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Chen G, Zhang Y, Trinidad JC, Dann C 3rd. Distinguishing Sulfotyrosine Containing Peptides from their Phosphotyrosine Counterparts Using Mass Spectrometry.

J Am Soc Mass Spectrom. 2018 Jan 8.


Peng T, Nagy G, role="region" aria-label="content"Trinidad JC, Jackson JM, Pohl NLB. A High-Throughput Mass-Spectrometry-Based Assay for Identifying the Biochemical Functions of Putative Glycosidases. Chembiochem. 2017 Dec 5;18(23):2306-2311. PMCID: PMC5716848

DeHaan H, McCambridge A, Armstrong B, Cruse C, Solanki D, Trinidad JC, Arkov AL, Gao M. An in vivo proteomic analysis of the Me31B interactome in Drosophila germ granules. FEBS Lett. 2017 Nov;591(21):3536-3547.

Peng H, Zhang Y, Palmer LD, Kehl-Fie TE, Skaar EP, Trinidad JC, Giedroc DP. Hydrogen Sulfide and Reactive Sulfur Species Impact Proteome S-Sulfhydration and Global Virulence Regulation in Staphylococcus aureus. ACS Infect Dis. 2017 Oct 13;3(10):744-755.

Yan J, Beattie TR, Rojas AL, Schermerhorn K, Gristwood T, Trinidad JC, Albers SV, Roversi P, Gardner AF, Abrescia NGA, Bell SD. (2017) Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme. Nat Commun. 2017 May 2;8:15075. PMCID: PMC5418573

Shimizu T, Shen J, Fang M, Zhang Y, Hori K, Trinidad JC, Bauer CE, Giedroc DP, Masuda S. (2017) Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis. Proc Natl Acad Sci U S A. Feb 14. pii: 201614133. PMCID: PMC5338557

Lechler MC, Crawford ED, Groh N, Widmaier K, Jung R, Kirstein J, Trinidad JC, Burlingame AL, David DC. (2017) Reduced Insulin/IGF-1 Signaling Restores the Dynamic Properties of Key Stress Granule Proteins during Aging. Cell Rep. Jan 10;18(2):454-467. PMCID: PMC5263236

Lisher JP, Tsui HT, Ramos-Montañez S, Hentchel KL, Martin JE, Trinidad JC, Winkler ME, Giedroc DP. (2017) Biological and Chemical Adaptation to Endogenous Hydrogen Peroxide Production in Streptococcus pneumoniae D39. mSphere. Jan 4;2(1). pii: e00291-16. PMCID: PMC5214746

Ramsey J, Renzi EC, Arnold RJ, Trinidad JC, Mukhopadhyay S. (2017) Palmitoylation of Sindbis Virus TF Protein Regulates Its Plasma Membrane Localization and Subsequent Incorporation into Virions. J Virol. Jan 18;91(3). pii: e02000-16. PMCID: PMC5244351


Zhu F, Clemmer DE, Trinidad JC. (2016) Characterization of lectin binding affinities via direct LC-MS profiling: implications for glycopeptide enrichment and separation strategies. Analyst. Dec 19;142(1):65-74.

Xu Y, Gristwood T, Hodgson B, Trinidad JC, Albers SV, Bell SD. (2016) Archaeal orthologs of Cdc45 and GINS form a stable complex that stimulates the helicase activity of MCM. Proc Natl Acad Sci U S A. Nov 22;113(47):13390-13395 PMCID: PMC5127375

Shen J, Peng H, Zhang Y, Trinidad JC, Giedroc DP. (2016) Staphylococcus aureus sqr Encodes a Type II Sulfide:Quinone Oxidoreductase and Impacts Reactive Sulfur Speciation in Cells. Biochemistry. Nov 29;55(47):6524-6534. PMCID: PMC5423654

Cheng H, Burroughs-Garcia J, Birkness JE, Trinidad JC, Deans MR. (2016) Disparate Regulatory Mechanisms Control Fat3 and P75NTR Protein Transport through a Conserved Kif5-Interaction Domain. PLoS One. Oct 27;11(10):e0165519. PMCID: PMC5082931


Pirinelli AL, Trinidad JC, Pohl NLB. (2015) Introducing Students to Protein Analysis Techniques: Separation and Comparative Analysis of Gluten Proteins in Various Wheat Strains. J Chem Educ. Nov;93(2):33-334.

Zhu F, Trinidad JC, Clemmer DE. (2015) Glycopeptide Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques. J Am Soc Mass Spectrom. Jul;26(7):1092-102. PMCID: PMC4475505

Morris M, Knudsen GM, Maeda S, Trinidad JC, Ioanoviciu A, Burlingame AL, Mucke L. (2015) Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice. Nat Neurosci. Aug;18(8):1183-9.

Zhu F, Glover MS, Shi H, Trinidad JC, Clemmer DE. (2015) Populations of Metal-Glycan Structures Influence MS Fragmentation Patterns. J Am Soc Mass Spectrom. 26(1):25-35. PMCID: PMC4276451


Pekkurnaz G, Trinidad JC, Wang X, Kong D, Schwarz TL. (2014) Glucose regulates mitochondrial motility via Milton modification by O-GlcNAc transferase. Cell. 158(1):54-68. PMCID: PMC4224014


Trinidad JC, Schoepfer R, Burlingame AL, Medzihradszky KF. (2013) N- and O-glycosylation in the murine synaptosome. Mol Cell Proteomics. 12(12):3474-88. PMCID: PMC3861701

Gautam V, Trinidad JC, Rimerman RA, Costa BM, Burlingame AL, Monaghan DT. (2013) Nedd4 is a specific E3 ubiquitin ligase for the NMDA receptor subunit GluN2D. Neuropharmacology. 74:96-107. PMCID: PMC3855079

Liu W, Baker SS, Trinidad JC, Burlingame AL, Baker RD, Forte JG, Virtuoso LP, Egilmez NK, Zhu L. (2013) Inhibition of lysosomal enzyme activities by proton pump inhibitors. J Gastroenterol. 48(12):1343-52.

Trinidad JC, Thalhammer A, Burlingame AL, Schoepfer R. (2013) Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins. Mol Cell Proteomics. 12(1):29-41. PMCID: PMC3536907


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. PMCID: PMC3412957

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. PMCID: PMC:3412033

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. (2012) Trk Activation of the ERK1/2 Kinase Pathway Stimulates Intermediate Chain Phosphorylation and Recruits Cytoplasmic Dynein to Signaling Endosomes for Retrograde Axonal Transport. J Neurosci. 32(44):15495-510. PMCID: PMC:3500848

Medzihradszky KF, Trinidad JC. (2012) Unusual fragmentation of Pro-Ser/Thr-containing peptides detected in collision-induced dissociation spectra. J Am Soc Mass Spectrom. 23(4):602-7. PMCID: PMC:3384711

Just S, Illing S, Trester-Zedlitz M, Lau EK, Kototowski SJ, Miess E, Mann A, Doll C, Trinidad JC, Burlingame AL, von Zastrow M, Schulz S. (2012) Differentiation of Opioid Drug Effects by Hierarchical Multi-site Phosphorylation. Mol Pharmacol. 83(3):633-9. PMCID: PMC3583494.

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. PMCID: PMC:3277568

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

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

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

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

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


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

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

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

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

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

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

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

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


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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

Trinidad JC, Cohen JB. (2004) “Neuregulin Inhibits Acetylcholine Receptor Aggregation in Myotubes.” Journal of Biological Chemistry 279(30) 31622-8. PMID: 15155732

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

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