msDiaLogue
Resulting from an ongoing collaboration with UConn Statistical Consulting Services (SCS), we present msDiaLogue: a new R-based analysis tool designed for untargeted mass spectrometry-based proteomic datasets. msDiaLogue supports protein differential abundance analysis and a wide variety of visualization options for Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) datasets. For more information, visit the UConn SCS msDiaLogue Github. For in-depth descriptions of msDiaLogue processing steps including a full user guide plus relevant code for R beginners, visit our tutorial page: https://uconn-scs.github.io/msDiaLogue/
Featured Publications
We are compiling a list of publications that feature analytical experiments conducted in the UConn Proteomics & Metabolomics Facility. If your publication is missing, email the Facility Director to get yours included as well!
2023
Gillig, M.A., Brennick, C.A., George, M.M., Balsbaugh, J.L., Shcheglova, T.V., Mandoiu, I.I., Rosales, T., Baker, B.M, Srivastava, P.K., & Karandikar, S.H. CD8+ T cell-dependent antitumor activity in vivo of a mass spectrometry-identified neoepitope despite undetectable CD8+ immunogenicity in vitro. Jour of Immunology, 2023.
Kyle, K.E., Puckett, S.P., Mauricio Caraballo-Rodriguez, A., Rivera-Chavez, J., Samples, R.M., Earp, C.E., Raja, H.A., Pearce, C.J., Ernst, M., van der Hooft, J.J.J., Adam, M.E., Oberlies, N.H., Dorrestein, P.C., Klassen, J.L., & Balunas, M.J. Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma-derived metabolite cues. PNAS, 2023.
LaGree, T.J., Byrd, B.A., Quelle, R.M., Schofield, S.L., & Mok, W.W.K. Stimulating transcription in antibiotic-tolerant Escherichia coli sensitizes it to fluoroquinolone and nonfluoroquinolone topoisomerase inhibitors. Antimicrobial Agents & Chemotherapy, 2023.
Lipka, B.M., Honeycutt, D.S., Bassett, G.M., Kowal, T.N., Adamczyk, M., Cartnick, Z.C., Betti, V.M., Goldberg, J.M., & Wang, F. Ultra-rapid electrophilic cysteine arylation. JACS, 2023.
Liu, Q., Zhu, D., Li, N., Chen, S., Hu, L., Yu, J., & Xiong, Y. Regulation of LRRK2 mRNA stability by ATIC and its substrate AICAR through ARE-mediated mRNA decay in Parkinson’s disease. EMBO Journal, 2023.
Sakato-Antoku, M., Balsbaugh, J.L., King, S.M. N-Terminal Processing and Modification of Ciliary Dyneins. Cells, 2023.
Samples, R.M., Puckett, S.P., & Balunas, M.J. Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Visualization of Molecules from Complex Biological Samples. Analytical Chemistry, 2023.
Santorella, E., Balsbaugh, J.L., Ge, S., Saboori, P., Baker, D., & Pachter, J.S. Proteomic interrogation of the meninges reveals the molecular identities of structural components and regional distinctions along the CNS axis. Fluids Barriers CNS, 2023.
Schiller, H., Kouassi, J., Hong, Y., Rados, T., Kwak, J., DiLucido, A., Safer, D., Marchfelder, A., Pfeiffer, F., Bisson-Filho, A., Schulze, S., & Pohlschroder, M. Identification and characterization of structural and regulatory cell-shape determinants in Haloferax volcanii. bioRxiv, 2023.
Singh, U., Pawge, G., Rani, S., Hsiao, C-H.C., Wiemer, A.J., & Wiemer, D.F. Diester prodrugs of a phosphonate butyrophilin ligang display improved cell potency, plasma stability, and payload internalization. J Med Chem, 2023.
Ta, A., Ricci-Azevedo, R., Vasudevan, S.O., Wright, S.S., Kumari, P., Havira, M.S., Nair, M.S., Rathinam, V.A., & Vanaja, S.K. A bacterial autotransporter impairs innate immune responses by targeting the transcription factor TFE3. Nature Communications, 2023.
Voelkel-Meiman, K., Poppel, A.J., Liddle, J.C., Balsbaugh, J.L., & MacQueen, A.J. Proximity labeling reveals new insights into the relationships between meiotic recombination proteins in S. cerevisiae. bioRxiv, 2023.
