%0 Journal Article %J Genome Biology %D 2022 %T Enhanced protein isoform characterization through long-read proteogenomics %A Miller, R. M. %A Jordan, B. %A Mehlferber, M. M. %A Jeffery, E. D. %A Chatzipantsiou, C. %A Kaur, S. %A Millikin, R. J. %A Dai, Y. X. %A Tiberi, S. %A Castaldi, P. J. %A Shortreed, M. R. %A Luckey, C. J. %A Conesa, A. %A Smith, L. M. %A Mays, A. D. %A Sheynkman, G. M. %B Genome Biology %V 23 %8 Mar %@ 1474-760X %G eng %M WOS:000764049100002 %] 69 %R 10.1186/s13059-022-02624-y %0 Journal Article %J Journal of Proteome Research %D 2022 %T A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis %A Dai, Y. L. %A Millikin, R. J. %A Rolfs, Z. %A Shortreed, M. R. %A Smith, L. M. %B Journal of Proteome Research %V 21 %P 2609-2618 %@ 1535-3893 %G eng %M WOS:000866359200001 %R 10.1021/acs.jproteome.2c00305 %0 Journal Article %J Iscience %D 2021 %T Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet %A Yau, B. %A Naghiloo, S. %A Diaz-Vegas, A. %A Carr, A. V. %A Van Gerwen, J. %A Needham, E. J. %A Jevon, D. %A Chen, S. Y. %A Hoehn, K. L. %A Brandon, A. E. %A Macia, L. %A Cooney, G. J. %A Shortreed, M. R. %A Smith, L. M. %A Keller, M. P. %A Thorn, P. %A Larance, M. %A James, D. E. %A Humphrey, S. J. %A Kebede, M. A. %B Iscience %V 24 %8 Oct %G eng %M WOS:000713819900003 %] 103099 %R 10.1016/j.isci.2021.103099 %0 Journal Article %J Nature methods %D 2019 %T Best practices and benchmarks for intact protein analysis for top-down mass spectrometry %A D.P Donnelly %A C.M Rawlins %A C.J DeHart %A L Fornelli %A L.F Schachner %A Z Lin %A J.L Lippens %A K.C Aluri %A R Sarin %A B Chen %A C Lantz %A W Jung %A K.R Johnson %A A Koller %A J.J Wolff %A I. DG Campuzano %A J.R Auclair %A A.R Ivanov %A J.P Whitelegge %A L Pasa-Tolic %A J Chamot-Rooke %A P.O Danis %A L.M Smith %A Y.O Tsybin %A J.A Loo %A Y Ge %A N.L Kelleher %A J.N Agar %B Nature methods %V 16 %G eng %N 7 %0 Journal Article %J Journal of Proteome Research %D 2019 %T Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database %A Y. Dai %A K.E Buxton %A L.V Schaffer %A R.M Miller %A R.J Millikin %A M. Scalf %A B.L Frey %A M.R Shortreed %A L.M Smith %B Journal of Proteome Research %V 18 %G eng %N 10 %0 Journal Article %J Nature methods %D 2019 %T A five-level classification system for proteoform identifications %A L.M Smith %A P.M Thomas %A M.R Shortreed %A L.V Schaffer %A R.T Fellers %A R.D LeDuc %A T. Tucholski %A Y. Ge %A J.A Agar %A L.C Anderson %A J. Chamot-Rooke %A J. Gault %A J.A Loo %A L. Pasa-Tolic %A C.V Robinson %A H. Schluter %A Y.O Tsybin %A M. Bilaseca %A J.A Vizcaino %A P.O Danis %A N.L Kelleher %B Nature methods %V 16 %8 08/2019 %G eng %N 10 %& 939 %0 Journal Article %J Nature genetics %D 2018 %T EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis %A Z. Yang %A S. Qian %A R.N Scheid %A L. Lu %A X. Chen %A R. Liu %A X. Du %A X. Lv %A M.D Boersma %A M. Scalf %A L.M Smith %A J.M Denu %A J.Du %A X. Zhong %B Nature genetics %V 50 %G eng %N 9 %0 Journal Article %J Journal of Proteome