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, 97(1), 324–332.

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., Hruban, R. H., & Zhang, H. (2025). Cancer Cell, 43(2), 245–261.

SPOT: spatial proteomics through on-site tissue-protein-labeling
Li, Q., Jiao, L., Sun, Z., Wang, Y., Lih, T. M., Hu, Y., & 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.

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.

Proteogenomic data and resources for pan-cancer analysis
Li, Y., Dou, Y., Leprevost, F. D. V.,... & Zhang, H. (2023). Cancer Cell, 41(8), 1397-1406.

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.

Standardized practices for the enrichment of neoplastic cells from tumor tissues for proteomic and genomic analyses
Li, Q. K., Hu, Y., Chen, L., Schnaubelt, M., Clark, D. J., Chan, D. W., & Zhang, H. (2022). Clinical Proteomics, 19(1), 22.

Proteogenomic characterization of pancreatic ductal adenocarcinoma
Cao, L., Huang, C., Cui Zhou, D.,... & Zhang, H. (2021). Cell, 184(19), 5031-5052.

Large-scale proteogenomic characterization of human invasive lobular carcinoma
Lih, T. M., Cho, K. C., Clark, D. J.,... & Zhang, H. (2021). Cancer Discovery, 11(9), 2226-2245.

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.

Integrated proteogenomic characterization of glioblastoma
Wang, L. B., Karpova, A., Gritsenko, M. A.,... & Zhang, H. (2020). Cancer Cell, 37(4), 569-589.

Proteogenomic characterization of human colon and rectal cancer reveals therapeutic vulnerabilities
Vasaikar, S. V., Huang, C., Wang, X.,... & Zhang, H. (2019). Cell, 177(4), 1035-1049.

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.

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.

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.

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Collins, B. C., Hunter, C. L., Liu, Y., Rosenberger, G., Gillet, L. C., Williams, E. G., Röst, H. L., & Zhang, H. (2017). Nature Communications, 8, 291.

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.

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.

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.

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.

CPTAC Assay Portal: A repository of targeted proteomic assays
Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Mani, D. R., Meavena, S. T., & Zhang, H. (2014). Molecular & Cellular Proteomics, 13(11), 907–917.

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.

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.

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.

A novel multiplex PCR assay for peripheral blood gene expression profiling
Jia, X., Tian, Y., & Zhang, H. (2012). BMC Cardiovascular Disorders, 12, 42.

Solid-phase extraction of N-linked glycopeptides
Tian, Y., Zhou, Y., Elliott, S., Aebersold, R., & Zhang, H. (2007). Nature Protocols 2(2): 334–339 

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., & Zhang, H. (2003). Nature Biotechnology, 21(6), 660–666.