academic article

• Riva, A., Kuzyk, O., Forsberg, E., Siuzdak, G., Pfann, C., Herbold, C., Daims, H., Loy, A., Warth, B., Berry, D. A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome Nature Communications  2019 10  DOI:10.1038/s41467-019-12413-0  PMID:31554820  PMCID:PMC6761162
• Domingo-Almenara, X., Montenegro-Burke, J. R., Guijas, C., Majumder, E. L. W., Benton, H. P., Siuzdak, G. Autonomous METLIN-guided in-source fragment annotation for untargeted metabolomics Analytical Chemistry  2019 91:3246-3253  DOI:10.1021/acs.analchem.8b03126  PMID:30681830
• Krantz, G. P., Lucas, K., Wunderlich, E. L., Hoang, L. T., Avci, R., Siuzdak, G., Fields, M. W. Bulk phase resource ratio alters carbon steel corrosion rates and endogenously produced extracellular electron transfer mediators in a sulfate-reducing biofilm Biofouling  2019 1-15  DOI:10.1080/08927014.2019.1646731  PMID:31402749
• Rinschen, M. M., Ivanisevic, J., Giera, M., Siuzdak, G. Identification of bioactive metabolites using activity metabolomics Nature Reviews Molecular Cell Biology  2019 20:353-367  DOI:10.1038/s41580-019-0108-4  PMID:30814649
• Montenegro-Burke, J. R., Woldstad, C. J., Fang, M., Bade, A. N., McMillan, J., Edagwa, B., Boska, M. D., Gendelman, H. E., Siuzdak, G. Nanoformulated antiretroviral therapy attenuates brain metabolic oxidative stress Molecular Neurobiology  2019 56:2896-2907  DOI:10.1007/s12035-018-1273-8  PMID:30069830  PMCID:PMC6403019
• Warth, B., Palermo, A., Rattray, N. J. W., Lee, N. V., Zhu, Z., Hoang, L. T., Cai, Y., Mazurek, A., Dann, S., VanArsdale, T., Fantin, V. R., Shields, D., et al. Palbociclib and fulvestrant act in synergy to modulate central carbon metabolism in breast cancer cells Metabolites  2019 9  DOI:10.3390/metabo9010007  PMID:30609717  PMCID:PMC6359333
• Domingo-Almenara, X., Montenegro-Burke, J. R., Benton, H. P., Siuzdak, G. Annotation: A computational solution for streamlining metabolomics analysis Analytical Chemistry  2018 90:480-489  DOI:10.1021/acs.analchem.7b03929  PMID:29039932  PMCID:PMC5750104
• Huan, T., Palermo, A., Ivanisevic, J., Rinehart, D., Edler, D., Phommavongsay, T., Benton, H. P., Guijas, C., Domingo-Almenara, X., Warth, B., Siuzdak, G. Autonomous multimodal metabolomics data integration for comprehensive pathway analysis and systems biology Analytical Chemistry  2018 90:8396-8403  DOI:10.1021/acs.analchem.8b00875  PMID:29893550
• Domingo-Almenara, X., Montenegro-Burke, J. R., Ivanisevic, J., Thomas, A., Sidibe, J., Teav, T., Guijas, C., Aisporna, A. E., Rinehart, D., Hoang, L., Nordstrom, A., Gomez-Romero, M., et al. CMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules Nature Methods  2018 15:681-684  DOI:10.1038/s41592-018-0110-3  PMID:30150755
• Forsberg, E. M., Huan, T., Rinehart, D., Benton, H. P., Warth, B., Hilmers, B., Siuzdak, G. Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online Nature Protocols  2018 13:633-651  DOI:10.1038/nprot.2017.151  PMID:29494574
• Palermo, A., Forsberg, E. M., Warth, B., Aisporna, A. E., Billings, E., Kuang, E., Benton, H. P., Berry, D., Siuzdak, G. Fluorinated gold nanoparticles for nanostructure imaging mass spectrometry ACS Nano  2018 12:6938-6948  DOI:10.1021/acsnano.8b02376  PMID:29966083
• Kok, B. P., Galmozzi, A., Littlejohn, N. K., Albert, V., Godio, C., Kim, W., Kim, S. M., Bland, J. S., Grayson, N., Fang, M. L., Meyerhof, W., Siuzdak, G., et al. Intestinal bitter taste receptor activation alters hormone secretion and imparts metabolic benefits Molecular Metabolism  2018 16:76-87  DOI:10.1016/j.molmet.2018.07.013  PMID:30120064  PMCID:PMC6158035
• Guijas, C., Montenegro-Burke, J. R., Domingo-Almenara, X., Palermo, A., Warth, B., Hermann, G., Koellensperger, G., Huan, T., Uritboonthai, W., Aisporna, A. E., Wolan, D. W., Spilker, M. E., et al. METLIN: A technology platform for identifying knowns and unknowns Analytical Chemistry  2018 90:3156-3164  DOI:10.1021/acs.analchem.7b04424  PMID:29381867
• Giera, M., dos Santos, F. B., Siuzdak, G. Metabolite-induced protein expression guided by metabolomics and systems biology Cell Metabolism  2018 27:270-272  DOI:10.1016/j.cmet.2018.01.002  PMID:29414681
• Guijas, C., Montenegro-Burke, J. R., Warth, B., Spilker, M. E., Siuzdak, G. Metabolomics activity screening for identifying metabolites that modulate phenotype Nature Biotechnology  2018 36:316-320  DOI:10.1038/nbt.4101  PMID:29621222
• Warth, B., Raffeiner, P., Granados, A., Huan, T., Fang, M., Forsberg, E. M., Benton, H. P., Goetz, L., Johnson, C. H., Siuzdak, G. Metabolomics reveals that dietary xenoestrogens alter cellular metabolism induced by palbociclib/letrozole combination cancer therapy Cell Chemical Biology  2018 25:291-300.e3  DOI:10.1016/j.chembiol.2017.12.010  PMID:29337187  PMCID:PMC5856613
• Beyer, B. A., Fang, M., Sadrian, B., Montenegro-Burke, J. R., Plaisted, W. C., Kok, B. P. C., Saez, E., Kondo, T., Siuzdak, G., Lairson, L. L. Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation Nature Chemical Biology  2018 14:22-28  DOI:10.1038/nchembio.2517  PMID:29131145
• Giera, M., Spilker, M. E., Siuzdak, G. Metabolomics: the omics' superglue The Analytical Scientist  2018 218
• Guijas, C., Siuzdak, G. Reply to comment on METLIN: A technology platform for identifying knowns and unknowns Analytical Chemistry  2018 90:13128-13129  DOI:10.1021/acs.analchem.8b04081  PMID:30299932
• Robinson, A. R., Yousefzadeh, M. J., Rozgaja, T. A., Wang, J., Li, X., Tilstra, J. S., Feldman, C. H., Gregg, S. Q., Johnsong, C. H., Skoda, E. M., Frantz, M. C., Bell-Temin, H., et al. Spontaneous DNA damage to the nuclear genome promotes senescence, redox imbalance and aging Redox Biology  2018 17:259-273  DOI:10.1016/j.redox.2018.04.007  PMID:29747066  PMCID:PMC6006678
• Montenegro-Burke, J. R., Aisporna, A. E., Benton, H. P., Rinehart, D., Fang, M., Huan, T., Warth, B., Forsberg, E., Abe, B. T., Iyanisevic, J., Wolan, D. W., Teyton, L., et al. Data streaming for metabolomics: accelerating data processing and analysis from days to minutes Analytical Chemistry  2017 89:1254-1259  DOI:10.1021/acs.analchem.6b03890  PMID:27983788  PMCID:PMC5244434
• Gendelman, H. E., Zhang, Y., Santamaria, P., Olson, K. E., Schutt, C. R., Bhatti, D., Shetty, B. L. D., Lu, Y., Estes, K. A., Standaert, D. G., Heinrichs-Graham, E., Larson, L., et al. Evaluation of the safety and immunomodulatory effects of sargramostim in a randomized, double-blind phase 1 clinical Parkinson's disease trial NPJ Parkinson's Disease  2017 3  DOI:10.1038/s41531-017-0013-5  PMID:28649610  PMCID:PMC5445595
• Warth, B., Spangler, S., Fang, M., Johnson, C., Forsberg, E., Granados, A., Martin, R. L., Domingo, X., Huan, T., Rinehart, D., Montenegro-Burke, J. R., Hilmers, B., et al. Exposing the exposome with global metabolomics and cognitive computing bioRxiv  2017  DOI:10.1101/145722
