Publications

Search current Trinidad publications in PubMed

2012

Shimbo K, Hsu GW, Nguyen H, Mahrus S, Trinidad JC, Burlingame AL, Wells JA. (2012) “Quantitative Profiling of Caspase Cleaved Substrates Reveals Different Drug-Induced and Cell Type Patterns in Apoptosis.” Proc Natl Acad Sci USA. 109(31):12432-7. PMID: 22802652
PubMed link

Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. (2012) “Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.” Mol Cell Proteomics (8):215-29. PMID: 22645316
PubMed link

Agard NJ, Mahrus S, Trinidad JC, Lynn A, Burlingame AL, Wells JA. (2012) “Global kinetic analysis of proteolysis via quantitative targeted proteomics.” Proc Natl Acad Sci USA. 109(6):1913-8. PMID: 22308409
PubMed link

Medzihradsky KF, Trinidad JC. (2012) “Unusual Fragmentation of Pro-Ser/Thr-Containing Peptides Detected in Collision-Induced Dissociation Spectra.” Journal of the American Society for Mass Spectrometry 23(4):602-7. PMID: 21952759
PubMed link

Curtis PD, Quardokus EM, Lawler ML, Guo X, Klein D, Chen JC, Arnold RJ, Brun YV. (2012) “The scaffolding and signaling functions of a localization factor impact polar development” Mol. Microbiol. 84, 712-735. PMID: 22512778
PubMed link

Yang Y, Li Z, Mo W, Ambadipudi R, Arnold RJ, Hrncirova P, Novotny MV, Georges E, Zhang JT. (2012) “Human ABCC1 interacts and colocalizes with ATP synthase alpha, revealed by interactive proteomics analysis” J. Proteome Res. 11, 1364-1372. PMID: 22188235
PubMed link

Carrasco MA, Buechler SA, Arnold RJ, Sformo T, Barnes BM, Duman JG. (2012) “Investigating the deep supercooling ability of an Alaskan beetle, Cucujus clavipes puniceus, via high throughput proteomics” J. Proteomics 75, 1220-1234. PMID: 22094879
PubMed link

Cooper BS; Hammad LA; Fisher NP; Karty JA; Montooth KL. (2012) “A variable thermal environment selectively favors increased cellular plasticity” Evolution 66(6):1976-84. PMID: 22671561
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Cheng Z; Wu J; Setterdahl A; Reddie K; Carroll K; Hammad LA; Karty JA; Bauer CE. (2012) “Activity of the tetrapyrrole regulator CrtJ is controlled by oxidation of a redox active cysteine located in the DNA binding domain” Mol. Microbiol. 85, 734-746. PMID: 22715852
PubMed link

2011

Lau EK, Trester-Zedlitz M, Trinidad JC, Kotowski SJ, Krutchinsky AN, Burlingame AL, von Zastrow M. (2011) “Quantitative Encoding of the Effect of a Partial Agonist on Individual Opioid Receptors by Multisite Phosphorylation and Threshold Detection” Science Signaling 4 (185). PMID: 21868358
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Baker PR, Trinidad JC, Chalkley RJ (2011) “ Modification site localization scoring integrated into a search engine.” Molecular & Cell Proteomics 10(7):M111.008078. PMID: 21490164
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Tan Y, Arnold RJ, Luo ZQ. (2011) “Legionella pneumophila regulates the small GTPase Rab1 activity by reversible phosphorylcholination” Proc. Natl. Acad. Sci. USA 108, 21212-21217. PMID: 22158903
PubMed link

Liu X, Li YF, Bohrer BC, Arnold RJ, Radivojac P, Tang H, Reilly JP. (2011) “Investigation of VUV Photodissociation Propensities Using Peptide Libraries” Int. J. Mass Spectrom. 308, 142-154. PMID: 22125417
PubMed link

Carrasco MA, Buechler SA, Arnold RJ, Sformo T, Barnes BM, Duman JG.  (2011) “Elucidating the Biochemical Overwintering Adaptations of Larval Cucujus clavipes puniceus, a Nonmodel Organism, via High Throughput Proteomics” J. Proteome Res. 10, 4634-4646. PMID: 21923194
PubMed link

Li S, Arnold RJ, Tang H, Radivojac P. (2011) “On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction” Anal. Chem. 83, 790-796. PMID: 21175207
PubMed link

Sari Y, Segu ZM, Youssef AA, Karty JA, Isailovic D. (2011) “Neuroprotective peptide ADNF-9 in fetal brain of C57BL/6 mice exposed prenatally to alcohol” J. Biomed. Sci. (London, U. K.) 18:77. PMID: 22017746
PubMed link

Hammad LA, Cooper BS, Fisher NP, Montooth KL, Karty JA. (2011) “Profiling and quantification of Drosophila melanogaster lipids using liquid chromatography/mass spectrometry” Rapid Commun. Mass Spectrom. 25:2959-2968. PMID: 21913275
PubMed link

