Center for Biomarker
Discovery & Translation
Featured Publications
2025
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues
Li, Q. K., Lih, T. M., Clark, D. J., Chen, L., Schnaubelt, M., & Zhang, H. (2025). Nature Protocols, 20(2), 1184–1201.AUTO-SP: Automated sample preparation for analyzing proteins and protein modifications
Lih, T. M., Jiao, L., Chen, L., Woo, J., Wang, Y., & Zhang, H. (2025). Analytical Chemistry.Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct patterns and potential markers of progression
Wang, Y., Lih, T.-S. M., Lee, J. W., Ohtsuka, T., Hozaka, Y., Mino-Kenudson, M., Adsay, N. V., Luchini, C., Scarpa, A., Maker, A. V., Kim, G. E., Paulino, J., Chen, L., Woo, J., Jiao, L., Sun, Z., Goodman, D., Pflüger, M. J., Roberts, N. J., . . . Zhang, H., & Hruban, R. H. (2025). Cancer Cell, 43(2), 245–261.
2024
SPOT: spatial proteomics through on-site tissue-protein-labeling
Xu, Y., Lih, T. M., De Marzo, A. M., Li, Q. K., & Zhang, H. (2024). Nature Communications, 15, 9193.Improving glycoproteomic analysis workflow by systematic evaluation of glycopeptide enrichment, quantification, MS approach, and data analysis strategies
Sun, Z., Lih, T. M., Woo, J., Jiao, L., Hu, Y., Wang, Y., Liu, H., & Zhang, H. (2024). Analytical Chemistry, 96(50), 20042–20051.
2023
Integrated glycoproteomic characterization of clear cell renal cell carcinoma
Lih, T. M., Cho, K. C., Hu, Y.,... & Zhang, H. (2023). Cell Reports, 42(5), 112443.
2022
Sonication-assisted protein extraction improves proteomic analysis of FFPE tissue
Li, Q. K., Lih, T. M., Cho, K. C., Clark, D. J., & Zhang, H. (2022). Journal of Proteomics, 265, 104618.
2021
Proteogenomic characterization of pancreatic ductal adenocarcinoma
Cao, L., Huang, C., Cui Zhou, D.,... & Zhang, H. (2021). Cell, 184(19), 5031-5052.
2020
Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer
Hu, Y., Lih, T. M., Cho, K. C.,... & Zhang, H. (2020). Nature Communications, 11, 6139.
2019
Integrated proteogenomic characterization of clear cell renal cell carcinoma.
Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., … & Zhang, H. (2019). Cell, 179(4), 964–983.e31.Multiplexed targeted mass spectrometry-based assays for the quantification of N-glycopeptides in human serum
Cao, L., Lih, T. M., & Zhang, H. (2019). Analytical Chemistry, 91(16), 10543–10550.
2018
Reanalysis of global proteomic and phosphoproteomic data identified a large number of glycopeptides
Hu, Y., Shah, P., Clark, D. J., Ao, M., & Zhang, H. (2018). Analytical Chemistry, 90(13), 8065–8071.Mapping the O‐glycoproteome using site‐specific extraction of O‐linked glycopeptides (EXoO)
Yang, W., Ao, M., Hu, Y., Li, Q. K., & Zhang, H. (2018). Molecular Systems Biology, 14(11), e8486.
2017
Simultaneous quantification of N- and O-glycans using a solid-phase method
Yang, S., Hu, Y., Sokoll, L., & Zhang, H. (2017). Nature Protocols, 12(6), 1229–1244.Single-cell proteomic characterization of drug-resistant prostate cancer cells
Woo, J., Loycano, M. A., Amanullah, M., Qian, J., Amend, S. R., Pienta, K. J., & Zhang, H. (2017). Molecular & Cellular Proteomics, 16(10), 1766–1778.
2016
Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides
Sun, S., Shah, P., Toghi Eshghi, S., Yang, W., Trikannad, N., Höti, N., Chen, L., Chan, D. W., & Zhang, H. (2016). Nature Biotechnology, 34(1), 84–88.Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J. E., Zhou, J. Y., Petyuk, V. A., Chen, L., Ray, D., Sun, S., Yang, F., Chen, L., Wang, J., Shah, P., Cha, S. W., ... & CPTAC. (2016). Cell, 166(3), 755–765.
2015
Integrated proteomic and glycoproteomic analyses of prostate cancer cells
Shah, P., Wang, X., Yang, W., Toghi Eshghi, S., & Zhang, H. (2015). Molecular & Cellular Proteomics, 14(11), 2753–2763.MRMPlus: An open source quality control and assessment tool for SRM/MRM assay development
Aiyetan, P., Thomas, S. N., Zhang, Z., & Zhang, H. (2015). BMC Bioinformatics, 16, 231.
2014
Glycoform analysis of recombinant and HIV gp120 via HCD and spectral-aligning strategy
Yang, W., Shah, P., Toghi Eshghi, S., Yang, S., & Zhang, H. (2014). Journal of Proteome Research, 13(11), 4974–4985.XGlycScan: An open source software for N-linked glycosite assignment, quantification and quality assessment
Aiyetan, P., Zhang, B., Zhang, Z., & Zhang, H. (2014). MOJ Proteomics & Bioinformatics, 1(3), 65–75.Glycoproteomic analysis identifies human glycoproteins secreted from HIV-latently infected T cells
Yang, W., Zhou, J. Y., Chen, L., & Zhang, H. (2014). Clinical Proteomics, 11(1), 28.Imaging of N-linked glycans from formalin-fixed paraffin-embedded tissue sections using MALDI MS
Eshghi, S. T., Yang, S., Wang, X., Shah, P., Li, X., & Zhang, H. (2014). ACS Chemical Biology, 9(12), 2856–2862.
2013
Analysis of N-glycoproteins using genomic N-glycosite prediction
Sun, S., Zhang, B., Aiyetan, P., & Zhang, H. (2013). Journal of Proteome Research, 12(4), 1618–1628.Mass spectrometric analysis of sialylated glycans with use of solid-phase labeling of sialic acids
Shah, P. K., Shuang, Y., Sun, S., & Zhang, H. (2013). Analytical Chemistry, 85(7), 3606–3613.Glycomic analysis by glycoprotein immobilization for glycan extraction and LC on microfluidic chip
Yang, S., Toghi Eshghi, S., Chiu, H., & Zhang, H. (2013). Analytical Chemistry, 85(10), 4478–4486.
2012
Targeted analyte detection by standard addition improves detection limits in MALDI MS
Toghi Eshghi, S., Li, X., & Zhang, H. (2012). Analytical Chemistry, 84(15), 6510–6516.Altered expression of sialylated glycoproteins in breast cancer using hydrazide chemistry and mass spectrometry
Tian, Y., Esteva, F. J., Song, J., & Zhang, H. (2012). Molecular & Cellular Proteomics, 11(4), M111.011403.
2007
Solid-phase extraction of N-linked glycopeptides
Tian, Y., Zhou, Y., Elliott, S., Aebersold, R., & Zhang, H. (2007). Nature Protocols 2(2), 334–339
2003
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
Zhang, H., Li, X. J., Martin, D. B., & Aebersold, R. (2003). Nature Biotechnology, 21(6), 660–666.