• Warth, B., Spangler, S., Fang, M., Johnson, C. H., Forsberg, E. M., Granados, A., Martin, R. L., Domingo-Almenara, X., Huan, T., Rinehart, D., Montenegro-Burke, J. R., Hilmers, B., et al. Exposome-scale investigations guided by global metabolomics, pathway analysis, and cognitive computing Analytical Chemistry  2017 89:11505-11513  DOI:10.1021/acs.analchem.7b02759  PMID:28945073
• Warth, B., Levin, N., Rinehart, D., Teijaro, J., Benton, H. P., Siuzdak, G. Metabolizing data in the cloud Trends in Biotechnology  2017 35:481-483  DOI:10.1016/j.tibtech.2016.12.010  PMID:28117091
• Johnson, C. H., Santidrian, A. F., LeBoeuf, S. E., Kurczy, M. E., Rattray, N. J. W., Rattray, Z., Warth, B., Ritland, M., Hoang, L. T., Loriot, C., Higa, J., Hansen, J. E., et al. Metabolomics guided pathway analysis reveals link between cancer metastasis, cholesterol sulfate, and phospholipids Cancer & Metabolism  2017 5  DOI:10.1186/s40170-017-0171-2  PMID:29093815  PMCID:PMC5663111
• Gao, J., Louie, K. B., Steinke, P., Bowen, B. P., de Raad, M., Zuckermann, R. N., Siuzdak, G., Northen, T. R. Morphology-driven control of metabolite selectivity using nanostructure-initiator mass spectrometry Analytical Chemistry  2017 89:6521-6526  DOI:10.1021/acs.analchem.7b00599  PMID:28520405
• Liu, J., Suel, G., Stevens, T. J., Lando, D., Basu, S., Atkinson, L. P., Laue, E. D., Corson, F., Schweisguth, F., Goni-Moreno, A., de Lorenzo, V., Koonin, E., et al. Principles of Systems Biology, No. 17 Cell Systems  2017 4:472-475  PMID:28544876
• Forsberg, E., Fang, M. L., Siuzdak, G. Staying alive: measuring intact viable microbes with electrospray ionization mass spectrometry Journal of the American Society for Mass Spectrometry  2017 28:14-20  DOI:10.1007/s13361-016-1440-y  PMID:27456857  PMCID:PMC5177535
• Huan, T., Forsberg, E. M., Rinehart, D., Johnson, C. H., Ivanisevic, J., Benton, H. P., Fang, M., Aisporna, A., Hilmers, B., Poole, F. L., Thorgersen, M. P., Adams, M. W. W., et al. Systems biology guided by XCMS Online metabolomics Nature Methods  2017 14:461-462  PMID:28448069
• Kurczy, M. E., Forsberg, E. M., Thorgersen, M. P., Poole II, F. L., Benton, H. P., Ivanisevic, J., Tran, M. L., Wall, J. D., Elias, D. A., Adams, M. W. W., Siuzdak, G. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation ACS Chemical Biology  2016 11:1677-1685  DOI:10.1021/acschembio.6b00082  PMID:27045776
• Paris, L. P., Johnson, C. H., Aguilar, E., Usui, Y., Cho, K., Hoang, L. T., Feitelberg, D., Benton, H. P., Westenskow, P. D., Kurihara, T., Trombley, J., Tsubota, K., et al. Global metabolomics reveals metabolic dysregulation in ischemic retinopathy Metabolomics  2016 12:15  DOI:10.1007/s11306-015-0877-5  PMID:26617478  PMCID:PMC4651979
• Kurihara, T., Westenskow, P. D., Gantner, M. L., Usui, Y., Schultz, A., Bravo, S., Aguilar, E., Wittgrove, C., Friedlander, M. S. H., Paris, L. P., Chew, E., Siuzdak, G., et al. Hypoxia-induced metabolic stress in retinal pigment epithelial cells is sufficient to induce photoreceptor degeneration Elife  2016 5  DOI:10.7554/eLife.14319  PMID:26978795  PMCID:PMC4848091
• Ivanisevic, J., Stauch, K. L., Petrascheck, M., Benton, H. P., Epstein, A. A., Fang, M., Gorantla, S., Tran, M., Hoang, L., Kurczy, M. E., Boska, M. D., Gendelman, H. E., et al. Metabolic drift in the aging brain Aging  2016 8:1000-1020  DOI:10.18632/aging.100961  PMID:27182841  PMCID:PMC4931850
• Johnson, C. H., Spilker, M. E., Goetz, L., Peterson, S. N., Siuzdak, G. Metabolite and microbiome interplay in cancer immunotherapy Cancer Research  2016 76:6146-6152  DOI:10.1158/0008-5472.can-16-0309  PMID:27729325  PMCID:PMC5093024
• Johnson, C. H., Ivanisevic, J., Siuzdak, G. Metabolomics: beyond biomarkers and towards mechanisms Nature Reviews Molecular Cell Biology  2016 17:451-459  DOI:10.1038/nrm.2016.25  PMID:26979502
• Wang, J. H., Westenskow, P. D., Fang, M., Friedlander, M., Siuzdak, G. Quantitative metabolomics of photoreceptor degeneration and the effects of stem cell-derived retinal pigment epithelium transplantation Philosophical Transactions of the Royal Society a-Mathematical Physical and Engineering Sciences  2016 374  DOI:10.1098/rsta.2015.0376  PMID:27644974  PMCID:PMC5031641
• Montenegro-Burke, J. R., Phommavongsay, T., Aisporna, A. E., Huan, T., Rinehart, D., Forsberg, E., Poole, F. L., Thorgersen, M. P., Adams, M. W., Krantz, G., Fields, M. W., Northen, T. R., et al. Smartphone analytics: mobilizing the lab into the cloud for omicscale analyses Analytical Chemistry  2016 88:9753-9758  DOI:10.1021/acs.analchem.6b02676  PMID:27560777  PMCID:PMC5054939
• Deguchi, H., Banerjee, Y., Trauger, S., Siuzdak, G., Kalisiak, E., Fernandez, J. A., Hoang, L., Tran, M., Yegneswaran, S., Elias, D. J., Griffin, J. H. Acylcarnitines are anticoagulants that inhibit factor Xa and are reduced in venous thrombosis, based on metabolomics data Blood  2015 126:1595-1600  DOI:10.1182/blood-2015-03-636761  PMID:26175037  PMCID:PMC4582336
• Johnson, C., Patti, G., Courade, J. P., Shriver, L., Hoang, L., Manchester, M., Siuzdak, G. Alterations in spinal cord metabolism during treatment of neuropathic pain Journal of Neuroimmune Pharmacology  2015 10:396-401  DOI:10.1007/s11481-015-9624-y  PMID:26232265  PMCID:PMC4548716
• Ivanisevic, J., Benton, H. P., Rinehart, D., Epstein, A., Kurczy, M. E., Boska, M. D., Gendelman, H. E., Siuzdak, G. An interactive cluster heat map to visualize and explore multidimensional metabolomic data Metabolomics  2015 11:1029-1034  DOI:10.1007/s11306-014-0759-2  PMID:26195918  PMCID:PMC4505375
• Ivanisevic, J., Elias, D., Deguchi, H., Averell, P. M., Kurczy, M., Johnson, C. H., Tautenhahn, R., Zhu, Z., Watrous, J., Jain, M., Griffin, J., Patti, G. J., et al. Arteriovenous blood metabolomics: a readout of intra-tissue metabostasis Scientific Reports  2015 5:12757  DOI:10.1038/srep12757  PMID:26244428  PMCID:PMC4525490
• Benton, H. P., Ivanisevic, J., Mahieu, N. G., Kurczy, M. E., Johnson, C. H., Franco, L., Rinehart, D., Valentine, E., Gowda, H., Ubhi, B. K., Tautenhahn, R., Gieschen, A., et al. Autonomous metabolomics for rapid metabolite identification in global profiling Analytical Chemistry  2015 87:884-891  DOI:10.1021/ac5025649  PMID:25496351  PMCID:PMC4303330
• Johnson, C. H., Ivanisevic, J., Benton, H. P., Siuzdak, G. Bioinformatics: the next frontier of metabolomics Analytical Chemistry  2015 87:147-156  DOI:10.1021/ac5040693  PMID:25389922  PMCID:PMC4287838
• Kurczy, M. E., Zhu, Z. J., Ivanisevic, J., Schuyler, A. M., Lalwani, K., Santidrian, A. F., David, J. M., Giddabasappa, A., Roberts, A. J., Olivos, H. J., O'Brien, P. J., Franco, L., et al. Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids Nature Communications  2015 6:5998  DOI:10.1038/ncomms6998  PMID:25601659  PMCID:PMC4454288