2010

David DC, Ollikainen N, Trinidad JC, Cary MP, Burlingame AL, Kenyon C. (2010) “Widespread protein aggregation as an inherent part of aging in C. elegans.” PLoS Biology 8(8): :e1000450. PMID: 20711477
PubMed link

Li YF, Arnold RJ, Tang H, Radivojac P. (2010) “The Importance of Peptide Detectability for Protein Identification, Quantification, and Experimental Design in MS/MS Proteomics” J. Proteome Res. 9, 6288-6297. PMID: 21067214
PubMed link

Bohrer BC, Li YF, Reilly JP, Clemmer DE, DiMarchi RD, Radivojac P, Tang H, Arnold RJ. (2010) “Combinatorial libraries of synthetic peptides as a model for shotgun proteomics” Anal. Chem. 82, 6559-6568. PMID: 20669997
PubMed link

Sari Y; Hammad LA; Saleh MS; Rebec GA; Mechref Y. (2010) “Alterations in selective neurotransmitters in fetal brains of prenatally alcohol-treated 7BL/6 mice: Quantitative analysis using liquid chromatography/tandem mass spectrometry” Int. J. Devl. Neuroscience 28, 263. PMID: 20123123
PubMed link

Hammad LA; Derryberry DZ; Jmeian Y; Mechref Y. (2010) “Quantification of monosaccharides through multiple-reaction monitoring liquid chromatography/mass spectrometry using an aminopropyl column” Rapid Commun. Mass Spectrom. 24(11) 1565-74. PMID: 20486252
PubMed link

Segu ZM; Hammad LA; Mechref Y. (2010) “Rapid and efficient glycoprotein identification through microwave-assisted enzymatic digestion” Rapid Commun. Mass spectrum. 24, 3461-3465. PMID: 21072803
PubMed link

2009

Beltrao P, Trinidad JC, Fiedler D, Toguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ. (2009) “Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species” PLoS Biology 7(6): e1000134. PMID: 19547744
PubMed link

Fernandez F, Trinidad JC, Blank M, Feng DD, Burlingame AL, Garner CC. (2009) "Normal protein composition of synapses in Ts65Dn mice: a mouse model of Down syndrome." Journal of Neurochemistry 110(1):157-69. PMID: 19453946
PubMed link

Zhang W, St-Gelais F, Grabner CP, Trinidad JC, Sumioka A, Morimoto-Tomita M, Kim KS, Straub C, Burlingame AL, Howe JR, Tomita S. (2009) "A transmembrane accessory subunit that modulates kainate-type glutamate receptors." Neuron 61(3): 385-396. PMID: 19217376
PubMed link

Thalhammer A, Trinidad JC, Burlingame AL, Schoepfer R. (2009) "Densin-180: revised membrane topology, domain structure and phosphorylation status." Journal of Neurochemistry 109(2): 297-302. PMID: 19187442
PubMed link

Ma Z, Cowart DM, Ward BP, Arnold RJ, DiMarchi RD, Zhang L, George GN, Scott RA, Giedroc DP. (2009) “Unnatural amino acid substitution as a probe of the allosteric coupling pathway in a mycobacterial Cu(I) sensor” J. Am. Chem. Soc. 131, 18044-18045. PMID: 19928961
PubMed link

Li YF, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H. (2009) “A Bayesian approach to protein inference problem in shotgun proteomics” J. Comput. Biol. 16, 1183-1193. PMID: 19645593
PubMed link

Li Y, Weitzel CS, Arnold RJ, Oakley MG. (2009) “Identification of interacting regions within the coiled coil of the Escherichia coli structural maintenance of chromosomes protein MukB” J. Mol. Biol. 391, 57-73. PMID: 19482037
PubMed link

Barendt SM, Land AD, Sham LT, Ng WL, Tsui HC, Arnold RJ, Winkler ME. (2009) “Influences of Capsule on the Cell Shape and Chaining of Wild-Type and pcsB Mutants of Serotype 2 Streptococcus pneumonia” J. Bacteriol. 191, 3024-3040. PMID: 19270090
PubMed link

Parrott MM, Sitarski SA, Arnold RJ, Picton LK, Hill RB, Mukhopadhyay S. (2009) “Role of Conserved Cysteines in The Alphavirus E3 Protein” J. Virology 83, 2584-2591. PMID: 19109378
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Hammad LA, Wu G, Saleh MM, Klouckova I, Dobrolecki LE, Hickey RJ, Schnaper L, Novotny MV, Mechref Y. (2009) “Elevated levels of hydroxylated phosphocholine lipids in the blood serum of breast cancer patients” Rapid Commun. Mass Spectrom. 23, 863. PMID: 19224569
PubMed link

Hammad LA, Saleh MM, Novotny MV, Mechref Y. (2009) “Monosaccharide compositional analysis of glycoproteins using multiple-reaction monitoring liquid chromatography mass spectrometry” J. Am. Soc. Mass Spectrom. 20, 1224. PMID: 19318280
PubMed link

