Publications of Proteomics and Mass Spectrometry Core Data
Co-authorship earned by the staff of the UF Scripps Mass Spectrometry and Proteomics Core.

Concerted Antibody and Antigen Discovery by Differential Whole-cell Phage Display Selections and Multi-omic Target Deconvolution. Cyr MG, Wilson HD, Spierling A-L, Chang J, Peng H, Steinberger P, Rader C. J. Mol. Biol. Volume 435, Issue 10, 15 May 2023, 168085.

Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics. Xu H, Bensalel J, Raju S, Capobianco E, Lu ML, Wei J. J Neurochem. 2023 Feb;164(4):512-528.

Optimized protocol for in vivo affinity purification proteomics and biochemistry using C. elegans. Desbois M, Pak JS, Opperman KJ, Giles AC, Grill B. Star Protocols Volume 4, Issue 2, 16 June 2023, 102262.

Cell Surface Engineering Enables Surfaceome Profiling. Vilen Z, Reeves AE, O’Leary TR, Jeoh E, Kammassawa N, Huang ML. ACS Chem. Biol. 2023, 18, 4, 701–710,

Short-Term and Long-Term Sensitization Differentially Alters the Composition of an Anterograde Transport Complex in Aplysia. Sadhu A, Badah KK, Zhao Y, Ali AA, Swarnkar A, Tsaprailis G, Crynen GC, Puthanveettil SV. eNuero 22 December 2022,  10 (1) ENEURO.0266-22.2022.

Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Cerullo F, Filbeck S, Patil PR, Hung H-C, Xu H, Vornberger J, Hofer FW, Schmitt J, Kramer G, Bukau B, Hofmann K, Pfeffer S, Joazeiro CAP. Nature 2022, volume 603, pages 509–514. DOI: 10.1038/s41586-022-04487-6

Proximity interactome analysis of Lassa polymerase reveals eRF3a/GSPT1 as a druggable target for host-directed antivirals. Fang J, Pietzsch C, Witwit H, Tsaprailis G, Crynen G, Cho KF, Ting AY, Bukreyev A, Saphire EO, de la Torre JC. Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2201208119. doi: 10.1073/pnas.2201208119.

Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome-related protein 1. Khamoui AV, Tokmina-Roszyk D, Feresin RG, Fields GB, Visavadiya NP. Proteomics 22(1), May 2022, 2100157.

Performing mass spectrometry-based proteomics in organisms with minimal reference protein databases. Chou S, Poskanzer KE, Thuy-Boun PS. 2022.

Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis. Thuy-Boun PS, Wang AY, Crissien-Martinez A, Xu JH, Chatterjee S, Stupp GS, Su AI, Coyle WJ, Wolan DW. Mol. Cell Prot. 21(3), March 2022, 100197.

Ubiquitin ligase activity inhibits Cdk5 to control axon termination. Desbois M, Opperman KJ, Amezquita J, Gaglio O, Grill B. PLOS Genetics 2022, 18(4): e1010152.

Active forgetting requires Sickie function in a dedicated dopamine circuit in Drosophila. Zhang Z, Sabandal JM, Tsaprailis G, Davis RL. PNAS 2022, 19 (38), e2204229119.

Functional interactomes of the Ebola virus polymerase identified by proximity proteomics in the context of viral replication. Fang J, Pietzsch C, Tsaprailis G, Crynen G, Cho KF, Ting AY, Bukreyev A, de la Torre JC, Ollmann Saphire E. Cell Reports 2022, 38(12), 110544. doi: 10.1016/j.celrep.2022.110544

Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing. Thrun A, Garzia A, Kigoshi-Tansho Y, Patil PR , Umbaugh CS, Dallinger T , Liu J, Kreger S, Patrizi A, Cox GA, Tuschl T, Joazeiro CAP. Mol Cell. 2021 May 20;81(10):2112-2122.e7. DOI: 10.1016/j.molcel.2021.03.004.