• Kurczy, M. E., Ivanisevic, J., Johnson, C. H., Uritboonthai, W., Hoang, L., Fang, M., Hicks, M., Aldebot, A., Rinehart, D., Mellander, L. J., Tautenhahn, R., Patti, G. J., et al. Determining conserved metabolic biomarkers from a million database queries Bioinformatics  2015 31:3721-3724  DOI:10.1093/bioinformatics/btv475  PMID:26275895  PMCID:PMC4836397
• Nikolskiy, I., Siuzdak, G., Patti, G. J. Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry Bioinformatics  2015 31:2017-2023  DOI:10.1093/bioinformatics/btv085  PMID:25691443  PMCID:PMC4481697
• Johnson, C. H., Dejea, C. M., Edler, D., Hoang, L. T., Santidrian, A. F., Felding, B. H., Ivanisevic, J., Cho, K., Wick, E. C., Hechenbleikner, E. M., Uritboonthai, W., Goetz, L., et al. Metabolism links bacterial biofilms and colon carcinogenesis Cell Metabolism  2015 21:891-897  DOI:10.1016/j.cmet.2015.04.011  PMID:25959674  PMCID:PMC4456201
• Ivanisevic, J., Siuzdak, G. The role of metabolomics in brain metabolism research Journal of Neuroimmune Pharmacology  2015 10:391-395  DOI:10.1007/s11481-015-9621-1  PMID:26201839  PMCID:PMC4546538
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• Ivanisevic, J., Epstein, A. A., Kurczy, M. E., Benton, P. H., Uritboonthai, W., Fox, H. S., Boska, M. D., Gendelman, H. E., Siuzdak, G. Brain region mapping using global metabolomics Chemistry & Biology  2014 21:1575-1584  DOI:10.1016/j.chembiol.2014.09.016  PMID:25457182  PMCID:PMC4304924
• Gowda, H., Ivanisevic, J., Johnson, C. H., Kurczy, M. E., Benton, H. P., Rinehart, D., Nguyen, T., Ray, J., Kuehl, J., Arevalo, B., Westenskow, P. D., Wang, J. H., et al. Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses Analytical Chemistry  2014 86:6931-6939  DOI:10.1021/ac500734c  PMID:24934772  PMCID:PMC4215863
• Johnson, C. H., Fisher, T. S., Hoang, L. T., Felding, B. H., Siuzdak, G., O'Brien, P. J. Luciferase does not alter metabolism in cancer cells Metabolomics  2014 10:354-360  DOI:10.1007/s11306-014-0622-5  PMID:24791164  PMCID:PMC4002053
• Patti, G. J., Tautenhahn, R., Johannsen, D., Kalisiak, E., Ravussin, E., Bruning, J. C., Dillin, A., Siuzdak, G. Meta-analysis of global metabolomic data identifies metabolites associated with life-span extension Metabolomics  2014 10:737-743  DOI:10.1007/s11306-013-0608-8  PMID:25530742  PMCID:PMC4267291
• Rinehart, D., Johnson, C. H., Nguyen, T., Ivanisevic, J., Benton, H. P., Lloyd, J., Arkin, A. P., Deutschbauer, A. M., Patti, G. J., Siuzdak, G. Metabolomic data streaming for biology-dependent data acquisition Nature Biotechnology  2014 32:524-527  DOI:10.1038/nbt.2927  PMID:24911492  PMCID:PMC4112958
• Deguchi, H., Elias, D. J., Trauger, S., Zhang, H. M., Kalisiak, E., Siuzdak, G., Griffin, J. H. Warfarin untargeted metabolomics study identifies novel procoagulant ethanolamide plasma lipids British Journal of Haematology  2014 165:409-412  DOI:10.1111/bjh.12720  PMID:24450944  PMCID:PMC3984601
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• Marchetti, V., Yanes, O., Aguilar, E., Wang, M., Friedlander, D., Moreno, S., Storm, K., Zhan, M., Naccache, S., Nemerow, G., Siuzdak, G., Friedlander, M. Differential macrophage polarization promotes tissue remodeling and repair in a model of ischemic retinopathy Scientific Reports  2011 1:76  DOI:10.1038/srep00076  PMID:22355595  PMCID:PMC3216563
• Yanes, O., Tautenhahn, R., Patti, G. J., Siuzdak, G. Expanding coverage of the metabolome for global metabolite profiling Analytical Chemistry  2011 83:2152-2161  DOI:10.1021/ac102981k  PMID:21329365  PMCID:PMC3285547
• Patti, G. J., Tautenhahn, R., Fonslow, B. R., Cho, Y., Deutschbauer, A., Arkin, A., Northen, T., Siuzdak, G. Meta-analysis of global metabolomics and proteomics data to link alterations with phenotype Spectroscopy-an International Journal  2011 26:151-154  DOI:10.3233/spe-2011-0534
• Long, J. Z., Cisar, J. S., Milliken, D., Niessen, S., Wang, C., Trauger, S. A., Siuzdak, G., Cravatt, B. F. Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids Nature Chemical Biology  2011 7:763-765  DOI:10.1038/nchembio.659  PMID:21926997  PMCID:PMC3201731
• Greving, M. P., Patti, G. J., Siuzdak, G. Nanostructure-initiator mass spectrometry metabolite analysis and imaging Analytical Chemistry  2011 83:2-7  DOI:10.1021/ac101565f  PMID:21049956  PMCID:PMC3012143
• Pendyala, G., Trauger, S. A., Siuzdak, G., Fox, H. S. Short communication: Quantitative proteomic plasma profiling reveals activation of host defense to oxidative stress in chronic SIV and methamphetamine comorbidity AIDS Research and Human Retroviruses  2011 27:179-182  DOI:10.1089/aid.2010.0090  PMID:20929344  PMCID:PMC3045074
• Powers, M. E., Smith, P. A., Roberts, T. C., Fowler, B. J., King, C. C., Trauger, S. A., Siuzdak, G., Romesberg, F. E. Type I signal peptidase and protein secretion in Staphylococcus epidermidis Journal of Bacteriology  2011 193:340-348  DOI:10.1128/jb.01052-10  PMID:21075926  PMCID:PMC3019839
• Tautenhahn, R., Patti, G. J., Kalisiak, E., Miyamoto, T., Schmidt, M., Lo, F. Y., McBee, J., Baliga, N. S., Siuzdak, G. metaXCMS: second-order analysis of untargeted metabolomics data Analytical Chemistry  2011 83:696-700  DOI:10.1021/ac102980g  PMID:21174458  PMCID:PMC3654666
• Lowe, R. D., Szili, E. J., Kirkbride, P., Thissen, H., Siuzdak, G., Voelcker, N. H. Combined immunocapture and laser desorption/ionization mass spectrometry on porous silicon Analytical Chemistry  2010 82:4201-4208  DOI:10.1021/ac100455x  PMID:20411919
• Patti, G. J., Woo, H. K., Yanes, O., Shriver, L., Thomas, D., Uritboonthai, W., Apon, J. V., Steenwyk, R., Manchester, M., Siuzdak, G. Detection of carbohydrates and steroids by cation-enhanced nanostructure-initiator mass spectrometry (NIMS) for biofluid analysis and tissue imaging Analytical Chemistry  2010 82:121-128  DOI:10.1021/ac9014353  PMID:19961200  PMCID:PMC2802282
• Facciotti, M. T., Pang, W. L., Lo, F. Y., Whitehead, K., Koide, T., Masumura, K., Pan, M., Kaur, A., Larsen, D. J., Reiss, D. J., Hoang, L., Kalisiak, E., et al. Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis BMC Systems Biology  2010 4:64  DOI:10.1186/1752-0509-4-64  PMID:20470417  PMCID:PMC2880973
• Dorrell, M. I., Aguilar, E., Jacobson, R., Trauger, S. A., Friedlander, J., Siuzdak, G., Friedlander, M. Maintaining retinal astrocytes normalizes revascularization and prevents vascular pathology associated with oxygen-induced retinopathy Glia  2010 58:43-54  DOI:10.1002/glia.20900  PMID:19544395  PMCID:PMC2814838
