Research

Introduction

Our lab research centers on cellular signaling and the use of advanced quantitative proteomics to uncover the molecular mechanisms underlying immune cell function and cancer. Over the past decade, our laboratory has developed and applied cutting-edge mass spectrometry workflows to analyze complex phosphorylation networks, enabling precise identification of regulatory pathways. Our current work focuses on T cell receptor and CAR T cell signaling, with particular emphasis on defining phosphorylation-dependent networks that control T cell activation, feedback regulation, and pathway crosstalk, and on determining how CAR design reshapes signaling in both effector and target cells. By integrating biochemical, molecular, and computational approaches with state-of-the-art LC-MS phosphoproteomic analysis, we aim to identify signaling mechanisms that govern immune responses and influence the efficacy, specificity, and safety of immune-based therapies for cancer and other human diseases.

Proteomics-guided dissection of CAR T-induced signaling in targets.

We use state-of-the-art quantitative phosphoproteomics to understand how CAR T cells alter signaling in both effector and target cells. By developing bidirectional coculture workflows that assign phosphorylation events to their cell of origin, we have mapped CAR-specific signaling networks, uncovered suppression of target-cell pathways in some settings, and shown that certain CAR designs can induce pro-growth signaling in tumor targets. This work provides critical mechanistic insight into how CAR structure shapes therapeutic responses and helps identify strategies to engineer safer, more effective cancer immunotherapies.

Our publications in this Area

  1. A. Callahan, R. Puterbaugh, T. Ro, X. Zhang, X. Su, A. Salomon. (2026). “Phosphoproteomic analysis of successive Jurkat CD19-CAR generations reveals TCRζ-driven signalling.” Cell. Signal., 138:112204. doi:10.1016/j.cellsig.2025.112204.

  2. A. Callahan, S.S. Trychanh, T. Ro, A. Mojumdar, A.R. Salomon*. (2026). “Phosphotyrosine proteomics reveals novel Zap70 and Itk pathway targets downstream of TCR and CAR in Jurkat T cells.” Sci. Rep., in press. doi:10.1038/s41598-026-47234-x. (*corresponding author)

  3. A. Callahan, X. Zhang, A. Wang, A. Mojumdar, L. Zeng, X. Su*, A. Salomon*. (2025). “CSF1R-CAR T cells induce CSF1R signaling and can promote cancer cell growth.” Sci. Signal., 18(913):eadv4112. doi:10.1126/scisignal.adv4112. (*corresponding authors)

  4. A. Griffith, K. Callahan, N. King, Q. Xiao, X. Su, A. Salomon. (2022). “SILAC phosphoproteomics reveals unique signaling circuits in CAR-T cells and the inhibition of B cell-activating phosphorylation in target cells.” J. Proteome Res., 21(2):395–409. PMCID: PMC8830406.

Quantitative Dissection of Proximal TCR Signaling Networks

Our laboratory has helped define how proximal T cell receptor (TCR) signaling is organized through feedback control, pathway crosstalk, and phosphotyrosine network regulation. Using quantitative phosphoproteomics and complementary biochemical approaches, we have identified new signaling proteins and phosphosites, revealed dynamic feedback mechanisms involving SLP-76, ZAP-70, Vav1, PLC-γ1, ERK, and key phosphatases, and clarified how these pathways shape T cell activation thresholds and signaling output. This work has advanced the field from static pathway models toward a systems-level understanding of how T cells balance sensitivity with control. Because these regulatory mechanisms influence immune activation in cancer, infection, and autoimmune disease, they provide an important foundation for understanding immune dysfunction and for developing strategies to therapeutically modulate T cell responses.

Our publications in this Area

    1. A. Callahan, A. Mojumdar, M. Hu, A. Wang, A. Griffith, N. Huang, X. Chua, N. Mroz, R. Puterbaugh, S. Reilly, A. Salomon. (2025). “The phosphatases TCPTP, PTPN22, and SHP1 play unique roles in T cell phosphotyrosine maintenance and feedback regulation of the TCR.” Sci. Rep., 15:27747. PMCID: PMC12311025.

    2. X. Chua, A. Salomon. (2021). “Ovalbumin antigen-specific activation of human T cell receptor closely resembles soluble antibody stimulation as revealed by BOOST phosphotyrosine proteomics.” J. Proteome Res., 20(6):3330–3344. PMCID: PMC8626127.