Dyrk1a Mutations Cause Undergrowth of Cortical Pyramidal Neurons via Dysregulated Growth Factor Signaling. Levy JA, LaFlamme CW, Tsaprailis G, Crynen G, Page DT. Biol. Psych. 2021, 90(5), 295-306.

Activity-regulated synaptic targeting of lncRNA ADEPTR mediates structural plasticity by localizing Sptn1 and AnkB in dendrites. Grinman E, Nakahata Y, Avchalumov Y, Espadas I, Swarnkar S, Yasuda R, Puthanveettil SV. Sci Adv. 2021, Apr 16;7(16):eabf0605. DOI: 10.1126/sciadv.abf0605

Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S. Mol. Cell 2021, Jan 7;81(1):104-114. DOI: 10.1016/j.molcel.2020.11.001

Proximity tagging identified the glycan-mediated glycoprotein interactors of galectin-1 in muscle stem cells. Vilen Z, Joeh E, Critcher M, Parker CG, Huang ML. ACS Chem. Biol. 2021, 16, 10, 1994–2003.

A photoaffinity probe that targets folate-binding proteins. Takamura A, Thuy-Boun PS, Kitamura S, Han Z, Wolan DW. Bioorg Med Chem Lett. 2021 May 15; 40: 127903.

Interplay between cell adhesion molecules governs synaptic wiring of cone photoreceptors. Cao Y, Wang Y, Dunn HA, Orlandi C, Shultz N, Kamasawa N, Fitzpatrick D, Li W, Zeitz C, Hauswirth W, Martemyanov KA. Proc. Natl. Acad. Sci. USA 2020, 117, 23914-23924.

RasGRP1 is a causal factor in the development of L-DOPA-induced dyskinesia in Parkinson’s disease. Eshraghi M, Ramírez-Jaruín UN, Shahani N, Nuzzo T, De Rosa A, Swarnkar S, Galii N, Rivera O, Tsaprailis G, Scharager-Tapia C, Crynen G, Li Q, Thiolat ML, Bezard E, Usiello A, Subramaniam S. Sci. Adv. 2020, 1 May 2020, 6(18), eaaz7001. DOI: 10.1126/sciadv.aaz7001

Chemically Programmable and Switchable CAR-T Therapy. Qi J, Tsuji K, Hymel D, Burke Jr., TR, Rader C, Peng H. Angew.Chem. Int. Ed. April 2020, 59,12178–12185.

Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control. Lytvynenko I, Paternoga H, Thrun A, Balke A, Müller TA, Chiang CH, Nagler K, Tsaprailis G, Anders S, Bischofs I, Maupin-Furlow JA, Spahn CMT, Joazeiro CAP. Cell 2019, Jun 27;178(1):76-90.e22.

Autophagy Is Inhibited by Ubiquitin Ligase Activity in the Nervous System. Crawley O, Opperman KJ, Desbois M, Adrados I, Borgen MA, Giles AC,  Duckett DR, Grill B. Nat. Commun. 2019, Nov 1; 10(1):5017. DOI: 10.1038/s41467-019-12804-3

A complex containing the O-GlcNAc transferase OGT-1 and the ubiquitin ligase EEL-1 regulates GABA neuron function. Giles AC, Desbois M, Opperman KJ, Tavora R, Maroni MJ, Grill B. J. Biol. Chem. 2019, Apr 26;294(17):6843-6856.

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database. Park SKR, Jung T, Thuy-Boun PS, Wang AY, Yates JR 3rd, Wolan DW. J. Proteome Res. 2019, Feb 1;18(2):616-622.

A DEAD-box protein regulates ribosome assembly through control of ribosomal protein synthesis. Iost I and Jain C. Nucleic Acids Res. 2019 Sep 5; 47(15): 8193–8206. doi: 10.1093/nar/gkz502

Chemical Crosslinking Mass Spectrometry Reveals the Conformational Landscape of the Activation Helix of PPARγ; a Model for Ligand-Dependent Antagonism. Zheng J, Corzo C, Chang MR, Shang J, Lam VQ, Brust R, Blayo AL, Bruning JB, Kamenecka TM, Kojetin DJ, Griffin PR. Structure 2018, Nov 6;26(11):1431-1439.e6.

