Publications

Mukherjee P, Zhou X, Galli S, Davidson B, Zhang L, Ahn J, Aljuhani R, Benicky J, Ailles L, Pomin VH, Olsen M, Goldman R. Aspartate β-Hydroxylase Is Upregulated in Head and Neck Squamous Cell Carcinoma and Regulates Invasiveness in Cancer Cell Models. Int J Mol Sci. 2024 May 3;25(9):4998. doi: 10.3390/ijms25094998. PMID: 38732216

Panigrahi A, Benicky J, Aljuhani R, Mukherjee P, Nováková Z, Bařinka C, Goldman R. Galectin-3-binding protein inhibits extracellular heparan 6-O-endosulfatase Sulf-2. Mol Cell Proteomics. 2024 May 31:100793. doi: 10.1016/j.mcpro.2024.100793. PMID: 38825040

Mukherjee P, Zhou X, Benicky J, Panigrahi A, Aljuhani R, Liu J, Ailles Pomin VH, Wang Z, Goldman R. Heparan-6-O-endosulfatase 2 promotes invasiveness of head and neck squamous carcinoma cell lines in co-cultures with cancer associated fibroblasts. Cancers. 2023 15(21):5168. doi: 10.3390/cancers15215168.

Benicky J, Sanda M, Panigrahi A, Liu J, Wang Z, Pagadala V, Su G, Goldman R. A 6-O-endosulfatase activity assay based on synthetic heparan sulfate oligomers. Glycobiology. 2023 Jun 3;33(5):384-395. doi: 10.1093/glycob/cwad026. PMID: 37052463; PMCID: PMC10243761.

Campos D, Girgis M, Yang Q, Zong G, Goldman R, Wang LX, Sanda M. “Ghost” Fragment Ions in Structure and Site-Specific Glycoproteomics Analysis. Anal Chem. 2023 Jul 11;95(27):10145-10148. doi: 10.1021/acs.analchem.3c02207. Epub 2023 Jun 29. PMID: 37382290.

Vora J, Navelkar R, Vijay-Shanker K, Edwards N, Martinez K, Ding X, Wang T, Su P, Ross K, Lisacek F, Hayes C, Kahsay R, Ranzinger R, Tiemeyer M, Mazumder R. (2023) The glycan structure dictionary-a dictionary describing commonly used glycan structure terms. Glycobiology. Online ahead of print. doi: 10.1093/glycob/cwad014. PMID: 36799723

Sanda M, Yang Q, Zong G, Chen H, Zheng Z, Dhani H, Khan K, Kroemer A, Wang LX, Goldman R (2023) LC-MS/MS-PRM Quantification of IgG Glycoforms Using Stable Isotope Labeled IgG1 Fc Glycopeptide Standard. J Proteome Res. 2023 Feb 10. doi: 10.1021/acs.jproteome.2c00475. PMID: 36763792

Panigrahi A, Zhang L, Benicky J, Sanda M, Ahn J, Goldman R. (2023) A multiplexed microflow LC-MS/MS-PRM assay for serologic quantification of IgG N- and HPX O- glycoforms in liver fibrosis. Sci Rep. 12;13(1):606. doi: 10.1038/s41598-023-27382-0. PMID: 36635317

Yang Y, Ahn J, Edwards NJ, Benicky J, Rozeboom AM, Davidson B, Karamboulas C, Nixon KCJ, Ailles L, Goldman R. (2022) Extracellular Heparan 6-O-Endosulfatases SULF1 and SULF2 in Head and Neck Squamous Cell Carcinoma and Other Malignancies. Cancers (Basel) 14(22):5553. doi: 10.3390/cancers14225553. PMID: 36428645

Panigrahi A, Benicky J, Wei R, Ahn J, Goldman R, Sanda M. (2022) A Rapid LC-MS/MS-PRM Assay for Serologic Quantification of Sialylated O-HPX Glycoforms in Patients with Liver Fibrosis. Molecules. 27(7):2213. doi: 10.3390/molecules27072213. PMID: 35408612

Navelkar R, Owen G, Mutherkrishnan V, Thiessen P, Cheng T, Bolton E, Edwards N, Tiemeyer M, Campbell MP, Martin M, Vora J, Kahsay R, Mazumder R. (2021) Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. Glycobiology. 2021 Dec 18;31(11):1510-1519. PMID: 34314492.