    3. X. Chua, T. Aballo, W. Elnemer, M. Tran, A. Salomon. (2021). “Quantitative interactomics of Lck-TurboID in living human T cells unveils T cell receptor stimulation-induced proximal Lck interactors.” J. Proteome Res., 20(1):715–726. PMCID: PMC7962135.

    4. W. Lo, N.H. Shah, N. Ahsan, V. Horkova, O. Stepanek, A.R. Salomon, J. Kuriyan, A. Weiss. (2018). “Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT.” Nat. Immunol., 19(7):733–741. PMCID: PMC6202249.

    5. J. Belmont, T. Gu, A. Mudd, A.R. Salomon. (2017). “A PLC-γ1 feedback pathway regulates Lck substrate phosphorylation at the T-cell receptor and SLP-76 complex.” J. Proteome Res., 16(8):2729–2742. PMCID: PMC5549626.

    6. Y. Helou, A. Petrashen, A. Salomon. (2015). “Vav1 regulates T cell activation through a feedback mechanism and crosstalk between the T cell receptor and CD28.” J. Proteome Res., 14:2963–2975. PMCID: PMC4490005.

    7. H. Goodfellow, M. Frushicheva, Q. Ji, D. Cheng, A. Cantor, J. Kuriyan, A. Chakraborty*, A. Salomon*, A. Weiss*. (2015). “Zap70 catalytic activity regulates basal signaling and negative feedback of the proximal TCR signaling pathway.” Sci. Signal., 8(377):ra49. PMCID: PMC4445242. (*corresponding authors)

    8. Q. Ji, Y. Ding, A. Salomon. (2015). “SRC homology 2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76) N-terminal tyrosine residues regulate a dynamic signaling equilibrium involving feedback of proximal T-cell receptor signaling.” Mol. Cell. Proteomics, 14:30–40. PMCID: PMC4288261.

    9. Y.A. Helou, V. Nguyen, S.P. Beik, A.R. Salomon. (2013). “ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.” PLoS One, 8(7):e69641. PMCID: PMC3714263.

    10. L. Cao, Y. Ding, N. Hung, K. Yu, A. Ritz, B.J. Raphael, A.R. Salomon. (2012). “Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells.” PLoS One, 7(10):e46725. PMCID: PMC3469622.

    11. V. Nguyen, L. Cao, J.T. Lin, N. Hung, A. Ritz, K. Yu, R. Jianu, S.P. Ulin, B.J. Raphael, D.H. Laidlaw, L. Brossay, A.R. Salomon. (2009). “A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation.” Mol. Cell. Proteomics, 8(11):2418–2431. PMCID: PMC2773711.

Advancing Quantitative Phosphoproteomics for Immune Signaling

Our laboratory has helped advance quantitative phosphoproteomics into a powerful framework for systems-level analysis of immune signaling. Early work from our group was among the first to demonstrate that mass spectrometry could be used to map tyrosine phosphorylation pathways on a broad scale in human cells, moving the field beyond one-protein-at-a-time studies toward global, quantitative analysis of signaling networks. We have since continued to expand the depth, reproducibility, and interpretability of these methods through improved phosphopeptide enrichment, optimized LC-MS workflows, BOOST-based strategies for deeper phosphotyrosine characterization, quantitative interactomics in living T cells, and recent evaluation of high-capacity first-pass desalting approaches that improve sample handling and support robust phosphoproteomics workflows. Together, these advances have strengthened the technical foundation for discovering signaling mechanisms in T cells and other immune systems and have provided broadly useful tools for studying cancer, infection, and immune-mediated disease.

Our publications in this Area

  1. A. Callahan, A. Mojumdar, A.R. Salomon, N.A. DaSilva*. (2025). “Evaluating first-pass, high protein capacity desalting techniques for phosphoproteomics applications.” bioRxiv, 2025.06.03.657744. doi:10.1101/2025.06.03.657744. PMCID: PMC12157578. (*corresponding author) 

  2. A. Callahan, X. Chua, A. Griffith, T. Hildebrandt, G. Fu, M. Hu, R. Wen, A. Salomon. (2024). “Deep phosphotyrosine characterization of primary murine T cells using broad spectrum optimization of selective triggering.” Proteomics, 24:e2400106. PMCID: PMC11684461.