2022
Bhattacharjee, M., Ivirico, J.L.E., Kan, H-M., Shah, S., Otsuka, T., Bordett, R., Barajaa, M., Nagiah, N., Pandey, R., Nair, L.S., and Laurencin, C.T. Injectable amnion hydrogel-mediated delivery of adipose-derived stem cells for osteoarthritis treatment. PNAS, 2022.
Caefer, D.M., Phan, N.Q, Liddle, J.C., Balsbaugh, J.L., O’Shea, J.P., Tzingounis, A.V., and Schwartz, D. The Okur-Chung Neurodevelopmental Syndrome Mutation CK2K198R Leads to a Rewiring of Kinase Specificity. Front Mol Biosci, 2022.
Karginov, T.A., Menoret, A.M., and Vella, A. Optimal CD8+ T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape. Nature Communications, 2022.
Karsmarski, O.P., Hawthorne, B.C., Cusano, A., LeVasseur, M.R., Wellington, I.J., McCarthy, M.B., Cote, M.P., and Mazzocca, A.D. Activated Serum Increases In Vitro Cellular Proliferation and Growth Factor Expression of Musculoskeletal Cells. Jour Clin Med, 2022.
Kraus, J.M., Giovannone, D., Rydzik, R., Balsbaugh, J.L., Moss, I.L., Schwedler, J.L., Bertrand, J.Y., Traver, D., Hankenson, K.D., Crump, J.G., and Youngstrom, D.W. Notch signaling enhances bone regeneration in the zebrafish mandible. Development, 2022.
Luxmi, R., Mains, R.E., Eipper, B.A., & King, S.M. Regulated processing and secretion of a peptide precursor in cilia. PNAS, 2022.
Reed, S.A., Balsbaugh, J., Li, X., Moore, T.E., Jones, A.K., Pillai, S.M., Hoffman, M.L., Govoni, K.E., and Zinn, S.A. Poor maternal diet during gestation alters offspring muscle proteome in sheep. Journal of Animal Sci, 2022.
Soh, H., Springer, K., Doci, K., Balsbaugh, J.L., and Tzingounis, A.V. KCNQ2 and KCNQ5 form heteromeric channels independent of KCNQ3. PNAS, 2022.
2021
Brennick, C.A., George, M.M., Moussa, M.R., Hagymasi, A.T., Al Seesi, S., Schceglova, T.V., Englander, R.P., Keller, G.L., Balsbaugh, J.L., Baker, B.M., Schietinger, A., Mandoui, I.I., and Srivastava, P.K. An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection. Jour Clin Investigation, 2021.
Caefer, D.M., Phan, N.Q., Liddle, J.C., Balsbaugh, J.L., O’Shea, J.P., Tzingounis, A.V., and Schwartz, D. The Okur-Chung Neurodevelopmental Syndrome (OCNDS) mutation CK2K198R Leads to a Rewiring of Kinase Specificity. bioRxiv Preprint, 2021.
Garcia Cruz, D., Giri, R.R., Gamiotea Turro, D., Balsbaugh, J.L., Adler, A.J., and Rodriguez, A. Lymphocyte Activation Gene-3 Regulates Dendritic Cell Metabolic Programing and T cell Priming Function. Jour of Immunology, 2021.
Luxmi, R., Mains, R.E., Eipper, B.A., King, S.M. Ciliary Generation of a Peptidergic Sexual Signal. bioRxiv Preprint, 2021.
Murphy, P.A., Jailkhani, N., Nicholas, S.A., Del Rosario, A.M., Balsbaugh, J.L., Begum, S., Kimble, A., and Hynes, R.O. Alternative Splicing of FN (Fibronectin) Regulates the Composition of the Arterial Wall Under Low Flow. Arteriosclerosis, Thrombosis, and Vascular Biology, 2021.
Luxmi, R., Mains, R.E., Eipper, B.A., King, S.M. Ciliary Generation of a Peptidergic Sexual Signal. bioRxiv Preprint, 2021.
Sinclair, A.N., Huynh, C.T., Sladewski, T.E., Zuromski, J.L., Ruiz, A.E., and de Graffenried, C.L. The Trypanosome brucei subpellicular microtubule array is organized into functionally discrete subdomains defined by microtubule associated proteins. PLoS Patholog, 2021.
