Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics
Andrew C. Yang, Haley du Bois, Niclas Olsson, David Gate, benoit lehallier, Daniela Berdnik, Kyle D. Brewer, Carolyn R Bertozzi, Joshua E. Elias, and Tony Wyss-Coray
Journal of the American Chemical Society. May 18, 2018 (Web); DOI: 10.1021/jacs.8b03074

T-cell immunopeptidomes reveal cell subtype surface markers derived from intracellular proteins
Niclas Olsson, Liora M Schultz, Lichao Zhang, Michael S. Khodadoust, Rupa Narayan, Debra K. Czerwinski, Ronald Levy, Joshua E. Elias
Proteomics. 2018 March 1; DOI: 10.1002/pmic.201700410


Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania.
Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL
Science. 2017 Aug 25;357(6353):802-806. doi: 10.1126/science.aan4834. PubMed PMID: 28839072.

RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation.
Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O.
J Biol Chem. 2017 Aug 11;292(32):13381-13390. doi: 10.1074/jbc.M117.784371. Epub 2017 Jun 27. PubMed PMID: 28655759; PubMed Central PMCID: PMC5555197.

From mystery to mechanism: can proteomics build systems-level understanding of our gut microbes?
Gonzalez CG, Zhang L, Elias JE
Expert Rev Proteomics. 2017 Jun;14(6):473-476. doi: 10.1080/14789450.2017.1311211. Epub 2017 Apr 3. PubMed PMID: 28335651

The Prenylated Proteome of Plasmodium falciparum Reveals Pathogen-specific Prenylation Activity and Drug Mechanism-of-action
Gisselberg JE, Zhang L, Elias JE, Yeh E.
Mol Cell Proteomics. 2017 Apr;16(4 suppl 1):S54-S64. doi: 10.1074/mcp.M116.064550. Epub 2016 Dec 31. PubMed PMID: 28040698; PubMed Central PMCID: PMC5393391

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.
Michael S. Khodadoust, Niclas Olsson, Lisa E. Wagar, Ole A. W. Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M. Newman, Debra K. Czerwinski, Victoria E. H. Carlton, Martin Moorhead, Malek Faham, Holbrook E. Kohrt, Jan Carette, Michael R. Green, Mark M. Davis, Ronald Levy, Joshua E. Elias & Ash A. Alizadeh
Nature. 2017

Relative Protein Quantification Using Tandem Mass Tag Mass Spectrometry.
Zhang L, Elias JE
Methods Mol Biol. 2017;1550:185-198. doi: 10.1007/978-1-4939-6747-6_14. PubMed PMID: 28188531.

Building proteomic tool boxes to monitor MHC class I and class II peptides.
Schumacher FR, Delamarre L, Jhunjhunwala S, Modrusan Z, Phung QT, Elias JE, Lill JR.
Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600061. Review. PubMed PMID: 27928884.


Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars.
Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR.
Analytical and bioanalytical chemistry. 2016

Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.
Lund PJ, Elias JE, Davis MM.
Journal of immunology (Baltimore, Md. : 1950). 2016

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens.
Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE.
Nature. 2016; 535(7610):159-63. NIHMSID: NIHMS794905

The effect of microbial colonization on the host proteome varies by gastrointestinal location.
Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE.
The ISME journal. 2016; 10(5):1170-81.

A PWWP Domain of Histone-Lysine N-Methyltransferase NSD2 Binds to Dimethylated Lys-36 of Histone H3 and Regulates NSD2 Function at Chromatin.
Sankaran SM, Wilkinson AW, Elias JE, Gozani O.
The Journal of biological chemistry. 2016; 291(16):8465-74.

Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.
Devabhaktuni A, Elias JE.
Journal of proteome research. 2016; 15(3):732-42.

Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases.
Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE.
Cell reports. 2016; 14(5):1049-61.


Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans.
Zimmerman SM, Hinkson IV, Elias JE, Kim SK.
PLoS genetics. 2015; 11(12):e1005725.

Quantitative Imaging of Gut Microbiota Spatial Organization.
Earle KA, Billings G, Sigal M, Lichtman JS, Hansson GC, Elias JE, Amieva MR, Huang KC, Sonnenburg JL.
Cell host & microbe. 2015; 18(4):478-88. NIHMSID: NIHMS728947

Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant's GI.
Elias JE.
Proteomics. 2015; 15(20):3407-8.

Monitoring host responses to the gut microbiota.
Lichtman JS, Sonnenburg JL, Elias JE.
The ISME journal. 2015; 9(9):1908-15.

A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme.
Carlson SM, Moore KE, Sankaran SM, Reynoird N, Elias JE, Gozani O.
The Journal of biological chemistry. 2015; 290(19):12040-7.

Calcineurin regulates the yeast synaptojanin Inp53/Sjl3 during membrane stress.
Guiney EL, Goldman AR, Elias JE, Cyert MS.
Molecular biology of the cell. 2015; 26(4):769-85.

2014 and Prior

Role of disease-associated tolerance in infectious superspreaders.
Gopinath S, Lichtman JS, Bouley DM, Elias JE, Monack DM.
Proceedings of the National Academy of Sciences of the United States of America. 2014; 111(44):15780-5.

Assessing subunit dependency of the Plasmodium proteasome using small molecule inhibitors and active site probes.
Li H, van der Linden WA, Verdoes M, Florea BI, McAllister FE, Govindaswamy K, Elias JE, Bhanot P, Overkleeft HS, Bogyo M.
ACS chemical biology. 2014; 9(8):1869-76.

The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.
Treeck M, Sanders JL, Gaji RY, LaFavers KA, Child MA, Arrizabalaga G, Elias JE, Boothroyd JC.
PLoS pathogens. 2014; 10(6):e1004197.

The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis.
Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P.
Cell cycle (Georgetown, Tex.). 2014; 13(18):2889-900.

Host-centric proteomics of stool: a novel strategy focused on intestinal responses to the gut microbiota.
Lichtman JS, Marcobal A, Sonnenburg JL, Elias JE.
Molecular & cellular proteomics : MCP. 2013; 12(11):3310-8.

A role for the MRN complex in ATR activation via TOPBP1 recruitment.
Duursma AM, Driscoll R, Elias JE, Cimprich KA.
Molecular cell. 2013; 50(1):116-22. NIHMSID: NIHMS455516

The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries.
Treeck M, Sanders JL, Elias JE, Boothroyd JC.
Cell host & microbe. 2011; 10(4):410-9. NIHMSID: NIHMS332451

A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers.
Jirawatnotai S, Hu Y, Michowski W, Elias JE, Becks L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Clark AB, Kunkel TA, van Harn T, Xia B, Correll M, Quackenbush J, Livingston DM, Gygi SP, Sicinski P.
Nature. 2011; 474(7350):230-4. NIHMSID: NIHMS309010

The dynamic state of protein turnover: It's about time.
Hinkson IV, Elias JE.
Trends in cell biology. 2011; 21(5):293-303.

A tissue-specific atlas of mouse protein phosphorylation and expression.
Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP.
Cell. 2010; 143(7):1174-89. NIHMSID: NIHMS257943

Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.
Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P.
Nature. 2010; 463(7279):374-8. NIHMSID: NIHMS209724

Target-decoy search strategy for mass spectrometry-based proteomics.
Elias JE, Gygi SP.
Methods in molecular biology (Clifton, N.J.). 2010; 604:55-71. NIHMSID: NIHMS222019

Identification of beta-secretase (BACE1) substrates using quantitative proteomics.
Hemming ML, Elias JE, Gygi SP, Selkoe DJ.
PloS one. 2009; 4(12):e8477.

The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.
Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP.
Journal of proteome research. 2008; 7(11):4756-65. NIHMSID: NIHMS130919

Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.
Hemming ML, Elias JE, Gygi SP, Selkoe DJ.
PLoS biology. 2008; 6(10):e257.

Assessing enzyme activities using stable isotope labeling and mass spectrometry.
Everley PA, Gartner CA, Haas W, Saghatelian A, Elias JE, Cravatt BF, Zetter BR, Gygi SP.
Molecular & cellular proteomics : MCP. 2007; 6(10):1771-7.

Catch-and-release reagents for broadscale quantitative proteomics analyses.
Gartner CA, Elias JE, Bakalarski CE, Gygi SP.
Journal of proteome research. 2007; 6(4):1482-91.

Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.
Li X, Gerber SA, Rudner AD, Beausoleil SA, Haas W, Villén J, Elias JE, Gygi SP.
Journal of proteome research. 2007; 6(3):1190-7.

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.
Elias JE, Gygi SP.
Nature methods. 2007; 4(3):207-14.

Optimization and use of peptide mass measurement accuracy in shotgun proteomics.
Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP.
Molecular & cellular proteomics : MCP. 2006; 5(7):1326-37.

Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation.
Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP.
Journal of proteome research. 2006; 5(5):1224-31.

Characterization of mouse spleen cells by subtractive proteomics.
Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP.
Molecular & cellular proteomics : MCP. 2005; 4(10):1459-70.

Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations.
Elias JE, Haas W, Faherty BK, Gygi SP.
Nature methods. 2005; 2(9):667-75.

The Parkinson's disease-associated DJ-1 protein is a transcriptional co-activator that protects against neuronal apoptosis.
Xu J, Zhong N, Wang H, Elias JE, Kim CY, Woldman I, Pifl C, Gygi SP, Geula C, Yankner BA.
Human molecular genetics. 2005; 14(9):1231-41.

BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number.
Starita LM, Machida Y, Sankaran S, Elias JE, Griffin K, Schlegel BP, Gygi SP, Parvin JD.
Molecular and cellular biology. 2004; 24(19):8457-66.

SILVER helps assign peptides to tandem mass spectra using intensity-based scoring.
Gibbons FD, Elias JE, Gygi SP, Roth FP.
Journal of the American Society for Mass Spectrometry. 2004; 15(6):910-2.

Intensity-based protein identification by machine learning from a library of tandem mass spectra.
Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP.
Nature biotechnology. 2004; 22(2):214-9.

A proteomics approach to understanding protein ubiquitination.
Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP.
Nature biotechnology. 2003; 21(8):921-6.

Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP.
Journal of proteome research. 2003; 2(1):43-50.