  3. X. Chua, A. Salomon. (2021). “Quantitative interactomics of Lck-TurboID in living human T cells unveils T cell receptor stimulation-induced proximal Lck interactors.” J. Proteome Res., 20(1):715–726. PMCID: PMC7962135.

  4. X. Chua, T. Mensah, T. Aballo, S. Mackintosh, R. Edmondson, A. Salomon. (2020). “Tandem mass tag approach utilizing pervanadate BOOST channels delivers deeper quantitative characterization of the tyrosine phosphoproteome.” Mol. Cell. Proteomics, 19:730–743. PMCID: PMC7124467.

  5. N. Ahsan, A. Salomon. (2017). “Quantitative phosphoproteomic analysis of T-cell receptor signaling.” Methods Mol. Biol., 1584:369–382. PMCID: PMC5573147.

  6. N. Ahsan, J. Belmont, Z. Chen, J. Clifton, A. Salomon. (2017). “Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction.” J. Proteomics, 165:69–74. PMCID: PMC5542054.

  7. Nühse, T., K. Yu, A. Salomon. (2007). “Isolation of phosphopeptides by immobilized metal ion affinity chromatography.” Curr. Protoc. Mol. Biol., Chapter 18:Unit 18.13.

  8. S.B. Ficarro, A.R. Salomon, L.M. Brill, D.E. Mason, M. Stettler-Gill, A. Brock, E.C. Peters. (2005). “Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites.” Rapid Commun. Mass Spectrom., 19(1):57–71.

  9. L.M. Brill, A.R. Salomon, S.B. Ficarro, M. Mukherji, M. Stettler-Gill, E.C. Peters. (2004). “Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry.” Anal. Chem., 76(10):2763–2772.

  10. A. Salomon, S. Ficarro, L. Brill, A. Brinker, Q. Phung, C. Ericson, K. Sauer, A. Brock, D. Horn, P. Schultz, E. Peters. (2003). “Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry.” Proc. Natl. Acad. Sci. U.S.A., 100(2):443–448. PMCID: PMC141014.

Computational Platforms Enabling Quantitative Proteomics and Network Analysis

Our laboratory has helped develop computational tools that make large-scale proteomics more rigorous, interpretable, and biologically informative. This work includes platforms for automated proteomic data processing, statistical validation of tandem mass spectra, relational database organization of quantitative datasets, discovery of phosphorylation motifs, and visualization of phosphoproteomic data in the context of signaling pathways and protein interaction networks. Together, these efforts have expanded the analytical infrastructure needed to move from raw mass spectrometry data to biological insight. More recent studies have integrated these computational advances with quantitative phosphoproteomic workflows to interpret complex T cell signaling responses at the systems level. These tools have helped advance the field by enabling deeper, more reproducible, and more mechanistic analysis of signaling networks relevant to immunology, cancer, and human disease.

Our publications in this Area

  1. X. Chua, A. Salomon. (2021). “Ovalbumin antigen-specific activation of human T cell receptor closely resembles soluble antibody stimulation as revealed by BOOST phosphotyrosine proteomics.” J. Proteome Res., 20(6):3330–3344. PMCID: PMC8626127.

  2. K. Yu, A. Salomon. (2010). “HTAPP: High-throughput autonomous proteomic pipeline.” Proteomics, 10:2113–2122.

  3. R. Jianu, K. Yu, L. Cao, V. Nguyen, A. Salomon, D. Laidlaw. (2010). “Visual integration of quantitative proteomic data, pathways and protein interactions.” IEEE Trans. Vis. Comput. Graph., 16(4):609–620. PMCID: PMC2872116.

  4. A. Ritz, G. Shakhnarovich, A. Salomon, B. Raphael. (2009). “Discovery of phosphorylation motif mixtures in phosphoproteomics data.” Bioinformatics, 25(1):14–21.

  5. K. Yu, A. Sabelli, L. DeKeukelaere, R. Park, S. Sindi, C.A. Gatsonis, A. Salomon. (2009). “Integrated platform for manual and high-throughput statistical validation of tandem mass spectra.” Proteomics, 9(11):3115–3125.

  6. K. Yu, A. Salomon. (2009). “PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information.” Proteomics, 9(23):5350–5358.

