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Hydrogen Sulfide Sensing through Reactive Sulfur Species (RSS) and Nitroxyl (HNO) in Enterococcus faecalis.

Shen J, Walsh BJC, Flores-Mireles AL, Peng H, Zhang Y, Zhang Y, Trinidad JC, Hultgren SJ, Giedroc DP.

ACS Chem Biol. 2018 Jun 15;13(6):1610-1620. doi: 10.1021/acschembio.8b00230. Epub 2018 May 17.


Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry.

Chen G, Zhang Y, Trinidad JC, Dann C 3rd.

J Am Soc Mass Spectrom. 2018 Mar;29(3):455-462. doi: 10.1007/s13361-017-1854-1. Epub 2018 Jan 8.


A High-Throughput Mass-Spectrometry-Based Assay for Identifying the Biochemical Functions of Putative Glycosidases.

Peng T, Nagy G, Trinidad JC, Jackson JM, Pohl NLB.

Chembiochem. 2017 Dec 5;18(23):2306-2311. doi: 10.1002/cbic.201700292. Epub 2017 Oct 27.


An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules.

DeHaan H, McCambridge A, Armstrong B, Cruse C, Solanki D, Trinidad JC, Arkov AL, Gao M.

FEBS Lett. 2017 Nov;591(21):3536-3547. doi: 10.1002/1873-3468.12854. Epub 2017 Oct 11.


Hydrogen Sulfide and Reactive Sulfur Species Impact Proteome S-Sulfhydration and Global Virulence Regulation in Staphylococcus aureus.

Peng H, Zhang Y, Palmer LD, Kehl-Fie TE, Skaar EP, Trinidad JC, Giedroc DP.

ACS Infect Dis. 2017 Oct 13;3(10):744-755. doi: 10.1021/acsinfecdis.7b00090. Epub 2017 Sep 6.


Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme.

Yan J, Beattie TR, Rojas AL, Schermerhorn K, Gristwood T, Trinidad JC, Albers SV, Roversi P, Gardner AF, Abrescia NGA, Bell SD.

Nat Commun. 2017 May 2;8:15075. doi: 10.1038/ncomms15075.


Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis.

Shimizu T, Shen J, Fang M, Zhang Y, Hori K, Trinidad JC, Bauer CE, Giedroc DP, Masuda S.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2355-2360. doi: 10.1073/pnas.1614133114. Epub 2017 Feb 14.


Reduced Insulin/IGF-1 Signaling Restores the Dynamic Properties of Key Stress Granule Proteins during Aging.

Lechler MC, Crawford ED, Groh N, Widmaier K, Jung R, Kirstein J, Trinidad JC, Burlingame AL, David DC.

Cell Rep. 2017 Jan 10;18(2):454-467. doi: 10.1016/j.celrep.2016.12.033.


Biological and Chemical Adaptation to Endogenous Hydrogen Peroxide Production in Streptococcus pneumoniae D39.

Lisher JP, Tsui HT, Ramos-Montañez S, Hentchel KL, Martin JE, Trinidad JC, Winkler ME, Giedroc DP.

mSphere. 2017 Jan 4;2(1). pii: e00291-16. doi: 10.1128/mSphere.00291-16. eCollection 2017 Jan-Feb.


Palmitoylation of Sindbis Virus TF Protein Regulates Its Plasma Membrane Localization and Subsequent Incorporation into Virions.

Ramsey J, Renzi EC, Arnold RJ, Trinidad JC, Mukhopadhyay S.

J Virol. 2017 Jan 18;91(3). pii: e02000-16. doi: 10.1128/JVI.02000-16. Print 2017 Feb 1.


Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM.

Xu Y, Gristwood T, Hodgson B, Trinidad JC, Albers SV, Bell SD.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):13390-13395. Epub 2016 Nov 7.


Staphylococcus aureus sqr Encodes a Type II Sulfide:Quinone Oxidoreductase and Impacts Reactive Sulfur Speciation in Cells.

Shen J, Peng H, Zhang Y, Trinidad JC, Giedroc DP.

Biochemistry. 2016 Nov 29;55(47):6524-6534. Epub 2016 Nov 16.


Disparate Regulatory Mechanisms Control Fat3 and P75NTR Protein Transport through a Conserved Kif5-Interaction Domain.

Cheng H, Burroughs-Garcia J, Birkness JE, Trinidad JC, Deans MR.

PLoS One. 2016 Oct 27;11(10):e0165519. doi: 10.1371/journal.pone.0165519. eCollection 2016.


Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice.

Morris M, Knudsen GM, Maeda S, Trinidad JC, Ioanoviciu A, Burlingame AL, Mucke L.

Nat Neurosci. 2015 Aug;18(8):1183-9. doi: 10.1038/nn.4067. Epub 2015 Jul 20.


Glycopeptide Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques.

Zhu F, Trinidad JC, Clemmer DE.

J Am Soc Mass Spectrom. 2015 Jul;26(7):1092-102. doi: 10.1007/s13361-015-1110-5. Epub 2015 Apr 4.


Populations of metal-glycan structures influence MS fragmentation patterns.

Zhu F, Glover MS, Shi H, Trinidad JC, Clemmer DE.

J Am Soc Mass Spectrom. 2015 Jan;26(1):25-35. doi: 10.1007/s13361-014-1000-2. Epub 2014 Oct 15.


Glucose regulates mitochondrial motility via Milton modification by O-GlcNAc transferase.

Pekkurnaz G, Trinidad JC, Wang X, Kong D, Schwarz TL.

Cell. 2014 Jul 3;158(1):54-68. doi: 10.1016/j.cell.2014.06.007.


N- and O-glycosylation in the murine synaptosome.

Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF.

Mol Cell Proteomics. 2013 Dec;12(12):3474-88. doi: 10.1074/mcp.M113.030007. Epub 2013 Jul 1.


Nedd4 is a specific E3 ubiquitin ligase for the NMDA receptor subunit GluN2D.

Gautam V, Trinidad JC, Rimerman RA, Costa BM, Burlingame AL, Monaghan DT.

Neuropharmacology. 2013 Nov;74:96-107. doi: 10.1016/j.neuropharm.2013.04.035. Epub 2013 Apr 29.


Differentiation of opioid drug effects by hierarchical multi-site phosphorylation.

Just S, Illing S, Trester-Zedlitz M, Lau EK, Kotowski SJ, Miess E, Mann A, Doll C, Trinidad JC, Burlingame AL, von Zastrow M, Schulz S.

Mol Pharmacol. 2013 Mar;83(3):633-9. doi: 10.1124/mol.112.082875. Epub 2012 Dec 13.


Trk activation of the ERK1/2 kinase pathway stimulates intermediate chain phosphorylation and recruits cytoplasmic dynein to signaling endosomes for retrograde axonal transport.

Mitchell DJ, Blasier KR, Jeffery ED, Ross MW, Pullikuth AK, Suo D, Park J, Smiley WR, Lo KW, Shabanowitz J, Deppmann CD, Trinidad JC, Hunt DF, Catling AD, Pfister KK.

J Neurosci. 2012 Oct 31;32(44):15495-510. doi: 10.1523/JNEUROSCI.5599-11.2012.


Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins.

Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R.

Mol Cell Proteomics. 2013 Jan;12(1):29-41. doi: 10.1074/mcp.M112.019976. Epub 2012 Oct 3.


Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis.

Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12432-7. doi: 10.1073/pnas.1208616109. Epub 2012 Jul 16.


Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.

Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL.

Mol Cell Proteomics. 2012 Aug;11(8):215-29. doi: 10.1074/mcp.O112.018366. Epub 2012 May 29.


Global kinetic analysis of proteolysis via quantitative targeted proteomics.

Agard NJ, Mahrus S, Trinidad JC, Lynn A, Burlingame AL, Wells JA.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):1913-8. doi: 10.1073/pnas.1117158109. Epub 2012 Jan 23.


Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra.

Medzihradszky KF, Trinidad JC.

J Am Soc Mass Spectrom. 2012 Apr;23(4):602-7. doi: 10.1007/s13361-011-0216-7. Epub 2011 Aug 5.


Quantitative encoding of the effect of a partial agonist on individual opioid receptors by multisite phosphorylation and threshold detection.

Lau EK, Trester-Zedlitz M, Trinidad JC, Kotowski SJ, Krutchinsky AN, Burlingame AL, von Zastrow M.

Sci Signal. 2011 Aug 9;4(185):ra52. doi: 10.1126/scisignal.2001748.


Modification site localization scoring integrated into a search engine.

Baker PR, Trinidad JC, Chalkley RJ.

Mol Cell Proteomics. 2011 Jul;10(7):M111.008078. doi: 10.1074/mcp.M111.008078. Epub 2011 Apr 13.


Widespread protein aggregation as an inherent part of aging in C. elegans.

David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C.

PLoS Biol. 2010 Aug 10;8(8):e1000450. doi: 10.1371/journal.pbio.1000450.


Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.

Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ.

PLoS Biol. 2009 Jun 16;7(6):e1000134. doi: 10.1371/journal.pbio.1000134. Epub 2009 Jun 23. Erratum in: PLoS Biol. 2009 Nov;7(11). doi: 10.1371/annotation/66479889-5e57-4213-bf25-c4e8cf3d933b.


Normal protein composition of synapses in Ts65Dn mice: a mouse model of Down syndrome.

Fernandez F, Trinidad JC, Blank M, Feng DD, Burlingame AL, Garner CC.

J Neurochem. 2009 Jul;110(1):157-69. doi: 10.1111/j.1471-4159.2009.06110.x. Epub 2009 Apr 22.


A transmembrane accessory subunit that modulates kainate-type glutamate receptors.

Zhang W, St-Gelais F, Grabner CP, Trinidad JC, Sumioka A, Morimoto-Tomita M, Kim KS, Straub C, Burlingame AL, Howe JR, Tomita S.

Neuron. 2009 Feb 12;61(3):385-96. doi: 10.1016/j.neuron.2008.12.014.


Densin-180: revised membrane topology, domain structure and phosphorylation status.

Thalhammer A, Trinidad JC, Burlingame AL, Schoepfer R.

J Neurochem. 2009 Apr;109(2):297-302. doi: 10.1111/j.1471-4159.2009.05951.x. Epub 2009 Feb 2. Review.


Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA.

Cell. 2008 Sep 5;134(5):866-76. doi: 10.1016/j.cell.2008.08.012. Epub 2008 Aug 21.


Human Proteinpedia enables sharing of human protein data.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A.

Nat Biotechnol. 2008 Feb;26(2):164-7. doi: 10.1038/nbt0208-164. No abstract available.


Quantitative analysis of synaptic phosphorylation and protein expression.

Trinidad JC, Thalhammer A, Specht CG, Lynn AJ, Baker PR, Schoepfer R, Burlingame AL.

Mol Cell Proteomics. 2008 Apr;7(4):684-96. Epub 2007 Dec 3.


Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice.

Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS.

J Cell Biol. 2007 Oct 8;179(1):151-64.


Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome.

Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA.

Am J Respir Crit Care Med. 2007 May 15;175(10):1006-13. Epub 2007 Mar 15.


O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.

Vosseller K, Trinidad JC, Chalkley RJ, Specht CG, Thalhammer A, Lynn AJ, Snedecor JO, Guan S, Medzihradszky KF, Maltby DA, Schoepfer R, Burlingame AL.

Mol Cell Proteomics. 2006 May;5(5):923-34. Epub 2006 Feb 1.


Comprehensive identification of phosphorylation sites in postsynaptic density preparations.

Trinidad JC, Specht CG, Thalhammer A, Schoepfer R, Burlingame AL.

Mol Cell Proteomics. 2006 May;5(5):914-22. Epub 2006 Feb 1.


Neurotransmitter release regulated by a MALS-liprin-alpha presynaptic complex.

Olsen O, Moore KA, Fukata M, Kazuta T, Trinidad JC, Kauer FW, Streuli M, Misawa H, Burlingame AL, Nicoll RA, Bredt DS.

J Cell Biol. 2005 Sep 26;170(7):1127-34.


Molecular constituents of neuronal AMPA receptors.

Fukata Y, Tzingounis AV, Trinidad JC, Fukata M, Burlingame AL, Nicoll RA, Bredt DS.

J Cell Biol. 2005 May 9;169(3):399-404.


Phosphorylation state of postsynaptic density proteins.

Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL.

J Neurochem. 2005 Mar;92(6):1306-16.


Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol.

Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL.

Proteomics. 2005 Feb;5(2):388-98.


[Association between membranous glomerulonephritis and Crohn's disease].

Díaz Rodríguez C, Granja E, Vázquez Martul E, Sacristán F, Moreno Fernández A, González Rivero C, del Río Romero D, Trinidad JC.

Nefrologia. 2004;24(4):368-71. Review. Spanish.


Neuregulin inhibits acetylcholine receptor aggregation in myotubes.

Trinidad JC, Cohen JB.

J Biol Chem. 2004 Jul 23;279(30):31622-8. Epub 2004 May 20.


[Tuberous sclerosis. Description of a family study].

Trinidad JC, Iraburu M, Martínez A, Espiñeira M, Bañales T, Alvarez I.

An Med Interna. 1997 Jul;14(7):351-4. Spanish.


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