LRIT1 Modulates Adaptive Changes in Synaptic Communication of Cone Photoreceptors. Sarria I, Cao Y, Wang Y, Ingram NT, Orlandi C, Kamasawa N, Kolesnikov AV, Pahlberg J, Kefalov VJ, Sampath AP, Martemyanov KA. Cell Reports 2018, 22(13), 27 March 2018, 3562-3573.

Transsynaptic Binding of Orphan Receptor GPR179 to Dystroglycan-Pikachurin Complex Is Essential for the Synaptic Organization of Photoreceptors. Orlandi C, Omori Y, Wang Y, Cao Y, Ueno A, Roux MJ, Condomitti G, de Wit J, Kanagawa M, Furukawa T, Martemyanov KA. Cell Reports 2018, 25(1), 2 October 2018, Pages 130-145.e5.

Orphan receptor GPR158 controls stress-induced depression. Sutton LP, Orlandi C, Song C, Oh WC, Muntean BS, Xie K, Fillipini A, Xie X, Satterfield R, Yaeger JDW, Renner KJ, Young SM Jr., Xu B,Kwon H, Martemaynov KA. eLife 2018, Feb 8;7:e33273

Stable and Potent Selenomab-Drug Conjugates. Li X, Nelson CG, Nair RR, Hazlehurst L, Moroni T, Martinez-Acedo P, Nanna AR, Hymel D, Burke TR Jr, Rader C. Cell. Chem. Biol. 2017, 4(24), 433-442.

Unique Interactome Network Signatures for Peroxisome Proliferator-activated Receptor Gamma (PPARγ) Modulation by Functional Selective Ligands. Lam VQ, Zheng J, Griffin PR. Mol. Cell. Proteomics 2017, Dec;16(12):2098-2110.

RasGRP1 promotes amphetamine-induced motor behavior through a Rhes interaction network (“Rhesactome”) in the striatum. Shahani N, Swarnkar S, Giovinazzo V, Morgenweck J, Bohn L, Scharager-Tapia C, Pascal B, Martinez-Acedo P, Khar K, Subramaniam S. Sci. Signal.  2016, Nov;9(454), ra111. DOI: 10.1126/scisignal.aaf6670

Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications. Pascal BD, West GM, Scharager-Tapia C, Flefil R, Moroni T, Martínez-Acedo P, Griffin PR, Carvalloza AC. J. Am. Soc. Mass Spectrom. 2015, Dec;26(12):2133-2140. DOI: 10.1007/s13361-015-1229-4

SERBP1 Is a Component of the Liver Receptor Homologue-1 Transcriptional Complex.
Mari Y, West GM, Scharager-Tapia C, Pascal BD, Garcia-Ordonez RD, Griffin PR. J. Proteome Res. 2015, Nov 6;14(11):4571-4580.

Site-Specific Proteomic Mapping Identifies Selectively Modified Regulatory Cysteine Residues in Functionally Distinct Protein Networks. Gould NS, Evans P, Martínez-Acedo P, Marino SM, Gladyshev VN, Carroll KS, Ischiropoulos H. Chem. Biol. 2015, Jul 23;22(7):965-975.

Mass spectrometry approach and ELISA reveal the effect of codon optimization on N-linked glycosylation of HIV-1 gp120. Honarmand Ebrahimi K, West GM, Flefil R. J. Proteome Res. 2014, Dec 5;13(12):5801-5811.

New approach to capture and characterize synaptic proteome. Liu XA, Kadakkuzha B, Pascal B, Steckler C, Akhmedov K, Yan L, Chalmers M, Puthanveettil SV. Proc. Natl. Acad. Sci. USA 2014, Nov 11;111(45):16154-16159.