Collaborative Applications of Quantitative Proteomics in Human Disease

Our laboratory has a strong track record of collaborative research that applies quantitative proteomics, phosphoproteomics, and signaling-network analysis to important problems across biomedicine. Working with investigators in cancer biology, immunology, metabolism, liver biology, and mitochondrial research, we have helped define signaling mechanisms that regulate tumor growth and metastasis, cancer stemness, adipose inflammation, hepatic signaling, and mitochondrial respiration and apoptosis. These studies illustrate the broad utility of proteomic approaches for uncovering mechanisms of human disease and reflect our lab’s role as a collaborative partner in translating complex signaling data into biological and biomedical insight.

Our publications in this Area

  1. M. Curtis, H. Kenny, B. Ashcroft, A. Mukherjee, A. Johnson, Y. Zhang, Y. Helou, R. Batlle, X. Liu, N. Gutierrez, X. Gao, S. Yamada, R. Lastra, A. Montag, N. Ahsan, J. Locasale, A. Salomon, A. Nebreda, E. Lengyel. (2019). “Fibroblasts mobilize tumor cell glycogen to promote proliferation and metastasis.” Cell Metab., 29:141–155. PMCID: PMC6326875.

  2. J. Wan, H. Kalpage, A. Vaishnav, J. Liu, I. Lee, G. Mahapatra, A. Turner, M. Zurek, Q. Ji, C. Moraes, M. Recanati, L. Grossman, A. Salomon, B. Edwards, M. Hüttemann. (2019). “Regulation of respiration and apoptosis by cytochrome c threonine 58 phosphorylation.” Sci. Rep., 9(1):15815. PMCID: PMC6825195.

  3. H.A. Kalpage, A. Vaishnav, J. Liu, A. Varughese, J. Wan, A.A. Turner, Q. Ji, M.P. Zurek, A.A. Kapralov, V.E. Kagan, J.S. Brunzelle, M.A. Recanati, L.I. Grossman, T.H. Sanderson, I. Lee, A.R. Salomon, B.F.P. Edwards, M. Hüttemann. (2019). “Serine-47 phosphorylation of cytochrome c in the mammalian brain regulates cytochrome c oxidase and caspase-3 activity.” FASEB J., 33(12):13503–13514. PMCID: PMC6894086.

  4. J. Li, B. Feng, Y. Nie, P. Jiao, X. Lin, M. Huang, R. An, Q. He, H.E. Zhou, A. Salomon, K.S. Sigrist, Z. Wu, S. Liu, H. Xu. (2018). “Sucrose nonfermenting-related kinase regulates both adipose inflammation and energy homeostasis in mice and humans.” Diabetes, 67(3):400–411. PMCID: PMC5828454.

  5. A.O. Adebayo Michael, N. Ahsan, V. Zabala, H. Francois-Vaughan, S. Post, K.E. Brilliant, A.R. Salomon, J.A. Sanders, P.A. Gruppuso. (2017). “Proteomic analysis of laser capture microdissected focal lesions in a rat model of progenitor marker-positive hepatocellular carcinoma.” Oncotarget, 8(16):26041–26056. PMCID: PMC5432236.

  6. A. Qadir, P. Ceppi, S. Brockway, C. Law, L. Mu, N. Khodarev, J. Kim, J. Zhao, W. Putzbach, A. Murmann, Z. Chen, W. Chen, X. Liu, A. Salomon, H. Liu, R. Weichselbaum, J. Yu, M. Peter. (2017). “CD95/Fas increases stemness in cancer cells by inducing a STAT1-dependent type I interferon response.” Cell Rep., 18(10):2373–2386. PMCID: PMC5474321.

  7. G. Mahapatra, A. Varughese, Q. Ji, I. Lee, J. Liu, A. Vaishnav, C. Sinkler, A.A. Kapralov, C.T. Moraes, T.H. Sanderson, T.L. Stemmler, L.I. Grossman, V.E. Kagan, J.S. Brunzelle, A.R. Salomon, B.F. Edwards, M. Hüttemann. (2017). “Phosphorylation of cytochrome c threonine 28 regulates electron transport chain activity in kidney: implications for AMP kinase.” J. Biol. Chem., 292(1):64–79. PMCID: PMC5217700.

  8. J.M. Boylan, A.R. Salomon, U. Tantravahi, P.A. Gruppuso. (2015). “Adaptation of HepG2 cells to a steady-state reduction in the content of protein phosphatase 6 (PP6) catalytic subunit.” Exp. Cell Res., 335(2):224–237. PMCID: PMC4485549.