2020
Agliano, F., Karlinsey, K.S., Ragazzi, M., Menoret, A., Vella, A.T. A benzimidazole inhibitor attenuates sterile inflammation induced in a model of systemic autoinflammation in female mice. Sci Reports, 2020.
Devarakonda, C.K.V., Shearier, E.R., Hu, C., Grady, J., Balsbaugh, J.L., Makari, J.H., Ferrer, F.A., and Shapiro, L.H. A Novel Urinary Biomarker Protein Panel to Identify Children with Ureteropelvic Junction Obstruction – A Pilot Study. Jour Pediatric Urology, 2020.
Gu, D., Zhang, Y., Wang, Q., and Zhou, X. S-nitrosylation-mediated activation of a histidine kinase represses the type 3 secretion system and promotes virulence of an enteric pathogen. Nature Communications, 2020.
Mara, A.B., Gavitt, T.D., Tullman, E.R., Geary, S.J., and Szczepanek, S.M. Lipid moieties of Mycoplasma pneumoniae lipoproteins are the causative factor of vaccine-enhanced disease. Vaccines, 2020.
Martin, I.J., Shih, K.C., Nieh, M.P., and Kasi, R.M. Templated Supramolecular Structures of Multichromic, Multiresponsive Perylene Diimide-Polydiacetylene Films. Macromolecules, 2020.
Nichols, F.C., Clark, R.B., Maciejewski, M.W., Provatas, A.A., Balsbaugh, J.L., Dewhirst, F.E., Smith, M.B., and Rahmlow, A. A Novel Phosphoglycerol Serine-Glycine Lipodipeptide of Prophryomonoas gingivalis is a TLR2 Ligand. Jour Lipid Research, 2020.
Podgorski, J., Calabrese, J., Alexandrescu, L., Jacobs-Sera, D., Pope, W., Hatfull, G., and White, S. Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins. Viruses, 2020.
Suria, A.M., Tan, K.C., Kerwin, A.H., Gitzel, L., Abini-Agbomson, L., Bertenshaw, J.M., Sewell, J., Nyholm, S.V., and Balunas, M.J. Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D’. mSphere, 2020.
2019
Foust, B.J., Li, J., Hsaio, C.C., Wiemer, D.F., and Wiemer, A.J. Stability and Efficiency of Mixed Aryl Phosphonate Prodrugs. ChemMedChem, 2019.
Kerwin, A.H., Gromek, S.M., Suria, A.M., Samples, R.M., Deoss, D.J., O’Donnell, K., Frasca, Jr., S., Sutton, D.A., Widerhold, N.P., Balunas, M.J., and Nyholm, S.V. Shielding the Next Generation: Symbiotic Bacteria from a Reproductive Organ Protect Bobtail Squid Eggs from Fungal Fouling. mBio, 2019.
Lentini, N.A., Hsaio, C.C., Crull, G.B., Wiemer, A.J., and Wiemer, D.F. Synthesis and Bioactivity of the Alanyl Phosphonamidate Stereoisomers Derived from a Butyrophilin Ligand. ACS Med Chem Lett, 2019.
Poe, M.M., Agabiti, S.S., Liu, C., Li, V., Teske, K.A., Hsaio, C.C., and Wiemer, A.J. Probing the Ligand-Binding Pocket of BTN3A1. J Med Chem, 2019.
Tetz, G., Tetz, V. Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma. Sci Reports, 2019.
Wang, L., Dietz, C., Zhou, F., Erfanzadeh, M., Zhu, Q., Smith, M.B., Yao, X. Treasure hunt for peptides with undefined chemical modifications: Proteomics identification of differential albumin adducts of 2-nitroimidazole-indocyanine green in hypoxic tumor. Jour Mass Spec, 2019.
2018
Lentini, N.A., Foust, B.J., Hsaio, C.C., Wiemer, A.J., and Wiemer, D.F. Phosphonamidate Prodrugs of a Butyrophilin Ligand Display Plasma Stability and Potent Vy9 Vg2 T Cell Stimulation. J Med Chem, 2018.
Lubner, J.M., Balsbaugh, J.L., Church, G.M., Chou, M.F., Schwartz, D. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. Curr Protoc Chem Biol, 2018.