Hammad LA, Neely M, Bridge B, Mechref Y. (2009) “Fast liquid chromatography separation and multiple-reaction monitoring mass spectrometric detection of neurotransmitters” J. Sep. Sci. 32, 2369. PMID: 19569096
PubMed link

2008

Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. (2008) “Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini.” Cell 134(4): 868-876. PMID: 18722006
PubMed link

Trinidad JC, Thalhammer A, Specht CG, Lynn AJ, Baker PR, Schoepfer R, Burlingame AL. (2008) “Quantitative Analysis of Synaptic Phosphorylation and Protein Expression.” Molecular & Cellular Proteomics 7(4): 684-696. PMID: 18056256
PubMed link

Saha S, Harrison SH, Shen C, Tang H, Radivojac P, Arnold RJ, Zhang X, Chen JY. (2008) “HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals” BMC Medical Genomics 1, 12. PMID: 18439290
PubMed link

Alves P, Arnold RJ, Clemmer DE, Li Y, Reilly JP, Sheng Q, Tang H, Xun Z, Zeng R, Radivojac P. (2008) “Fast and accurate identification of semi-tryptic peptides in shotgun proteomics” Bioinformatics  24, 102-109. PMID: 18033797
PubMed link

2007 and earlier

Olsen O, Funke L, Long JF, Fukata M, Kazuta T, Trinidad JC, Moore KA, Misawa H, Welling PA, Burlingame AL, Zhang M, Bredt DS. (2007) “Renal defects associated with improper polarization of the CRB and DLG polarity complexes in MALS-3 knockout mice.” Journal of Cell Biology 179(1) 151-64. PMID: 17923534
PubMed link

Hirsch J, Hansen KC, Sapru A, Frank JA, Chalkley RJ, Fang X, Trinidad JC, Baker P, Burlingame AL, Matthay MA. (2007) “Impact of low and high tidal volumes on the rat alveolar epithelial type II cell proteome.” American Journal of Respiratory and Critical Care Medicine 175 1006-1013. PMID: 17363773
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Vosseller K, Trinidad JC, Chalkley R, Specht CG, Thalhammer A, Lynn AJ, Snedecor AO, Guan S, Medzihradszky KF, Maltby D, Schoepfer R, Burlingame AL. (2006) “O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry.” Molecular & Cellular Proteomics 5(5) 923-934. PMID: 16452088
PubMed link

Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL. (2006) “Comprehensive Identification of Phosphorylation Sites in Postsynaptic Density Preparations.” Molecular & Cellular Proteomics 5(5) 914-922. PMID: 16452087
PubMed link

Olsen O, Moore KA, Fukata M, Kazuta T, Trinidad JC, Kauer FW, Streuli M, Misawa H, Burlingame AL, Nicoll RA, Bredt DS. (2005) “Neurotransmitter Release Regulated by a MALS / Liprin-α Presynaptic Complex.” Journal of Cell Biology 170(7) 1127-1134. PMID: 16186258
PubMed link

Fukata Y, Tzingounis AV, Trinidad JC, Fukata M, Burlingame AL, Nicoll RA, Bredt DS (2005) “Molecular Constituents of Neuronal AMPA Receptors.” Journal of Cell Biology 169(3) 399-404. PMID: 15883194
PubMed link

Trinidad JC, Thalhammer A, Specht CG, Schoepfer R, Burlingame AL. (2005) “Phosphorylation State of Postsynaptic Density Proteins.” Journal of Neurochemistry 92(6) 1306-16. PMID: 15748150
PubMed link

Vosseller K, Hansen KC, Chalkley RJ, Trinidad JC, Wells L, Hart GW, Burlingame AL. (2005) “Quantitative Analysis of Both Protein Expression and Serine / Threonine Post-translational Modifications Through Stable Isotope Labeling with Dithiothreitol.” Proteomics 5(2) 388-98. PMID: 15648052
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Trinidad JC, Cohen JB. (2004) “Neuregulin Inhibits Acetylcholine Receptor Aggregation in Myotubes.” Journal of Biological Chemistry 279(30) 31622-8. PMID: 15155732
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Chiara DC, Trinidad JC, Wang D, Ziebell MR, Sullivan D, Cohen JB. (2003) “Identification of Amino Acids in the Nicotinic Acetylcholine Receptor Agonist Binding Site and Ion Channel Photolabeled by 4-[(3-trifluoromethyl)-3H-diazirin-3-yl] benzoylcholine, a Novel Photoaffinity Antagonist.” Biochemistry 42(2) 271-83. PMID: 12525154
PubMed link

Trinidad JC, Fischbach GD, Cohen JB. (2000) “The Agrin/MuSK Signaling Pathway is Spatially Segregated from the Neuregulin/erbB Receptor Signaling Pathway at the Neuromuscular Junction.” Journal of Neuroscience 20(23) 8762-8770. PMID: 11102484
PubMed link