Research %D 2018 %T ProForma: A Standard Proteoform Notation %A Leduc, R. D. %A Schwammle, V. %A Shortreed, M. R. %A Cesnik, A. J. %A Solntsev, S. K. %A Shaw, J. B. %A Martin, M. J. %A Vizcaino, J. A. %A Alpi, E. %A Danis, P. %A Kelleher, N. L. %A Smith, L. M. %A Ge, Y. %A Agar, J. N. %A Chamot-Rooke, J. %A Loo, J. A. %A Pasa-Tolic, L. %A Tsybin, Y. O. %B Journal of Proteome Research %V 17 %P 1321-1325 %8 Mar %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00851 %0 Journal Article %J Journal of Proteome Research %D 2018 %T Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families %A Cesnik, A. J. %A Shortreed, M. R. %A Schaffer, L. V. %A Knoener, R. A. %A Frey, B. L. %A Scalf, M. %A Solntsev, S. K. %A Dai, Y. X. %A Gasch, A. P. %A Smith, L. M. %B Journal of Proteome Research %V 17 %P 568-578 %8 Jan %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00685 %0 Journal Article %J Journal of Proteome Research %D 2017 %T Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database %A Dai, Y. X. %A Shortreed, M. R. %A Scalf, M. %A Frey, B. L. %A Cesnik, A. J. %A Solntsev, S. %A Schaffer, L. V. %A Smith, L. M. %B Journal of Proteome Research %V 16 %P 4156-4165 %8 Nov %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00516 %0 Journal Article %J Analytical Chemistry %D 2017 %T Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins %A Dai, Yunxiang %A Kennedy-Darling, Julia %A Shortreed, Michael R. %A Scalf, Mark %A Gasch, Audrey P. %A Smith, L. M. %B Analytical Chemistry %V 89 %P 7841-7846 %@ 0003-2700 %G eng %R 10.1021/acs.analchem.7b01784 %0 Journal Article %J Genomics %D 2016 %T HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae %A Guillen-Ahlers, H. %A Rao, P. K. %A Levenstein, M. E. %A Kennedy-Darling, J. %A Perumalla, D. S. %A Jadhav, A. Y. %A Glenn, J. P. %A Ludwig-Kubinski, A. %A Drigalenko, E. %A Montoya, M. J. %A Goring, H. H. %A Anderson, C. D. %A Scalf, M. %A Gildersleeve, H. I. %A Cole, R. %A Greene, A. M. %A Oduro, A. K. %A Lazarova, K. %A Cesnik, A. J. %A Barfknecht, J. %A Cirillo, L. A. %A Gasch, A. P. %A Shortreed, M. R. %A Smith, L. M. %A Olivier, M. %B Genomics %V 107 %P 267-273 %G eng %0 Journal Article %J Science Translational Medicine %D 2015 %T Bioengineered vocal fold mucosa for voice restoration %A Ling, C. Y. %A Li, Q. Y. %A Brown, M. E. %A Kishimoto, Y. %A Toya, Y. %A Devine, E. E. %A Choi, K. O. %A Nishimoto, K. %A Norman, I. G. %A Tsegyal, T. %A Jiang, J. J. %A Burlingham, W. J. %A Gunasekaran, S. %A L. M. Smith %A Frey, B. L. %A Welham, N. V. %B Science Translational Medicine %V 7 %8 Nov %@ 1946-6234 %G eng %] 314ra187 %R 10.1126/scitranslmed.aab4014 %0 Journal Article %J Nature Methods %D 2013 %T Proteoform: a single term describing protein complexity %A L. M. Smith %A Kelleher, N. L. %A Ge, Y. %A Consortium Top Down, Proteomics %B Nature Methods %V 10 %P 186-187 %8 Mar %@ 1548-7091 %G eng %R 10.1038/nmeth.2369 %0 Journal Article %J Molecular Cell %D 2011 %T Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction %A