20032020

Research output per year

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Research Output

Article
41 Scopus citations

Alzheimer amyloid precursor aspartyl proteinase activity in CHAPSO homogenates of Spodoptera frugiperda cells

Carter, T. L., Verdile, G., Groth, D., Bogush, A., Thomas, S., Shen, P., Fraser, P. E., Mathews, P., Nixon, R. A., Ehrlich, M. E., Kwok, J. B. J., St. George-Hyslop, P., Schofield, P., Li, Y., Yang, A., Martins, R. N. & Gandy, S., Oct 1 2004, In : Alzheimer disease and associated disorders. 18, 4, p. 261-263 3 p.

Research output: Contribution to journalArticle

6 Scopus citations

Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation

Cripps, D., Thomas, S. N., Jeng, Y., Yang, F., Davies, P. & Yang, A. J., Apr 21 2006, In : Journal of Biological Chemistry. 281, 16, p. 10825-10838 14 p.

Research output: Contribution to journalArticle

Open Access
178 Scopus citations
Open Access
7 Scopus citations

Comparative analysis of the catalytic regulation of NEDD4-1 and WWP2 ubiquitin ligases

Jiang, H., Thomas, S. N., Chen, Z., Chiang, C. Y. & Cole, P. A., Nov 15 2019, In : Journal of Biological Chemistry. 294, 46, p. 17421-17436 16 p.

Research output: Contribution to journalArticle

1 Scopus citations
Open Access
83 Scopus citations

Dual modification of Alzheimer's disease PHF-tau protein by lysine methylation and ubiquitylation: A mass spectrometry approach

Thomas, S. N., Funk, K. E., Wan, Y., Liao, Z., Davies, P., Kuret, J. & Yang, A. J., Jan 1 2012, In : Acta Neuropathologica. 123, 1, p. 105-117 13 p.

Research output: Contribution to journalArticle

Open Access
50 Scopus citations

Enzymatic Analysis of PTEN Ubiquitylation by WWP2 and NEDD4-1 E3 Ligases

Chen, Z., Thomas, S. N., Bolduc, D. M., Jiang, X., Zhang, X., Wolberger, C. & Cole, P. A., Jul 5 2016, In : Biochemistry. 55, 26, p. 3658-3666 9 p.

Research output: Contribution to journalArticle

16 Scopus citations

High-Throughput Proteomic-Based Identification of Oxidatively Induced Protein Carbonylation in Mouse Brain

Soreghan, B. A., Yang, F., Thomas, S. N., Hsu, J. & Yang, A. J., Nov 1 2003, In : Pharmaceutical research. 20, 11, p. 1713-1720 8 p.

Research output: Contribution to journalArticle

96 Scopus citations

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

the CPTAC Investigators, Jul 28 2016, In : Cell. 166, 3, p. 755-765 11 p.

Research output: Contribution to journalArticle

Open Access
286 Scopus citations

IsoQuant: A software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation

Liao, Z., Wan, Y., Thomas, S. N. & Yang, A. J., May 15 2012, In : Analytical chemistry. 84, 10, p. 4535-4543 9 p.

Research output: Contribution to journalArticle

17 Scopus citations

Lysine methylation is an endogenous post-translational modification of tau protein in human brain and a modulator of aggregation propensity

Funk, K. E., Thomas, S. N., Schafer, K. N., Cooper, G. L., Liao, Z., Clark, D. J., Yang, A. J. & Kuret, J., Jul 15 2014, In : Biochemical Journal. 462, 1, p. 77-88 12 p.

Research output: Contribution to journalArticle

46 Scopus citations

Modification of Sialic Acids on Solid Phase: Accurate Characterization of Protein Sialylation

Yang, S., Zhang, L., Thomas, S., Hu, Y., Li, S., Cipollo, J. & Zhang, H., Jun 20 2017, In : Analytical chemistry. 89, 12, p. 6330-6335 6 p.

Research output: Contribution to journalArticle

16 Scopus citations

Molecular features of phosphatase and tensin homolog (PTEN) Regulation by C-terminal phosphorylation

Chen, Z., Dempsey, D. R., Thomas, S. N., Hayward, D., Bolduc, D. M. & Cole, P. A., Jul 1 2016, In : Journal of Biological Chemistry. 291, 27, p. 14160-14169 10 p.

Research output: Contribution to journalArticle

Open Access
14 Scopus citations

MRMPlus: An open source quality control and assessment tool for SRM/MRM assay development

Aiyetan, P., Thomas, S. N., Zhang, Z. & Zhang, H., Dec 12 2015, In : BMC bioinformatics. 16, 1, 411.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A. C., Held, J. M., Hirayama-Kurogi, M., Hou, G., Krisp, C., Larsen, B., Lin, L., Liu, S., Molloy, M. P., Moritz, R. L., Ohtsuki, S., Schlapbach, R. & 5 others, Selevsek, N., Thomas, S. N., Tzeng, S. C., Zhang, H. & Aebersold, R., Dec 1 2017, In : Nature communications. 8, 1, 291.