• Yanes, O., Clark, J., Wong, D. M., Patti, G. J., Sanchez-Ruiz, A., Benton, H. P., Trauger, S. A., Desponts, C., Ding, S., Siuzdak, G. Metabolic oxidation regulates embryonic stem cell differentiation Nature Chemical Biology  2010 6:411-417  DOI:10.1038/nchembio.364  PMID:20436487  PMCID:PMC2873061
• Cvetkovic, A., Menon, A. L., Thorgersen, M. P., Scott, J. W., Poole, F. L., Jenney, F. E., Lancaster, W. A., Praissman, J. L., Shanmukh, S., Vaccaro, B. J., Trauger, S. A., Kalisiak, E., et al. Microbial metalloproteomes are largely uncharacterized Nature  2010 466:779-782  DOI:10.1038/nature09265  PMID:20639861
• Patti, G. J., Shriver, L. P., Wassif, C. A., Woo, H. K., Uritboonthai, W., Apon, J., Manchester, M., Porter, F. D., Siuzdak, G. Nanostructure-initiator mass spectrometry (NIMS) imaging of brain cholesterol metabolites in Smith-Lemli-Opitz syndrome Neuroscience  2010 170:858-864  DOI:10.1016/j.neuroscience.2010.07.038  PMID:20670678  PMCID:PMC2952448
• Pendyala, G., Trauger, S. A., Siuzdak, G., Fox, H. S. Quantitative plasma proteomic profiling identifies the vitamin E binding protein afamin as a potential pathogenic factor in SIV induced CNS disease Journal of Proteome Research  2010 9:352-358  DOI:10.1021/pr900685u  PMID:19908921  PMCID:PMC2801767
• Kopp, F., Komatsu, T., Nomura, D. K., Trauger, S. A., Thomas, J. R., Siuzdak, G., Simon, G. M., Cravatt, B. F. The glycerophospho metabolome and its influence on amino acid homeostasis revealed by brain metabolomics of GDE1(-/-) mice Chemistry & Biology  2010 17:831-840  DOI:10.1016/j.chembiol.2010.06.009  PMID:20797612  PMCID:PMC2931592
• Dorrell, M. I., Aguilar, E., Jacobson, R., Yanes, O., Gariano, R., Heckenlively, J., Banin, E., Ramirez, G. A., Gasmi, M., Bird, A., Siuzdak, G., Friedlander, M. Antioxidant or neurotrophic factor treatment preserves function in a mouse model of neovascularization-associated oxidative stress Journal of Clinical Investigation  2009 119:611-623  DOI:10.1172/jci35977  PMID:19188685  PMCID:PMC2648679
• Pendyala, G., Trauger, S. A., Kalisiak, E., Ellis, R. J., Siuzdak, G., Fox, H. S. Cerebrospinal fluid proteomics reveals potential pathogenic changes in the brains of SIV-infected monkeys Journal of Proteome Research  2009 8:2253-2260  DOI:10.1021/pr800854t  PMID:19281240  PMCID:PMC2682714
• Koudelka, K. J., Destito, G., Plummer, E. M., Trauger, S. A., Siuzdak, G., Manchester, M. Endothelial targeting of cowpea mosaic virus (CPMV) via surface vimentin PLoS Pathogens  2009 5:e1000417  DOI:10.1371/journal.ppat.1000417  PMID:19412526  PMCID:PMC2670497
• Zhou, H. Y., Wu, S. L., Joo, J. Y., Zhu, S. Y., Han, D. W., Lin, T. X., Trauger, S., Bien, G., Zhu, Y., Yao, S., Siuzdak, G. Generation of induced pluripotent stem cells using recombinant proteins Cell Stem Cell  2009 4:381-384  DOI:10.1016/j.stem.2009.04.005  PMID:19398399
• Kalisiak, J., Trauger, S. A., Kalisiak, E., Morita, H., Fokin, V. V., Adams, M. W. W., Sharpless, K. B., Siuzdak, G. Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach Journal of the American Chemical Society  2009 131:378-386  DOI:10.1021/ja808172n  PMID:19055353  PMCID:PMC2735399
• Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., Siuzdak, G. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites Proceedings of the National Academy of Sciences of the United States of America  2009 106:3698-3703  DOI:10.1073/pnas.0812874106  PMID:19234110  PMCID:PMC2656143
• Yanes, O., Woo, H. K., Northen, T. R., Oppenheimer, S. R., Shriver, L., Apon, J., Estrada, M. N., Potchoiba, M. J., Steenwyk, R., Manchester, M., Siuzdak, G. Nanostructure initiator mass spectrometry: Tissue imaging and direct biofluid analysis Analytical Chemistry  2009 81:2969-2975  DOI:10.1021/ac802576q  PMID:19301920  PMCID:PMC2676195
• Menon, A. L., Poole, F. L., Cvetkovic, A., Trauger, S. A., Kalisiak, E., Scott, J. W., Shanmukh, S., Praissman, J., Jenney, F. E., Wikoff, W. R., Apon, J. V., Siuzdak, G., et al. Novel multiprotein complexes identified in the hyperthermophilic archaeon pyrococcus furiosus by non-denaturing fractionation of the native proteome Molecular & Cellular Proteomics  2009 8:735-751  DOI:10.1074/mcp.M800246-MCP200  PMID:19043064  PMCID:PMC2668238
• Woo, H. K., Go, E. P., Hoang, L., Trauger, S. A., Bowen, B., Siuzdak, G., Northen, T. R. Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry Rapid Communications in Mass Spectrometry  2009 23:1849-1855  DOI:10.1002/rcm.4076  PMID:19449318  PMCID:PMC3052201
• Wikoff, W. R., Kalisak, E., Trauger, S., Manchester, M., Siuzdak, G. Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response Journal of Proteome Research  2009 8:3578-3587  DOI:10.1021/pr900275p  PMID:19496611  PMCID:PMC3437991
• Crews, B., Wikoff, W. R., Patti, G. J., Woo, H. K., Kalisiak, E., Heideker, J., Siuzdak, G. Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data Analytical Chemistry  2009 81:8538-8544  DOI:10.1021/ac9014947  PMID:19764780  PMCID:PMC3058611
• Northen, T. R., Lee, J. C., Hoang, L., Raymond, J., Hwang, D. R., Yannone, S. M., Wong, C. H., Siuzdak, G. A nanostructure-initiator mass spectrometry-based enzyme activity assay Proceedings of the National Academy of Sciences of the United States of America  2008 105:3678-3683  DOI:10.1073/pnas.0712332105  PMID:18319341  PMCID:PMC2268803
• Trauger, S. A., Kalisak, E., Kalisiak, J., Morita, H., Weinberg, M. V., Menon, A. L., Poole, F. L., Adams, M. W. W., Siuzdak, G. Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile Journal of Proteome Research  2008 7:1027-1035  DOI:10.1021/pr700609j  PMID:18247545
• Wikoff, W. R., Pendyala, G., Siuzdak, G., Fox, H. S. Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques Journal of Clinical Investigation  2008 118:2661-2669  DOI:10.1172/jci34138  PMID:18521184  PMCID:PMC2398736
• O'Maille, G., Go, E. P., Hoang, L., Want, E. J., Smith, C., O'Maille, P., Nordstrom, A., Morita, H., Qin, C., Uritboonthai, W., Apon, J., Moore, R., et al. Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling Spectroscopy-an International Journal  2008 22:327-343  DOI:10.3233/spe-2008-0361
• Nordstrom, A., Want, E., Northen, T., Lehtio, J., Siuzdak, G. Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics Analytical Chemistry  2008 80:421-429  DOI:10.1021/ac:701982e  PMID:18085752
• Eraly, S. A., Vallon, V., Rieg, T., Gangoiti, J. A., Wikoff, W. R., Siuzdak, G., Barshop, B. A., Nigam, S. K. Multiple organic anion transporters contribute to net renal excretion of uric acid Physiological Genomics  2008 33:180-192  DOI:10.1152/physiolgenomics.00207.2007  PMID:18270321  PMCID:PMC3016923
• Woo, H. K., Northen, T. R., Yanes, O., Siuzdak, G. Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis Nature Protocols  2008 3:1341-1349  DOI:10.1038/nprot.2008.110  PMID:18714302