Proteomic analysis of peptides tagged with dimedone and related probes. Martínez-Acedo P, Gupta V, Carroll KS. J. Mass Spectrom. 2014, Apr;49(4):257-265. doi: 10.1002/jms.3336

Using unnatural amino acid mutagenesis to probe the regulation of PRMT1. Rust HL, Subramanian V, West GM, Young DD, Schultz PG, Thompson PR. ACS Chem. Biol. 2014, Mar 21;9(3):649-655.

General statistical framework for quantitative proteomics by stable isotope labeling. Navarro P, Trevisan-Herraz M, Bonzon-Kulichenko E, Núñez E, Martínez-Acedo P, Pérez-Hernández D, Jorge I, Mesa R, Calvo E, Carrascal M, Hernáez ML, García F, Bárcena JA, Ashman K, Abian J, Gil C, Redondo JM, Vázquez J. J. Proteome Res. 2014, Mar 7;13(3):1234-1247.

Ischemic preconditioning protects cardiomyocyte mitochondria through mechanisms independent of cytosol. Ruiz-Meana M, Núñez E, Miro-Casas E, Martínez-Acedo P, Barba I, Rodriguez-Sinovas A, Inserte J, Fernandez-Sanz C, Hernando V, Vázquez J, Garcia-Dorado D. J. Mol. Cell. Cardiol. 2014, Mar;68:79-88.

Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry. Sarkar M, Pascal BD, Steckler C, Aquino C, Micalizio GC, Kodadek T, Chalmers MJ. J. Am. Soc. Mass Spectrom. 2013, Jul;24(7):1026-1036.

Direct interaction between AR and PAK6 in androgen-stimulated PAK6 activation. Liu X, Busby J, John C, Wei J, Yuan X, Lu ML. PLoS One 2013, Oct 10;8(10):e77367.

A novel strategy for global analysis of the dynamic thiol redox proteome. Martínez-Acedo P, Núñez E, Gómez FJ, Moreno M, Ramos E, Izquierdo-Álvarez A, Miró-Casas E, Mesa R, Rodriguez P, Martínez-Ruiz A, Dorado DG, Lamas S, Vázquez J. Mol. Cell Proteomics 2012, Sep;11(9):800-813. DOI:

Probing adenylation: using a fluorescently labelled ATP probe to directly label and immunoprecipitate VopS substrates. Lewallen DM, Steckler CJ, Knuckley B, Chalmers MJ, Thompson PR. Mol. Biosyst. 2012, Jun;8(6):1701-1706. DOI

Application of iTRAQ Reagents to Relatively Quantify the Reversible Redox State of Cysteine Residues. McDonagh B, Martínez-Acedo P, Vázquez J, Padilla CA, Sheehan D, Bárcena JA. Int. J. Proteomics 2012, 2012: 514847.

Phosphorylation of Y372 is critical for Jak2 tyrosine kinase activation. Sayyah J, Gnanasambandan K, Kamarajugadda S, Tsuda S, Caldwell-Busby J, Sayeski PP. Cell Signal 2011, Nov;23(11):1806-1815.

A biomimetic polyketide-inspired approach to small-molecule ligand discovery. Aquino C, Sarkar M, Chalmers MJ, Mendes K, Kodadek T, Micalizio GC. Nat. Chem. 2011, Nov 20;4(2):99-104.

Cell death induced by the Jak2 inhibitor, G6, correlates with cleavage of vimentin filaments. Majumder A, Kirabo A, Karrupiah K, Tsuda S, Caldwell-Busby J, Cardounel AJ, Keseru GM, Sayeski PP. Biochemistry 2011, Sep 13;50(36):7774-7786.

A robust method for quantitative high-throughput analysis of proteomes by (18)O- labeling. Bonzon-Kulichenko E, Pérez-Hernández D, Núñez E, Martínez-Acedo P, Navarro P, Trevisan-Herraz M, Ramos Mdel C, Sierra S, Martínez-Martínez S, Ruiz-Meana M, Miró-Casas E, García-Dorado D, Redondo JM, Burgos JS, Vázquez J. Mol. Cell Proteomics 2011, Jan;10(1):M110.003335.