  9. W. Wimuttisuk, M. West, B. Davidge, K. Yu, A. Salomon, J.D. Singer. (2014). “Novel Cul3 binding proteins function to remodel E3 ligase complexes.” BMC Cell Biol., 15:28. PMCID: PMC4107866.

  10. B. Feng, P. Jiao, Y. Helou, Y. Li, Q. He, M.S. Walters, A. Salomon, H. Xu. (2014). “Mitogen-activated protein kinase phosphatase 3 (MKP-3)-deficient mice are resistant to diet-induced obesity.” Diabetes, 63(9):2924–2934. PMCID: PMC4141371.

  11. B.D. DeNardo, M.P. Holloway, Q. Ji, K.T. Nguyen, Y. Cheng, M.B. Valentine, A. Salomon, R.A. Altura. (2013). “Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma.” PLoS One, 8(12):e82513. PMCID: PMC3859635.

  12. T.H. Sanderson, G. Mahapatra, P. Pecina, Q. Ji, K. Yu, C. Sinkler, A. Varughese, R. Kumar, M.J. Bukowski, R.N. Tousignant, A.R. Salomon, I. Lee, M. Hüttemann. (2013). “Cytochrome c is tyrosine 97 phosphorylated by neuroprotective insulin treatment.” PLoS One, 8(11):e78627. PMCID: PMC3818486.

  13. D.W. Lamming, G. Demirkan, J.M. Boylan, M.M. Mihaylova, T. Peng, J. Ferreira, N. Neretti, A. Salomon, D.M. Sabatini, P.A. Gruppuso. (2014). “Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2).” FASEB J., 28(1):300–315. PMCID: PMC3868844.

  14. Y. Li, Y. Nie, Y. Helou, G. Ding, B. Feng, H. Xu, A. Salomon, H. Xu. (2013). “Identification of sucrose non-fermenting-related kinase (SNRK) as a suppressor of adipocyte inflammation.” Diabetes, 62(7):2396–2409. PMCID: PMC3712026.

  15. G. Demirkan, A.R. Salomon, P.A. Gruppuso. (2012). “Phosphoproteomic analysis of liver homogenates.” Methods Mol. Biol., 909:151–163. PMCID: PMC3581044.

  16. X.M. O’Brien, K.E. Heflin, L.M. Lavigne, K. Yu, M. Kim, A.R. Salomon, J.S. Reichner. (2012). “Lectin site ligation of CR3 induces conformational changes and signaling.” J. Biol. Chem., 287(5):3337–3348. PMCID: PMC3270988.

  17. G. Demirkan, K. Yu, J.M. Boylan, A.R. Salomon, P.A. Gruppuso. (2011). “Phosphoproteomic profiling of in vivo signaling in liver by the mammalian target of rapamycin complex 1 (mTORC1).” PLoS One, 6(6):e21729. PMCID: PMC3125343.

  18. P. Agrawal, K. Yu, A.R. Salomon, J.M. Sedivy. (2010). “Proteomic profiling of Myc-associated proteins.” Cell Cycle, 9(24):4908–4921. PMCID: PMC3047814.

  19. J.A. Pezza, S.X. Langseth, R. Raupp Yamamoto, S.M. Doris, S.P. Ulin, A.R. Salomon, T.R. Serio. (2009). “The NatA acetyltransferase couples Sup35 prion complexes to the [PSI+] phenotype.” Mol. Biol. Cell, 20(3):1068–1080. PMCID: PMC2633373.

  20. H. Yu, I. Lee, A.R. Salomon, K. Yu, M. Hüttemann. (2008). “Mammalian liver cytochrome c is tyrosine-48 phosphorylated in vivo, inhibiting mitochondrial respiration.” Biochim. Biophys. Acta, 1777(7–8):1066–1071. PMCID: PMC2652845.

  21. I. Lee, A.R. Salomon, J.W. Doan, L.I. Grossman, M. Hüttemann. (2006). “New prospects for an old enzyme: mammalian cytochrome c is tyrosine-phosphorylated in vivo.” Biochemistry, 45(30):9121–9128.

  22. I. Lee, A.R. Salomon, S. Ficarro, I. Mathes, F. Lottspeich, L.I. Grossman, M. Hüttemann. (2005). “cAMP-dependent tyrosine phosphorylation of subunit I inhibits cytochrome c oxidase activity.” J. Biol. Chem., 280(7):6094–6100.

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