• Vallon, V., Eraly, S. A., Wikoff, W. R., Rieg, T., Kaler, G., Truong, D. M., Ahn, S. Y., Mahapatra, N. R., Mahata, S. K., Gangoiti, J. A., Wu, W., Barshop, B. A., et al. Organic anion transporter 3 contributes to the regulation of blood pressure Journal of the American Society of Nephrology  2008 19:1732-1740  DOI:10.1681/asn.2008020180  PMID:18508962  PMCID:PMC2518443
• Bunner, A. E., Trauger, S. A., Siuzdak, G., Williamson, J. R. Quantitative ESI-TOF analysis of macromolecular assembly kinetics Analytical Chemistry  2008 80:9379-9386  DOI:10.1021/ac8020505  PMID:19007188  PMCID:PMC2735594
• Benton, H. P., Wong, D. M., Trauger, S. A., Siuzdak, G. XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization Analytical Chemistry  2008 80:6382-6389  DOI:10.1021/ac800795f  PMID:18627180  PMCID:PMC2728033
• Pendyala, G., Want, E. J., Webb, W., Siuzdak, G., Fox, H. S. Biomarkers for neuroaids: The widening scope of metabolomics Journal of Neuroimmune Pharmacology  2007 2:72-80  DOI:10.1007/s11481-006-9041-3  PMID:18040828
• Northen, T. R., Yanes, O., Northen, M. T., Marrinucci, D., Uritboonthai, W., Apon, J., Golledge, S. L., Nordstrom, A., Siuzdak, G. Clathrate nanostructures for mass spectrometry Nature  2007 449:1033-1036  DOI:10.1038/nature06195  PMID:17960240
• Lissauer, M. E., Johnson, S. B., Siuzdak, G., Bochicchio, G., Whiteford, C., Nussbaumer, B., Moore, R., Scalea, T. M. Coagulation and complement protein differences between septic and uninfected systemic inflammatory response syndrome patients Journal of Trauma-Injury Infection and Critical Care  2007 62:1082-1092  DOI:10.1097/TA.0b013e31804d23e1  PMID:17495706
• Want, E. J., Nordstrom, A., Morita, H., Siuzdak, G. From exogenous to endogenous: The inevitable imprint of mass spectrometry in metabolomics Journal of Proteome Research  2007 6:459-468  DOI:10.1021/pr060505+  PMID:17269703
• Northen, T. R., Woo, H. K., Northen, M. T., Nordstrom, A., Uritboonthail, W., Turner, K. L., Siuzdak, G. High surface area of porous silicon drives desorption of intact molecules Journal of the American Society for Mass Spectrometry  2007 18:1945-1949  DOI:10.1016/j.jasms.2007.08.009  PMID:17881245  PMCID:PMC2080661
• Wikoff, W. R., Gangoiti, J. A., Barshop, B. A., Siuzdak, G. Metabolomics identifies perturbations in human disorders of propionate metabolism Clinical Chemistry  2007 53:2169-2176  DOI:10.1373/clinchem.2007.089011  PMID:17951291
• Mutch, D. M., O'Maille, G., Wikoff, W. R., Wiedmer, T., Sims, P. J., Siuzdak, G. Mobilization of pro-inflammatory lipids in obese plscr3-deficient mice Genome Biology  2007 8:R38  DOI:10.1186/gb-2007-8-3-r38  PMID:17355638  PMCID:PMC1868938
• Go, E. P., Uritboonthai, W., Apon, J. V., Trauger, S. A., Nordstrom, A., O'Maille, G., Brittain, S. M., Peters, E. C., Siuzdak, G. Selective metabolite and peptide capture/mass detection using fluorous affinity tags Journal of Proteome Research  2007 6:1492-1499  DOI:10.1021/pr060608s  PMID:17343404  PMCID:PMC2530906
• Steenwyk, R. C., Hutzler, J. M., Sams, J., Shen, Z. X., Siuzdak, G. Atmospheric pressure desorption/ionization on silicon ion trap mass spectrometry applied to the quantitation of midazolam in rat plasma and determination of midazolam 1 '-hydroxylation kinetics in human liver microsomes Rapid Communications in Mass Spectrometry  2006 20:3717-3722  DOI:10.1002/rcm.2796  PMID:17117443
• Go, E. P., Wikoff, W. R., Shen, Z. X., O'Maille, G., Morita, H., Conrads, T. P., Nordstrom, A., Trauger, S. A., Uritboonthai, W., Lucas, D. A., Chan, K. C., Veenstra, T. D., et al. Mass spectrometry reveals specific and global molecular transformations during viral infection Journal of Proteome Research  2006 5:2405-2416  DOI:10.1021/pr060215t  PMID:16944953  PMCID:PMC2566936
• Nordstrom, A., O'Maille, G., Qin, C., Siuzdak, G. Nonlinear data alignment for uplc-ms and hplc-ms based metabolomics: Quantitative analysis of endogenous and exogenous metabolites in human serum Analytical Chemistry  2006 78:3289-3295  DOI:10.1021/ac060245f  PMID:16689529  PMCID:PMC3705959
• Want, E. J., Smith, C. A., Qin, C. A., VanHorne, K. C., Siuzdak, G. Phospholipid capture combined with non-linear chromatographic correction for improved serum metabolite profiling Metabolomics  2006 2:145-154  DOI:10.1007/s11306-006-0028-0
• Lee, J. C., Wit, C. Y., Apon, J. V., Siuzdak, G., Wong, C. H. Reactivity-based one-pot synthesis of the tumor-associated antigen n3 minor octasaccharide for the development of a photocleavable dios-ms sugar array Angewandte Chemie-International Edition  2006 45:2753-2757  DOI:10.1002/anie.200504067  PMID:16548041
• Shen, Z. X., Want, E. J., Chen, W., Keating, W., Nussbaumer, W., Moore, R., Gentle, T. M., Siuzdak, G. Sepsis plasma protein profiling with immunodepletion, three-dimensional liquid chromatography tandem mass spectrometry, and spectrum counting Journal of Proteome Research  2006 5:3154-3160  DOI:10.1021/pr060327k  PMID:17081067
• Want, E. J., O'Maille, G., Smith, C. A., Brandon, T. R., Uritboonthai, W., Qin, C., Trauger, S. A., Siuzdak, G. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry Analytical Chemistry  2006 78:743-752  DOI:10.1021/ac051312t  PMID:16448047
• Nordstrom, A., Apon, J. V., Uritboonthal, W., Go, E. P., Siuzdak, G. Surfactant-enhanced desorption/ionization on silicon mass spectrometry Analytical Chemistry  2006 78:272-278  DOI:10.1021/ac051398q  PMID:16383337
• Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., Siuzdak, G. Xcms: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Analytical Chemistry  2006 78:779-787  DOI:10.1021/ac051437y  PMID:16448051
• Talkington, M. W. T., Siuzdak, G., Williamson, J. R. An assembly landscape for the 30S ribosomal subunit Nature  2005 438:628-632  DOI:10.1038/nature04261  PMID:16319883  PMCID:PMC1444899
• Go, E. P., Apon, J. V., Luo, G. H., Saghatelian, A., Daniels, R. H., Sahi, V., Dubrow, R., Cravatt, B. F., Vertes, A., Siuzdak, G. Desorption/ionization on silicon nanowires Analytical Chemistry  2005 77:1641-1646  DOI:10.1021/ac048460o  PMID:15762567
• Smith, C. A., O'Maille, G., Want, E. J., Qin, C., Trauger, S. A., Brandon, T. R., Custodio, D. E., Abagyan, R., Siuzdak, G. METLIN - a metabolite mass spectral database Therapeutic Drug Monitoring  2005 27:747-751  DOI:10.1097/01.ftd.0000179845.53213.39  PMID:16404815
• Bothner, B., Taylor, D., Jun, B., Lee, K. K., Siuzdak, G., Schlutz, C. P., Johnson, J. E. Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex Virology  2005 334:17-27  DOI:10.1016/j.virol.2005.01.017  PMID:15749119
• Lacy, E. R., Wang, Y. F., Post, J., Nourse, A., Webb, W., Mapelli, M., Musacchio, A., Siuzdak, G., Kriwacki, R. W. Molecular basis for the specificity of p27 toward cyclin-dependent kinases that regulate cell division Journal of Molecular Biology  2005 349:764-773  DOI:10.1016/j.jmb.2005.04.019  PMID:15890360