Yuan W, Liu B, Sanda M, Wei R, Benicky J, Novakova Z, Barinka C, Goldman R. (2021) Glycoforms of human prostate-specific membrane antigen (PSMA) in human cells and prostate tissue. Prostate. Jan;82(1):132-144. doi: 10.1002/pros.24254. Epub 2021 Oct 18. PMID: 34662441

Yamada I, Campbell MP, Edwards N, Castro LJ, Lisacek F, Mariethoz J, Ono T, Ranzinger R, Shinmachi D, Aoki-Kinoshita KF. (2021) The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. Glycobiology. 7;31(7):741-750. doi: 10.1093/glycob/cwab013. PMID: 33677548

Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. (2021) Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods. 2021 18(11):1304-1316. PMID: 34725484

Sanda M, Ahn J, Kozlik P, Goldman R. (2021). Analysis of site and structure specific core fucosylation in liver disease progression using exoglycosidase-assisted data-independent LC-MS/MS. Sci Rep 11, 23273. PMID: 34857845

Zhang W, Edwards N. (2021). GNOme – Glycan Naming and Subsumption Ontology. In Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO); pp1-5. September 14-16, 2021.

McIntosh AT, Wei R, Ahn J, Aouizerat BE, Kassaye SG, Augenbraun MH, Price JC, French AL, Gange SJ, Anastos KM, Goldman R. (2020). A genomic variant of ALPK2 is associated with increased liver fibrosis risk in HIV/HCV coinfected women. PLoS One. 2021 Mar 11;16(3):e0247277. PMID: 33705408

Sanda M, Morrison L, Goldman R. (2021) N and O glycosylation of the SARS-CoV-2 spike protein. Anal Chem. 2021 Feb 2;93(4):2003-2009. PMID: 33406838

Yang Y, Ahn J, Raghunathan R, Kallakury BV, Davidson B, Kennedy ZB, Zaia J, Goldman R (2021) Expression of the Extracellular Sulfatase SULF2 Affects Survival of Head and Neck Squamous Cell Carcinoma Patients, Front Oncol. 2021 Jan 8;10:582827. PMID: 33585200

Benicky J, Sanda M, Brnakova-Kennedy Z, Grant OC, Woods RJ, Alan Zwart A, Goldman R. (2020) PD-L1 glycosylation and its impact on binding to clinical antibodies. Journal of Proteome Research 20(1):485-497. PMID: 33073996

Sanda M, Benicky J, Goldman R. (2020) Low Collision Energy Fragmentation in Structure-Specific Glycoproteomics Analysis. Anal Chem. 92, 8262–8267. PMID: 32441515

Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. GlyGen data model and processing workflow. Bioinformatics. 2020 Jun 1;36(12):3941-3943. doi: 10.1093/bioinformatics/btaa238. PMID: 32324859; PMCID: PMC7320628.

Kozlik P, Molnarova K, Jecmen T, Krizek T, Goldman R. (2020) Glycan-specific precipitation of glycopeptides in high organic content sample solvents used in HILIC. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Aug 1;1150:122196. doi: 10.1016/j.jchromb.2020.122196. Epub 2020 May 28. PMID: 32485649

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W. (2020) GlyGen: Computational and Informatics Resources for Glycoscience. Glycobiology. 30, 72-73. PMID: 31616925

Deslattes Mays A, Schmidt M, Graham G, Tseng E, Baybayan P, Sebra R, Sanda M, Mazarati JB, Riegel A, Wellstein A. (2019) Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations. Genes (Basel). 10(4):253. PMID: 30934798

Benicky J, Sanda M, Brnakova Kennedy Z, Goldman R. (2019) N-Glycosylation is required for secretion of the precursor to brain-derived neurotrophic factor (proBDNF) carrying sulfated LacdiNAc structures. J Biol Chem, 294, 16816-16830. PMID: 31558607