Cyclosporine A-induced nitration of tyrosine 34 MnSOD in endothelial cells: role of mitochondrial superoxide. Redondo-Horcajo M, Romero N, Martínez-Acedo P, Martínez-Ruiz A, Quijano C, Lourenço CF, Movilla N, Enríquez JA, Rodríguez-Pascual F, Rial E, Radi R, Vázquez J, Lamas S. Cardiovasc. Res. 2010, Jul 15;87(2):356-365.

Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes. Dorus S, Wasbrough ER, Busby J, Wilkin EC, Karr TL
Mol. Biol. Evol. 2010, Jun;27(6):1235-1246.

A novel cross-talk in diacylglycerol signaling: the Rac-GAP beta2-chimaerin is negatively regulated by protein kinase Cdelta-mediated phosphorylation. Griner EM, Caino MC, Sosa MS, Colón-González F, Chalmers MJ, Mischak H, Kazanietz MG
J. Biol. Chem. 2010, May 28;285(22):16931-41

Activation domain-dependent degradation of somatic Wee1 kinase. Owens L, Simanski S, Squire C, Smith A, Cartzendafner J, Cavett V, Caldwell Busby J, Sato T, Ayad NG
J. Biol. Chem. 2010, Feb 26;285(9):6761-9

Mapping the phosphorylation sites of Ulk1. Dorsey FC, Rose KL, Coenen S, Prater SM, Cavett V, Cleveland JL, Caldwell-Busby J J. Proteome Res. 2009, Nov;8(11):5253-5263.

Statistical model to analyze quantitative proteomics data obtained by 18O/16O labeling and linear ion trap mass spectrometry: application to the study of vascular endothelial growth factor-induced angiogenesis in endothelial cells. Jorge I, Navarro P, Martínez-Acedo P*, Núñez E, Serrano H, Alfranca A, Redondo JM, Vázquez J Mol Cell Proteomics. 2009, May;8(5):1130-1149.

Strategies to recover proteins from ocular tissues for proteomics. Patel N, Solanki E, Picciani R, Cavett V, Caldwell-Busby JA, Bhattacharya SK Proteomics 2008, Mar;8(5):1055-1070. DOI: 10.1002/pmic.200700856

A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway. Amelio AL, Miraglia LJ, Conkright JJ, Mercer BA, Batalov S, Cavett V, Orth AP, Busby J, Hogenesch JB, Conkright MD Proc. Natl. Acad. Sci. USA 2007, Dec 18;104(51):20314-20319.

High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies. Jorge I, Casas E, Villar M, Ortega-Pérez I, López-Ferrer D, Martínez-Ruiz A, Carrera M, Marina A, Martínez P, Serrano H, Cañas B, Were F, Gallardo JM, Lamas S, Redondo JM, García-Dorado D, Vázquez J. J. Mass Spectrom. 2007, Nov;42(11):1391-1403. DOI: 10.1002/jms.1314

The N-terminal SH2 domain of the tyrosine phosphatase, SHP-2, is essential for Jak2-dependent signaling via the angiotensin II type AT1 receptor. Godeny MD, Sayyah J, VonDerLinden D, Johns M, Ostrov DA, Caldwell-Busby J, Sayeski PP.
Cell Signal. 2007 Mar;19(3):600-609.

Proteomic analyses of zebra finch optic tectum and comparative histochemistry. Sloley S, Smith S, Gandhi S, Busby JA, London S, Luksch H, Clayton DF, Bhattacharya SK.
J. Proteome Res. 2007, Jun;6(6):2341-2350.

Proteomic analyses of songbird (Zebra finch; Taeniopygia guttata) retina. Sloley S, Smith S, Algeciras M, Cavett V, Busby JA, London S, Clayton DF, Bhattacharya SK.
J. Proteome Res. 2007 Mar;6(3):1093-100

Trizol-based method for sample preparation and isoelectric focusing of halophilic proteins. Kirkland PA, Busby J, Stevens S Jr, Maupin-Furlow JA
Analytical Biochem. 2006 Apr 15;351(2):254-9