• Lowe, R., Go, E. P., Tong, G. C., Voelcker, N. H., Siuzdak, G. Monitoring edta and endogenous metabolite biomarkers from serum with mass spectrometry Spectroscopy-an International Journal  2005 19:137-146
• Luo, G. H., Chen, Y., Siuzdak, G., Vertes, A. Surface modification and laser pulse length effects on internal energy transfer in dios Journal of Physical Chemistry B  2005 109:24450-24456  DOI:10.1021/jp054311d  PMID:16375447
• Want, E. J., Cravatt, B. F., Siuzdak, G. The expanding role of mass spectrometry in metabolite profiling and characterization ChemBioChem  2005 6:1941-1951  DOI:10.1002/cbic.200500151  PMID:16206229
• Shen, Z. X., Thomas, J. J., Siuzdak, G., Blackledge, R. D. A case study on forensic polymer analysis by dios-ms: The suspect who gave us the slip (r) Journal of Forensic Sciences  2004 49:1028-1035  PMID:15461106
• Shen, Z. X., Go, E. P., Gamez, A., Apon, J. V., Fokin, V., Greig, M., Ventura, M., Crowell, J. E., Blixt, O., Paulson, J. C., Stevens, R. C., Finn, M. G., et al. A mass spectrometry plate reader: monitoring enzyme activity and inhibition with a desorption/ionization on silicon (DIOS) platform ChemBioChem  2004 5:921-927  DOI:10.1002/cbic.200400008  PMID:15239048
• Meng, J. C., Siuzdak, G., Finn, M. G. Affinity mass spectrometry from a tailored porous silicon surface Chemical Communications  2004 2108-2109  DOI:10.1039/b408200a
• Saghatelian, A., Trauger, S. A., Want, E. J., Hawkins, E. G., Siuzdak, G., Cravatt, B. F. Assignment of endogenous substrates to enzymes by global metabolite profiling Biochemistry  2004 43:14332-14339  DOI:10.1021/bi0480335  PMID:15533037
• Meng, J. C., Averbuj, C., Lewis, W. G., Siuzdak, G., Finn, M. G. Cleavable linkers for porous silicon-based mass spectrometry Angewandte Chemie-International Edition  2004 43:1255-1260  DOI:10.1002/anie.200352803  PMID:14991792
• Thomas, J. J., Bothner, B., Traina, J., Benner, W. H., Siuzdak, G. Electrospray ion mobility spectrometry of intact viruses Spectroscopy-an International Journal  2004 18:31-36
• Bothner, B., Siuzdak, G. Electrospray ionization of a whole virus: Analyzing mass, structure, and viability ChemBioChem  2004 5:258-260  DOI:10.1002/cbic.200300754  PMID:14997515
• Trauger, S. A., Go, E. P., Shen, Z. X., Apon, J. V., Compton, B. J., Bouvier, E. S. P., Finn, M. G., Siuzdak, G. High sensitivity and analyte capture with desorption/ionization mass spectrometry on silylated porous silicon Analytical Chemistry  2004 76:4484-4489  DOI:10.1021/ac049657j  PMID:15283591
• Wu, E., Trauger, S. A., Pache, L., Mullen, T. M., Von Seggern, D. J., Siuzdak, G., Nemerow, G. R. Membrane cofactor protein is a receptor for adenoviruses associated with epidemic keratoconjunctivitis Journal of Virology  2004 78:3897-3905  DOI:10.1128/jvi.78.8.3897-3905.2004  PMID:15047806
• Kriwacki, R., Reisdorph, N., Siuzdak, G. Protein structure characterization with mass spectrometry Spectroscopy-an International Journal  2004 18:37-47
• Trauger, S. A., Wu, E., Bark, S. J., Nemerow, G. R., Siuzdak, G. The identification of an adenovirus receptor by using affinity capture and mass spectrometry ChemBioChem  2004 5:1095-1099  DOI:10.1002/cbic.200400037  PMID:15300833
• Lewis, W. G., Shen, Z. X., Finn, M. G., Siuzdak, G. Desorption/ionization on silicon (DIOS) mass spectrometry: background and applications International Journal of Mass Spectrometry  2003 226:107-116  DOI:10.1016/s1387-3806(02)00973-9
• Go, E. P., Prenni, J. E., Wei, J., Jones, A., Hall, S. C., Witkowska, H. E., Shen, Z. X., Siuzdak, G. Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry Analytical Chemistry  2003 75:2504-2506  DOI:10.1021/ac026253n  PMID:12918997
• Reisdorph, N., Thomas, J. J., Katpally, U., Chase, E., Harris, K., Siuzdak, G., Smith, T. J. Human rhinovirus capsid dynamics is controlled by canyon flexibility Virology  2003 314:34-44  DOI:10.1016/s0042-6822(03)00452-5  PMID:14517058
• Trauger, S. A., Junker, T., Siuzdak, G. Investigating viral proteins and intact viruses with mass spectrometry Modern Mass Spectrometry  2003 225:265-282  DOI:10.1007/b10476
• Want, E., Greig, M., Compton, B., Bolanos, B., Siuzdak, G. Mass spectrometry in high throughput analysis Spectroscopy-an International Journal  2003 17:663-680
• Compton, B. J., Siuzdak, G. Mass spectrometry in nucleic acid, carbohydrate and steroid analysis Spectroscopy-an International Journal  2003 17:699-713
• Yao, S., Meng, J. C., Siuzdak, G., Finn, M. G. New catalysts for the asymmetric hydrosilylation of ketones discovered by mass spectrometry screening Journal of Organic Chemistry  2003 68:2540-2546  DOI:10.1021/jo026365e  PMID:12662022
• Prenni, J. E., Shen, Z. X., Trauger, S., Chen, W., Siuzdak, G. Protein characterization using liquid chromatography desorption ionization on silicon mass spectrometry (lc-dios-ms) Spectroscopy-an International Journal  2003 17:693-698
• Meyers, A., Trauger, S., Webb, W., Reisdorph, N., Wranik, C., Peters, E., Siuzdak, G. Protein identification and profiling with mass spectrometry Spectroscopy-an International Journal  2003 17:1-15
• Go, E. P., Shen, Z. X., Harris, K., Siuzdak, G. Quantitative analysis with desorption/ionization on silicon mass spectrometry using electrospray deposition Analytical Chemistry  2003 75:5475-5479  DOI:10.1021/ac034376h  PMID:14710827
• Want, E., Compton, B. J., Hollenbeck, T., Siuzdak, G. The application of mass spectrometry in pharmacokinetics studies Spectroscopy-an International Journal  2003 17:681-691
• Sonderegger, M., Staniszewski, K., Meyers, A., Siuzdak, G. A bioinformatics approach for mass spectrometry data processing: Applications to proteomics and small molecule analysis Spectroscopy-an International Journal  2002 16:81-87
• Bothner, B., Carmitchel, L., Staniszewski, K., Sonderegger, M., Siuzdak, G. Biomolecule structure characterization in the gas phase using mass spectrometry Spectroscopy-an International Journal  2002 16:71-79
• Trauger, S. A., Webb, W., Siuzdak, G. Peptide and protein analysis with mass spectrometry Spectroscopy-an International Journal  2002 16:15-28
• Smith, T. J., Schmidt, T., Fang, J., Wu, J., Siuzdak, G., Stanley, C. A. The structure of apo human glutamate dehydrogenase details subunit communication and allostery Journal of Molecular Biology  2002 318:765-777  DOI:10.1016/s0022-2836(02)00161-4  PMID:12054821
• Thomas, J. J., Shen, Z. X., Blackledge, R., Siuzdak, G. Desorption-ionization on silicon mass spectrometry: An application in forensics Analytica Chimica Acta  2001 442:183-190  DOI:10.1016/s0003-2670(01)01107-2