Research output: Contribution to journalArticle

Open Access
108 Scopus citations

Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N-Linked Glycosite-Containing Peptides in Serum

Thomas, S. N., Harlan, R., Chen, J., Aiyetan, P., Liu, Y., Sokoll, L. J., Aebersold, R., Chan, D. W. & Zhang, H., Oct 9 2015, In : Analytical chemistry. 87, 21, p. 10830-10838 9 p.

Research output: Contribution to journalArticle

16 Scopus citations

Neuronal endosomal/lysosomal membrane destabilization activates caspases and induces abnormal accumulation of the lipid secondary messenger ceramide

Ditaranto-Desimone, K., Saito, M., Tekirian, T. L., Saito, M., Berg, M., Dubowchik, G., Soreghan, B., Thomas, S., Marks, N. & Yang, A. J., Feb 15 2003, In : Brain Research Bulletin. 59, 6, p. 523-531 9 p.

Research output: Contribution to journalArticle

27 Scopus citations

N-GlycositeAtlas: A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping

Sun, S., Hu, Y., Ao, M., Shah, P., Chen, J., Yang, W., Jia, X., Tian, Y., Thomas, S. & Zhang, H., Sep 7 2019, In : Clinical Proteomics. 16, 1, 35.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Phosphorylation of serine 51 regulates the interaction of human DNA ligase I with replication factor C and its participation in DNA replication and repair

Peng, Z., Liao, Z., Dziegielewska, B., Matsumoto, Y., Thomas, S., Wan, Y., Yang, A. & Tomkinson, A. E., Oct 26 2012, In : Journal of Biological Chemistry. 287, 44, p. 36711-36719 9 p.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations

PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information

Wan, Y., Cripps, D., Thomas, S., Campbell, P., Ambulos, N., Chen, T. & Yang, A., Jul 1 2008, In : Journal of Proteome Research. 7, 7, p. 2803-2811 9 p.

Research output: Contribution to journalArticle

30 Scopus citations

Proteomic analysis of exfoliation deposits

Ovodenko, B., Rostagno, A., Neubert, T. A., Shetty, V., Thomas, S., Yang, A., Liebmann, J., Ghiso, J. & Ritch, R., Apr 1 2007, In : Investigative Ophthalmology and Visual Science. 48, 4, p. 1447-1457 11 p.

Research output: Contribution to journalArticle

Open Access
70 Scopus citations

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

Zhou, J. Y., Chen, L., Zhang, B., Tian, Y., Liu, T., Thomas, S. N., Chan, L., Schnaubelt, M., Boja, E., Hiltke, T., Kinsinger, C. R., Rodriguez, H., Davies, S. R., Li, S., Snider, J. E., Erdmann-Gilmore, P., Tabb, D. L., Townsend, R. R., Ellis, M. J., Rodland, K. D. & 5 others, Smith, R. D., Carr, S. A., Zhang, Z., Chan, D. W. & Zhang, H., Dec 1 2017, In : Journal of Proteome Research. 16, 12, p. 4523-4530 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Quantification of Tau Protein Lysine Methylation in Aging and Alzheimer's Disease

Huseby, C. J., Hoffman, C. N., Cooper, G. L., Cocuron, J. C., Alonso, A. P., Thomas, S. N., Yang, A. J. & Kuret, J., Jan 1 2019, In : Journal of Alzheimer's Disease. 71, 3, p. 979-991 13 p.

Research output: Contribution to journalArticle

Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability

Thomas, S. N., Waters, K. M., Morgan, W. F., Yang, A. J. & Baulch, J. E., Aug 1 2012, In : Free Radical Biology and Medicine. 53, 3, p. 618-628 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Rapid characterization of amyloid-β side-chain oxidation by tandem mass spectrometry and the scoring algorithm for spectral analysis

Schiewe, A. J., Margol, L., Soreghan, B. A., Thomas, S. N. & Yang, A. J., Jul 1 2004, In : Pharmaceutical research. 21, 7, p. 1094-1102 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays

Hoofnagle, A. N., Whiteaker, J. R., Carr, S. A., Kuhn, E., Liu, T., Massoni, S. A., Thomas, S. N., Reid Townsend, R., Zimmerman, L. J., Boja, E., Chen, J., Crimmins, D. L., Davies, S. R., Gao, Y., Hiltke, T. R., Ketchum, K. A., Kinsinger, C. R., Mesri, M., Meyer, M. R., Qian, W. J. & 35 others, Schoenherr, R. M., Scott, M. G., Shi, T., Whiteley, G. R., Wrobel, J. A., Wu, C., Ackermann, B. L., Aebersold, R., Barnidge, D. R., Bunk, D. M., Clarke, N., Fishman, J. B., Grant, R. P., Kusebauch, U., Kushnir, M. M., Lowenthal, M. S., Moritz, R. L., Neubert, H., Patterson, S. D., Rockwood, A. L., Rogers, J., Singh, R. J., Van Eyk, J. E., Wong, S. H., Zhang, S., Chan, D. W., Chen, X., Ellis, M. J., Liebler, D. C., Rodland, K. D., Rodriguez, H., Smith, R. D., Zhang, Z., Zhang, H. & Paulovich, A. G., Jan 2016, In : Clinical chemistry. 62, 1, p. 48-69 22 p.

Research output: Contribution to journalArticle

Open Access
77 Scopus citations

Reduced neuronal expression of synaptic transmission modulator HNK-1/neural cell adhesion molecule as a potential consequence of amyloid β-mediated oxidative stress: A proteomic approach

Thomas, S. N., Soreghan, B. A., Nistor, M., Sarsoza, F., Head, E. & Yang, A. J., Feb 1 2005, In : Journal of Neurochemistry. 92, 4, p. 705-717 13 p.

Research output: Contribution to journalArticle

21 Scopus citations

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry

Mertins, P., Tang, L. C., Krug, K., Clark, D. J., Gritsenko, M. A., Chen, L., Clauser, K. R., Clauss, T. R., Shah, P., Gillette, M. A., Petyuk, V. A., Thomas, S. N., Mani, D. R., Mundt, F., Moore, R. J., Hu, Y., Zhao, R., Schnaubelt, M., Keshishian, H., Monroe, M. E. & 9 others, Zhang, Z., Udeshi, N. D., Davies, S. R., Townsend, R. R., Chan, D. W., Smith, R. D., Zhang, H., Liu, T. & Carr, S. A., Jul 1 2018, In : Nature Protocols. 13, 7, p. 1632-1661 30 p.

Research output: Contribution to journalArticle

39 Scopus citations

Site-Specific Fucosylation Analysis Identifying Glycoproteins Associated with Aggressive Prostate Cancer Cell Lines Using Tandem Affinity Enrichments of Intact Glycopeptides Followed by Mass Spectrometry

Zhou, J., Yang, W., Hu, Y., Höti, N., Liu, Y., Shah, P., Sun, S., Clark, D., Thomas, S. & Zhang, H., Jul 18 2017, In : Analytical chemistry. 89, 14, p. 7623-7630 8 p.

Research output: Contribution to journalArticle

19 Scopus citations

Stable isotope labeling with amino acids in cell culture based mass spectrometry approach to detect transient protein interactions using substrate trapping

Thomas, S. N., Wan, Y., Liao, Z., Hanson, P. I. & Yang, A. J., Jul 15 2011, In : Analytical chemistry. 83, 14, p. 5511-5518 8 p.

Research output: Contribution to journalArticle

8 Scopus citations

Targeted proteomic analyses of histone H4 acetylation changes associated with homologous-recombination-deficient high-grade serous ovarian carcinomas

Thomas, S. N., Chen, L., Liu, Y., Höti, N. & Zhang, H., Oct 6 2017, In : Journal of Proteome Research. 16, 10, p. 3704-3710 7 p.

Research output: Contribution to journalArticle

3 Scopus citations

Type IV pilus secretins have extracellular C termini

Lieberman, J. A., Petro, C. D., Thomas, S., Yang, A. & Donnenberg, M. S., Mar 24 2015, In : mBio. 6, 2, e00322-15.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1+AβPP mouse model of Alzheimer's disease

Soreghan, B. A., Lu, B. W., Thomas, S. N., Duff, K., Rakhmatulin, E. A., Nikolskaya, T., Chen, T. & Yang, A. J., Jan 1 2005, In : Journal of Alzheimer's Disease. 8, 3, p. 227-241 15 p.

Research output: Contribution to journalArticle

23 Scopus citations

Using the cptac assay portal to identify and implement highly characterized targeted proteomics assays

Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V., MacLean, B., Yan, P., Wrobel, J. A., Kennedy, J., Mani, D. R., Zimmerman, L. J., Meyer, M. R., Mesri, M., Boja, E., Carr, S. A., Chan, D. W., Chen, X., Chen, J., Davies, S. R., Ellis, M. J. C., Fenyö, D. & 22 others, Hiltke, T., Ketchum, K. A., Kinsinger, C., Kuhn, E., Liebler, D. C., Liu, T., Loss, M., Maccoss, M. J., Qian, W. J., Rivers, R., Rodland, K. D., Ruggles, K. V., Scott, M. G., Smith, R. D., Thomas, S., Townsend, R. R., Whiteley, G., Wu, C., Zhang, H., Zhang, Z., Rodriguez, H. & Paulovich, A. G., Feb 1 2016, In : Methods in Molecular Biology. 1410, p. 223-236 14 p.

