Higdon R, Bauman A, von Haller PD, Kolker E.
<i>Proteomics.</i> 2010 Jun;10(12):2369-76.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20391536">PubMed</a>

<li>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.
<i>Anal Chem.</i> 2010 May 1;82(9):3556-66.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20373789">PubMed</a>

<li>Backbone and side-chain specific dissociations of z ions from non-tryptic peptides.
Chung TW, Turecek F.
<i>J Am Soc Mass Spectrom.</i> 2010 Aug;21(8):1279-95. Epub 2010 Feb 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20299240">PubMed</a>

<li>Comprehensive structure characterization of lipid A extracted from Yersinia pestis for determination of its phosphorylation configuration.
Jones JW, Cohen IE, Turecek F, Goodlett DR, Ernst RK.
<i>J Am Soc Mass Spectrom.</i> 2010 May;21(5):785-99. Epub 2010 Jan 25.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20185334">PubMed</a>

<li>Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation datasets.
Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R.
<i>Proteomics.</i> 2010 Mar;10(6):1190-5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/20082347">PubMed</a>

<p><h3>2009</h3>

<li>Proteomics data repositories.
Riffle M, Eng JK.
<i>Proteomics.</i> 2009 Oct;9(20):4653-63.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19795424">PubMed</a>

<li>Control of promatrilysin (MMP7) activation and substrate-specific activity by sulfated glycosaminoglycans.
Ra HJ, Harju-Baker S, Zhang F, Linhardt RJ, Wilson CL, Parks WC.
<i>J Biol Chem.</i> 2009 Oct 9;284(41):27924-32. Epub 2009 Aug 4.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19654318">PubMed</a>

<li>Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean.
Panchaud A, Scherl A, Shaffer SA, von Haller PD, Kulasekara HD, Miller SI, Goodlett DR.
<i>Anal Chem.</i> 2009 Aug 1;81(15):6481-8.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19572557">PubMed</a>

<li>Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures.
Hoopmann MR, Merrihew GE, von Haller PD, Maccoss MJ.
<i>J Proteome Res.</i> 2009 Apr;8(4):1870-5.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19256536">PubMed</a>

<li>Tandem Mass Spectrometry Investigation of ADP-ribosylated Kemptide.
Hengel SM, Shaffer SA, Nunn BL, Goodlett DR.
<i>J Am Soc Mass Spectrom.</i> 2009 Mar;20(3):477-83. Epub 2008 Nov 17.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19070509">PubMed</a>

<p><h3>2008</h3>

<li>New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening.
Major MB, Roberts BS, Berndt JD, Marine S, Anastas J, Chung N, Ferrer M, Yi X, Stoick-Cooper CL, von Haller PD, Kategaya L, Chien A, Angers S, MacCoss M, Cleary MA, Arthur WT, Moon RT.
<i>Sci Signal.</i> 2008 Nov 11;1(45):ra12.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/19001663">PubMed</a>

<li>A fast SEQUEST cross correlation algorithm.
Eng JK, Fischer B, Grossmann J, Maccoss MJ.
<i>J Proteome Res.</i> 2008 Oct;7(10):4598-602. Epub 2008 Sep 6.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/18774840">PubMed</a>

<li>Determination of pyrophosphorylated forms of lipid A in Gram-negative bacteria using a multivaried mass spectrometric approach.
Jones JW, Shaffer SA, Ernst RK, Goodlett DR, Turecek F.
<i>Proc Natl Acad Sci U S A.</i> 2008 Sep 2;105(35):12742-7. Epub 2008 Aug 27.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/18753624">PubMed</a>

<li>MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.
Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M.
<i>Mol Cell Proteomics.</i> 2008 Nov;7(11):2270-8. Epub 2008 Jul 18.
<a target="new" href="https://www.ncbi.nlm.nih.gov/pubmed/18641041">PubMed</a>
</ol>

</div>
</div>

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