• Thomas, J. J., Shen, Z. X., Crowell, J. E., Finn, M. G., Siuzdak, G. Desorption/ionization on silicon (dios): A diverse mass spectrometry platform for protein characterization Proceedings of the National Academy of Sciences of the United States of America  2001 98:4932-4937  DOI:10.1073/pnas.081069298  PMID:11296246  PMCID:PMC33141
• Shen, Z. X., Yao, S. L., Crowell, J. E., Siuzdak, G., Finn, M. G. Dios-mseed: A chip-based method for measurement of enantiomeric excess by kinetic resolution/mass spectrometry Israel Journal of Chemistry  2001 41:313-316  DOI:10.1560/tbxu-fd8h-fhm1-nr8h
• Bark, S. J., Muster, N., Yates, J. R., Siuzdak, G. High-temperature protein mass mapping using a thermophilic protease Journal of the American Chemical Society  2001 123:1774-1775  DOI:10.1021/ja002909n  PMID:11456785
• Fuerstenau, S. D., Benner, W. H., Thomas, J. J., Brugidou, C., Bothner, B., Siuzdak, G. Mass spectrometry of an intact virus Angewandte Chemie-International Edition  2001 40:542-544
• Shen, Z. X., Thomas, J. J., Averbuj, C., Broo, K. M., Engelhard, M., Crowell, J. E., Finn, M. G., Siuzdak, G. Porous silicon as a versatile platform for laser desorption/ionization mass spectrometry Analytical Chemistry  2001 73:612-619  DOI:10.1021/ac000746f  PMID:11217770
• Broo, K., Wei, J., Marshall, D., Brown, F., Smith, T. J., Johnson, J. E., Schneemann, A., Siuzdak, G. Viral capsid mobility: A dynamic conduit for inactivation Proceedings of the National Academy of Sciences of the United States of America  2001 98:2274-2277  DOI:10.1073/pnas.051598298  PMID:11226229  PMCID:PMC30128
• Thomas, J. J., Bakhtiar, R., Siuzdak, G. Mass spectrometry in viral proteomics Accounts of Chemical Research  2000 33:179-187  DOI:10.1021/ar9801200  PMID:10727207
• Bothner, B., Chavez, R., Wei, J., Strupp, C., Phung, Q., Schneemann, A., Siuzdak, G. Monitoring enzyme catalysis with mass spectrometry Journal of Biological Chemistry  2000 275:13455-13459  DOI:10.1074/jbc.275.18.13455  PMID:10788458
• Bothner, B., Schneemann, A., Marshall, D., Reddy, V., Johnson, J. E., Siuzdak, G. Crystallographically identical virus capsids display different properties in solution Nature Structural Biology  1999 6:114-116  PMID:10048920
• Wei, J., Buriak, J. M., Siuzdak, G. Desorption-ionization mass spectrometry on porous silicon Nature  1999 399:243-246  PMID:10353246
• Hollenbeck, T. P. E., Siuzdak, G., Blackledge, R. D. Electrospray and maldi mass spectrometry in the identification of spermicides in criminal investigations Journal of Forensic Sciences  1999 44:783-788  PMID:10432613
• Yang, C. Y., Gu, Z. W., Yang, M. L., Lin, S. N., Siuzdak, G., Smith, C. V. Identification of modified tryptophan residues in apolipoprotein b-100 derived from copper ion-oxidized low-density lipoprotein Biochemistry  1999 38:15903-15908  DOI:10.1021/bi991464g  PMID:10625456
• Schalley, C. A., Castellano, R. K., Brody, M. S., Rudkevich, D. M., Siuzdak, G., Rebek, J. Investigating molecular recognition by mass spectrometry: Characterization of calixarene-based self-assembling capsule hosts with charged guests Journal of the American Chemical Society  1999 121:4568-4579  DOI:10.1021/ja990276a
• Guo, J. H., Wu, J., Siuzdak, G., Finn, M. G. Measurement of enantiomeric excess by kinetic resolution and mass spectrometry Angewandte Chemie-International Edition  1999 38:1755-1758  DOI:10.1002/(sici)1521-3773(19990614)38:12<1755::aid-anie1755>3.3.co;2-h
• Chatman, K., Hollenbeck, T., Hagey, L., Vallee, M., Purdy, R., Weiss, F., Siuzdak, G. Nanoelectrospray mass spectrometry and precursor ion monitoring for quantitative steroid analysis and attomole sensitivity Analytical Chemistry  1999 71:2358-2363  DOI:10.1021/ac9806411  PMID:10405603
• Tsui, V., Garcia, C., Cavagnero, S., Siuzdak, G., Dyson, H. J., Wright, P. E. Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through an obligatory intermediate Protein Science  1999 8:45-49  DOI:10.1110/ps.8.1.45  PMID:10210182  PMCID:PMC2144105
• Marmey, P., Bothner, B., Jacquot, E., de Kochko, A., Ong, C. A., Yot, P., Siuzdak, G., Beachy, R. N., Fauquet, C. M. Rice tungro bacilliform virus open reading frame 3 encodes a single 37-kda coat protein Virology  1999 253:319-326  DOI:10.1006/viro.1998.9519  PMID:9918890
• Takayama, S., Chung, S. J., Igarashi, Y., Ichikawa, Y., Sepp, A., Lechler, R. I., Wu, J., Hayashi, T., Siuzdak, G., Wong, C. H. Selective inhibition of β-1,4- and α-1,3-galactosyltransferases: donor sugar-nucleotide based approach Bioorganic & Medicinal Chemistry  1999 7:401-409  DOI:10.1016/s0968-0896(98)00249-1  PMID:10218835
• Schalley, C. A., Rivera, J. M., Martin, T., Santamaria, J., Siuzdak, G., Rebek, J. Structural examination of supramolecular architectures by electrospray ionization mass spectrometry European Journal of Organic Chemistry  1999 1999:1325-1331  DOI:10.1002/(SICI)1099-0690(199906)1999:6<1325::AID-EJOC1325>3.0.CO;2-6
• Lewis, J. K., Bothner, B., Smith, T. J., Siuzdak, G. Antiviral agent blocks breathing of the common cold virus Proceedings of the National Academy of Sciences of the United States of America  1998 95:6774-6778  DOI:10.1073/pnas.95.12.6774  PMID:9618488
• Owens, D. R., Bothner, B., Phung, Q., Harris, K., Siuzdak, G. Aspects of oligonucleotide and peptide sequencing with maldi and electrospray mass spectrometry Bioorganic & Medicinal Chemistry  1998 6:1547-1554  DOI:10.1016/s0968-0896(98)00098-4  PMID:9801826
• Bothner, B., Dong, X. F., Bibbs, L., Johnson, J. E., Siuzdak, G. Evidence of viral capsid dynamics using limited proteolysis and mass spectrometry Journal of Biological Chemistry  1998 273:673-676  DOI:10.1074/jbc.273.2.673  PMID:9422714
• Lewis, J. K., Bendahmane, M., Smith, T. J., Beachy, R. N., Siuzdak, G. Identification of viral mutants by mass spectrometry Proceedings of the National Academy of Sciences of the United States of America  1998 95:8596-8601  DOI:10.1073/pnas.95.15.8596  PMID:9671723
• Siuzdak, G. Probing viruses with mass spectrometry Journal of Mass Spectrometry  1998 33:203-211  DOI:10.1002/(sici)1096-9888(199803)33:3<203::aid-jms653>3.0.co;2-q  PMID:9538522
• Siuzdak, G. What's your frequently asked mass spec question? R&D Magazine  1998 40:37-37
• Wu, J., Chatman, K., Harris, K., Siuzdak, G. An automated maldi mass spectrometry approach for optimizing cyclosporin extraction and quantitation Analytical Chemistry  1997 69:3767-3771  DOI:10.1021/ac970276y  PMID:9302875
• Takayama, S., Martin, R., Wu, J., Laslo, K., Siuzdak, G., Wong, C. H. Chemoenzymatic preparation of novel cyclic imine sugars and rapid biological activity evaluation using electrospray mass spectrometry and kinetic analysis Journal of the American Chemical Society  1997 119:8146-8151  DOI:10.1021/ja971695f