Yuan W, Wei R, Goldman R, Sanda M. (2019) Optimized Fragmentation for Quantitative Analysis of Fucosylated N-Glycoproteins by LC-MS-MRM. Anal Chem, 91, 9206-9212. PMID: 31268672

Gourgari E, Ma J, Playford MP, Mehta NN, Goldman R, Remaley AT, Gordon SM. (2019) Proteomic alterations of HDL in youth with type 1 diabetes and their associations with glycemic control: a case-control study. Cardiovasc Diabetol. 28, 43. PMID: 30922315

Yang W, Ramadan S, Orwenyo J, Kakeshpour T, Diaz T, Eken Y, Sanda M, Jackson JE, Wilson AK, Huang X. (2018) Chemoenzymatic synthesis of glycopeptides bearing rare N-glycan sequences with or without bisecting GlcNAc. Chem Sci. 9(43):8194-8206. eCollection 2018 Nov 21. PMID: 30542567

Yuan W, Benicky J, Wei R, Goldman R, Sanda M. (2018) Quantitative Analysis of Sex-Hormone-Binding Globulin Glycosylation in Liver Diseases by Liquid Chromatography-Mass Spectrometry Parallel Reaction Monitoring. J Proteome Res. 17, 2755-2766. PMID: 29972295

Kozlik P, Goldman R, Sanda M. (2018) Hydrophilic interaction liquid chromatography in the separation of glycopeptides and their isomers. Anal Bioanal Chem. 410, 5001-5008. PMID: 29806066

Fan Y, Hu Y, Yan C, Goldman R, Pan Y, Mazumder R, Dingerdissen HM. (2018) Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. Sci Rep. 12, 4322. PMID: 29531238

Ma J, Sanda M, Wei R, Zhang L, Goldman R. (2018) Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics. 189, 67-74. PMID: 29427759

Sanda M, Zhang L, Edwards NJ, Goldman R. (2017) Site-specific analysis of changes in the glycosylation of proteins in liver cirrhosis using data-independent workflow with soft fragmentation. Anal Bioanal Chem, 409, 619-627. PMID: 27822650

Kozlik P, Sanda M, Goldman R. (2017) Nano reversed phase versus nanohydrophilic interaction liquid chromatography on a chip in the analysis of hemopexin glycopeptides. J Chromatogr A, 13, 152-155. PMID: 28888681

Darebna P, Novak P, Kucera R, Topolcan O, Sanda M, Goldman R, Pompach P. (2017) Changes in the expression of N-and O-glycopeptides in patients with colorectal cancer and hepatocellular carcinoma quantified by full-MS scan FT-ICR and multiple reaction monitoring. J Proteomics, 153, 44-52. PMID: 27646713

Kozlik P, Goldman R, Sanda M. (2017) Study of structure-dependent chromatographic behavior of glycopeptides using reversed phase nanoLC. Electrophoresis, 38, 2193-21. PMID: 28444931

Wang M, Sanda M, Comunale MA, Herrera H, Swindell C, Kono Y, Singal AG, Marrero J, Block T,Goldman R, Mehta A. (2017) Changes in the Glycosylation of Kininogen and the Development of a Kininogen-Based Algorithm for the Early Detection of HCC. Cancer Epidemiol Biomarkers Prev, 26, 795-803 PMID: 28223431

Sanda M, Goldman R. (2016) Data Independent Analysis of IgG Glycoforms in Samples of Unfractionated Human Plasma. Anal Chem, 88, 10118-10125. PMID: 27649061

Sanda M, Benicky J, Wu J, Wang Y, Makambi K, Ahn J, Smith CI, Zhao P, Zhang L, Goldman R. (2016) Increased sialylation of site-specific O-glycoforms of hemopexin in liver disease. Clin Proteomics, 13, 24. PMID: 27688741

Flowers SA, Zhou X, Wu J, Wang Y, Makambi K, Kallakury BV, Singer MS, Rosen SD, Davidson B, Goldman R. (2016) Expression of the extracellular sulfatase SULF2 is associated with squamous cell carcinoma of the head and neck. Oncotarget, 7, 43177-43187. PMID: 27223083

Yuan W., Sanda M., Wu J., Koomen J., Goldman R. (2015) Quantitative analysis of immunoglobulin subclasses and subclass specific glycosylation by LC-MS-MRM in liver disease. J Proteomics, 116, 24-33 PMC4329072

Singer MS, Phillips JJ, Lemjabbar-Alaoui H, Wang YQ, Wu J, Goldman R, Rosen SD. (2015) SULF2, a heparan sulfate endosulfatase, is present in the blood of healthy individuals and increases in cirrhosis. Clin ChimActa. 440, 72-8. PMC430547

Goldman R. and Sanda M. (2014) Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl, 9, 17-32. PMC5780646

Benicky J, Sanda M, Pompach P, Wu J, Goldman R (2014) Quantification of Fucosylated Hemopexin and Complement Factor H in Plasma of Patients with Liver Disease. Anal Chem, 86, 10716-23 PMC4222631

White D.L, Liu Y., Garcia J., El-Serag H.B., Jiao L., Tsavachidis S., Franco L.M., Lee J.S., Tavakoli-Tabasi S., Moore D., Goldman R., Kuzniarek J., Ramsey D.J., Kanwal F., Marcelli M. (2014) Sex hormone pathway gene polymorphisms are associated with risk of advanced hepatitis C-related liver disease in males. Int J Mol Epidemiol Genet, 5, 164-76 PMC4214264

Nayak A., Pattabiraman N., Fadra N., Goldman R., Kosakovsky Pond S.L., Mazumder R. (2014) Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2. J Biomol Struct Dyn. Oct 15:1-13. PMC5896302

Pompach P., Ashline D.J., Brnakova Z., Benicky J., Sanda M., Goldman R. (2014) Protein and Site Specificity of Fucosylation in Liver-Secreted Glycoproteins. J Proteome Res., 13, 5561-9 PMC4261953

Wallace T.A., Downey R.F., Seufert C.J., Schetter A., Dorsey T.M., Johnson C.A., Goldman R., Loffredo C.A., Yan P., Sullivan F.J., Giles F.J., Wang-Johanning F., Ambs S., Glynn S.A. (2014) Elevated HERV-K mRNA expression in PBMC is associated with a prostate cancer diagnosis particularly in older men and smokers. Carcinogenesis, 35, 2074-83 PMC4146419

Chandler K., Brnakova Z., Sanda M., Wang S., Stalnaker S., Bridger R., Zhao P., Wells L., Edwards N., Goldman R. (2014) Site-Specific Glycan Microheterogeneity of Inter-alpha-Trypsin Inhibitor Heavy Chain H4. Journal of Proteome Research, 13, 3314-29 PMC4084840

Fu Y., Mi L., Sanda M., Silverstein S., Aggarwal M., Wang D., Gupta P., Goldman R., Appella, G., Chung, F.L (2014) A click chemistry approach to identify protein targets of chemopreventive phenethyl isothiocyanate. RSC Advances, 3920-3923. PMC5512166

Sanda M., Pompach P., Benicky J., Goldman, R. (2013) LC-MS3 Quantification of O-Glycopeptides in Human Serum. Electrophoresis, 34, 2342-2349 PMC3808000

Chandler K.B., Pompach P., Goldman R., Edwards N. (2013) Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. J Proteome Res. 12, 3652-66 PMC3777712

Lam P.V., Goldman R., Karagiannis K., Narsule T., Simonyan V., Soika V., Mazumder R. (2013) Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. Genomics Proteomics Bioinformatics, 1, 96-104 PMC3914773

Chandler K.B., Goldman R. (2013) Glycoprotein disease markers and single protein-omics. MolCell Proteomics, 12, 836-45 PMC3617330

Sanda M., Pompach P., Brnakova Z., Wu J., Makambi K., Goldman R. (2013) Quantitative LC-MS-MRM analysis of site-specific glycoforms of haptoglobin in liver disease. Mol Cell Proteomics, 12, 1294-305 PMC3650340