Research output: Contribution to journalArticle

16 Scopus citations
Chapter

Mass spectrometry analysis of lysine posttranslational modifications of Tau protein from Alzheimer’s disease brain

Thomas, S. N. & Yang, A. J., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 161-177 17 p. (Methods in Molecular Biology; vol. 1523).

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Scopus citations

MudPIT (Multidimensional Protein Identification Technology) for Identification of Post-Translational Protein Modifications in Complex Biological Mixtures

Thomas, S. N., Lu, B. W., Nikolskaya, T., Nikolsky, Y. & Yang, A. J., Jun 19 2006, Redox Proteomics: From Protein Modifications to Cellular Dysfunction and Diseases. John Wiley & Sons, Inc., p. 233-252 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Scopus citations

Proteomic analysis of protein phosphorylation and ubiquitination in Alzheimer's disease

Thomas, S., Cripps, D. & Yang, A. J., Dec 1 2009, Neuroproteomics: Methods and Protocols. Ottens, A., Wang, K. & Wang, K. (eds.). p. 109-121 13 p. (Methods in Molecular Biology; vol. 566).

Research output: Chapter in Book/Report/Conference proceedingChapter

19 Scopus citations
Comment/debate

Erratum: Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (Cell (2019) 179(4) (964–983.e31), (S0092867419311237), (10.1016/j.cell.2019.10.007))

Clinical Proteomic Tumor Analysis Consortium, Jan 9 2020, In : Cell. 180, 1, 1 p.

Research output: Contribution to journalComment/debate

Open Access

How sweet it is: The coming of age of continuous glucose monitoring

Thomas, S. N., Jan 1 2019, In : Clinical chemistry. 65, 9, p. 1184-1185 2 p.

Research output: Contribution to journalComment/debate

Editorial

Targeted proteomic assays for the verification of global proteomics insights

Thomas, S. N. & Zhang, H., Oct 2 2016, In : Expert Review of Proteomics. 13, 10, p. 897-899 3 p.

Research output: Contribution to journalEditorial

Open Access
3 Scopus citations
Letter

CPTAC Assay Portal: A repository of targeted proteomic assays

Whiteaker, J. R., Halusa, G. N., Hoofnagle, A. N., Sharma, V., MacLean, B., Yan, P., Wrobel, J. A., Kennedy, J., Mani, D. R., Zimmerman, L. J., Meyer, M. R., Mesri, M., Rodriguez, H., Paulovich, A. G., Abbatiello, S. E., Boja, E., Carr, S. A., Chan, D. W., Chen, X., Chen, J. & 24 others, Davies, S. R., Ellis, M. J. C., Fenyö, D., Hiltke, T., Ketchum, K. A., Kinsinger, C., Kuhn, E., Liebler, D. C., Lin, D., Liu, T., Loss, M., MacCoss, M. J., Qian, W. J., Rivers, R., Rodland, K. D., Ruggles, K. V., Scott, M. G., Smith, R. D., Thomas, S., Townsend, R. R., Whiteley, G., Wu, C., Zhang, H. & Zhang, Z., Jul 2014, In : Nature Methods. 11, 7, p. 703-704 2 p.

Research output: Contribution to journalLetter

66 Scopus citations
Other contribution

Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes

Thomas, S. N., Friedrich, B., Schnaubelt, M., Chan, D. W., Zhang, H. & Aebersold, R., Oct 3 2019

Research output: Other contribution

Open Access
Review article

Advances in mass spectrometry-based clinical biomarker discovery

Crutchfield, C. A., Thomas, S. N., Sokoll, L. J. & Chan, D. W., Jan 7 2016, In : Clinical Proteomics. 13, 1, 13.

Research output: Contribution to journalReview article

Open Access
87 Scopus citations

Advancing signaling networks through proteomics

Tekirian, T. L., Thomas, S. N. & Yang, A., Aug 1 2007, In : Expert Review of Proteomics. 4, 4, p. 573-583 11 p.

Research output: Contribution to journalReview article

7 Scopus citations

Exosomal proteome profiling: A potential multi-marker cellular phenotyping tool to characterize hypoxia-induced radiation resistance in breast cancer

Thomas, S. N., Liao, Z., Clark, D., Chen, Y., Samadani, R., Mao, L., Ann, D. K., Baulch, J. E., Shapiro, P. & Yang, A. J., Sep 1 2013, In : Proteomes. 1, 2, p. 87-108 22 p.

Research output: Contribution to journalReview article

Open Access
28 Scopus citations