• Kriwacki, R. W., Wu, J., Tennant, L., Wright, P. E., Siuzdak, G. Probing protein structure using biochemical and biophysical methods - proteolysis, matrix-assisted laser desorption/ionization mass spectrometry, high-performance liquid chromatography and size-exclusion chromatography of p21(waf1/cip1/sdi1) Journal of Chromatography A  1997 777:23-30  DOI:10.1016/s0021-9673(97)00527-x  PMID:9297835
• Wu, J., Takayama, S., Wong, C. H., Siuzdak, G. Quantitative electrospray mass spectrometry for the rapid assay of enzyme inhibitors Chemistry & Biology  1997 4:653-657  DOI:10.1016/s1074-5521(97)90220-9  PMID:9331404
• Chang, H. T., Chen, C. T., Kondo, T., Siuzdak, G., Sharpless, K. B. Asymmetric dihydroxylation enables rapid construction of chiral dendrimers based on 1,2-diols Angewandte Chemie-International Edition  1996 35:182-186  DOI:10.1002/anie.199601821
• Fitzgerald, M. C., Siuzdak, G. Biochemical mass spectrometry: Worth the weight? Chemistry & Biology  1996 3:707-715  DOI:10.1016/s1074-5521(96)90245-8  PMID:8939685
• Fitzgerald, M. C., Harris, K., Shevlin, C. G., Siuzdak, G. Direct characterization of solid phase resin-bound molecules by mass spectrometry Bioorganic & Medicinal Chemistry Letters  1996 6:979-982  DOI:10.1016/0960-894x(96)00152-7
• Siuzdak, G., Bothner, B., Yeager, M., Brugidou, C., Fauquet, C. M., Hoey, K., Chang, C. M. Mass spectrometry and viral analysis Chemistry & Biology  1996 3:45-48  DOI:10.1016/s1074-5521(96)90083-6  PMID:8807827
• Kriwacki, R. W., Wu, J., Siuzdak, G., Wright, P. E. Probing protein/protein interactions with mass spectrometry and isotopic labeling: Analysis of the p21/cdk2 complex Journal of the American Chemical Society  1996 118:5320-5321  DOI:10.1021/ja960752m
• Cravatt, B. F., Prosperogarcia, O., Siuzdak, G., Gilula, N. B., Henriksen, S. J., Boger, D. L., Lerner, R. A. Chemical characterization of a family of brain lipids that induce sleep Science  1995 268:1506-1509  DOI:10.1126/science.7770779  PMID:7770779
• Krebs, J. F., Siuzdak, G., Dyson, H. J., Stewart, J. D., Benkovic, S. J. Detection of a catalytic antibody species acylated at the active site by electrospray mass spectrometry Biochemistry  1995 34:720-723  DOI:10.1021/bi00003a002  PMID:7827028
• Siuzdak, G., Bothner, B. Gas-phase micelles Angewandte Chemie-International Edition  1995 34:2053-2055  DOI:10.1002/anie.199520531
• Bothner, B., Chatman, K., Sarkisian, M., Siuzdak, G. Liquid-chromatography mass-spectrometry of antisense oligonucleotides Bioorganic & Medicinal Chemistry Letters  1995 5:2863-2868  DOI:10.1016/0960-894x(95)00499-j
• Siuzdak, G., Krebs, J. F., Benkovic, S. J., Dyson, H. J. Binding of hapten to a single chain catalytic antibody demonstrated by electrospray mass spectrometry Journal of the American Chemical Society  1994 116:7937-7938  DOI:10.1021/ja00096a077
• Lerner, R. A., Siuzdak, G., Prosperogarcia, O., Henriksen, S. J., Boger, D. L., Cravatt, B. F. Cerebrodiene: A brain lipid isolated from sleep-deprived cats Proceedings of the National Academy of Sciences of the United States of America  1994 91:9505-9508  DOI:10.1073/pnas.91.20.9505  PMID:7937797  PMCID:PMC44841
• Stewart, J. D., Krebs, J. F., Siuzdak, G., Berdis, A. J., Smithrud, D. B., Benkovic, S. J. Dissection of an antibody-catalyzed reaction Proceedings of the National Academy of Sciences of the United States of America  1994 91:7404-7409  DOI:10.1073/pnas.91.16.7404  PMID:8052597
• Siuzdak, G., Zheng, Z. L., Rhamphal, J. Y., Ichikawa, Y., Nicolaou, K. C., Gaeta, F. C. A., Chatman, K. S., Wong, C. H. Examination of the sialyl-lewis-x calcium complex by electrospray mass-spectrometry Bioorganic & Medicinal Chemistry Letters  1994 4:2863-2866  DOI:10.1016/s0960-894x(01)80829-5
• Crano, J., Knowles, D., Kwiatkowski, P., Flood, T., Ross, R., Chiang, L., Lasch, J., Chadha, R., Siuzdak, G. Structure of three novel photochromic compounds; X-ray crystallographic and theoretical studies Acta Crystallographica Section B-Structural Science  1994 50:772-779  DOI:10.1107/s0108768194005938
• Siuzdak, G. The emergence of mass-spectrometry in biochemical-research Proceedings of the National Academy of Sciences of the United States of America  1994 91:11290-11297  DOI:10.1073/pnas.91.24.11290  PMID:7972052
• Rideout, D., Bustamante, A., Siuzdak, G. Cationic drug analysis using matrix-assisted laser-desorption ionization mass-spectrometry - application to influx kinetics, multidrug-resistance, and intracellular chemical-change Proceedings of the National Academy of Sciences of the United States of America  1993 90:10226-10229  DOI:10.1073/pnas.90.21.10226  PMID:8234281
• Siuzdak, G., Ichikawa, Y., Caulfield, T. J., Munoz, B., Wong, C. H., Nicolaou, K. C. Evidence of ca2+-dependent carbohydrate association through ion spray mass-spectrometry Journal of the American Chemical Society  1993 115:2877-2881  DOI:10.1021/ja00060a040
• Siuzdak, G., Wendeborn, S. V., Nicolaou, K. C. Cationization of organometallo carbonyl compounds by fast ion bombardment International Journal of Mass Spectrometry and Ion Processes  1992 112:79-91  DOI:10.1016/0168-1176(92)87033-b
• Siuzdak, G., Belbruno, J. J. Multiphoton ionization of nitrobenzene in nonaqueous solutions - characterization of the cation and ion-molecule chemistry Laser Chemistry  1991 11:83-93  DOI:10.1155/lc.11.83
• Siuzdak, G., North, S., Belbruno, J. J. Multiphoton ionization of phenol in nonaqueous solutions - characterization of the cation and ion molecule chemistry Journal of Physical Chemistry  1991 95:5186-5190  DOI:10.1021/j100166a050
• Belbruno, J. J., Siuzdak, G. Rempi-ms - application to the study of the gas-phase dynamics of radical cations Institute of Physics Conference Series  1991 177-180
• Belbruno, J. J., Siuzdak, G. Resonant ionization in solution - initiation of ion-molecule chemistry by rempi Institute of Physics Conference Series  1991 351-354
• Siuzdak, G., Belbruno, J. J. Laser multiphoton dissociation ionization of butylamines - competitive processes in radical cations Journal of Physical Chemistry  1990 94:4559-4565  DOI:10.1021/j100374a038
• Siuzdak, G., Belbruno, J. J. Multiphoton ionization studies of amines with uv-vis lasers Applied Physics B-Photophysics and Laser Chemistry  1990 50:221-226  DOI:10.1007/bf00357287
• Belbruno, J. J., Siuzdak, G., North, S. Multiphoton-induced chemistry of phenol in hexane at 266 nm Chemical Physics Letters  1990 166:167-172  DOI:10.1016/0009-2614(90)87271-r
• Belbruno, J. J., Siuzdak, G., North, S. Uv multiphoton induced chemistry of nitrobenzene in solution Laser Chemistry  1990 10:177-184  DOI:10.1155/1990/42676
• Marzzacco, C. J., Deckey, G., Colarulli, R., Siuzdak, G., Halpern, A. M. Excited-state protonation and photophysical properties of azaphenanthrenes Journal of Physical Chemistry  1989 93:2935-2939  DOI:10.1021/j100345a018