Pompach P., Brnakova Z., Sanda M., Wu J., Edwards N., Goldman R. (2013) Site specific glycoforms of haptoglobin in liver cirrhosis and hepatocellular carcinoma. Mol Cell Proteomics, 12, 1281-93 PMC3650339

Leymarie N … Goldman R. … Zou C. (2013) Interlaboratory Study on Differential Analysis of Protein Glycosylation by Mass Spectrometry: The ABRF Glycoprotein Research Multi-Institutional Study 2012. Mol Cell Proteomics, 12, 2935-2951 PMC3790302

Bekesova S., Kosti, O., Chandler K.B., Wu J., Madej H.J., Brown K.C., Simonyan, V., Goldman, R. (2012) N-glycans in liver-secreted and immunoglogulin-derived protein fractions. Journal of Proteomics,75, 2216-2224 PMC3568703

Mazumder R., Morampudi K.S., Motwani M., Vasudevan S., Goldman R. (2012) Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes. PLoS ONE, 7, e36212 PMC3346765

Xiao J.F., Tuli L., Varghese, R.S.; Zhou, B., Tsung-Heng Tsai, T-H., Ranjbar, M.N., Zhao, Y., Wang, J., Di Poto, C., Cheema, A.K., Tadesse,M.D., Goldman, R., Shetty, K. (2012) Utilization of Metabolomics to Identify Serum Biomarkers for Hepatocellular Carcinoma in Patients with Liver Cirrhosis. Anal Chim Acta, 743, 90-100. PMC3419576

Lenco J., Lan R., Edwards N.J., Goldman R. (2012) MS/MS library facilitated MRM quantification of native peptides prepared by denaturing ultrafiltration. Proteome Science, 10, 7 PMC3331852

Ressom H.W., Xiao J.F., Tuli L., Varghese R.S., Zhou B., Tsai T.H., Ranjbar M., Zhao Y., Wang J., Di Poto C., Cheema A.K., Tadesse M.G., Goldman R., Shetty K. (2012) Utilization of Metabolomics to Identify Serum Biomarkers for Hepatocellular Carcinoma in Patients with Liver Cirrhosis. Anal Chim Acta. 743C: 90–100 PMC3419576

PompachP., Chandler K., Lan R., Edwards N.J., Goldman, R. (2012) Semi-automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nanoReverse Phase LC-MS/MS, and Glycan Database Search. Journal of Proteome Research, 11, 1728-1740 PMC3292689

Isailovic D., Plasencia M.D., Gaye M.M., Stokes S.T., Kurulugama R.T., Pungpapong V., Zhang M., Kyselova Z., Goldman R., Mechref Y., Novotny M.V., Clemmer D.E. (2012) Delineating Diseases by IMS-MS Profiling of Serum N-linked Glycans. J Proteome Res., 11, 576-585 PMC3337085

Kosti, O., Xu X., Veenstra T.D., Hsing A.W., Chu L.W., Goldman L., Bebu I., Collins S., Dritschilo A., Lynch J.H., Goldman R. (2011) Urinary estrogen metabolites and prostate cancer risk: a pilot study. Prostate, 7, 507-16 PMC3037420

Kosti O., Goldman L., Saha D.T., Orden RA., Pollock A.J., Madej L.H., Hsing A.W., Chu, L.W., Lynch J.H., Goldman R. (2011) DNA damage phenotype and prostate cancer risk. Mutation Research, 719, 41-46. PMC3038618

Kang P., Madera M., Alley WR Jr., Goldman R., Mechref Y., Novotny MV. (2011) Glycomic alterations in the highly-abundant and lesser-abundant blood serum protein fractions for patients diagnosed with hepatocellular carcinoma. Int J Mass Spectrom, 305, 185-198. PMC3685172

Ahmadi, N., Goldman,R., Kosti, O., Seillier-Moiseiwitch, F., Davidson, B.J. (2010) Regular non-steroidal anti inflammatory drug use is less prevalent in head and neck cancer patients. Int. J. Otolaryngol., 2010, 424161-169. PMC290201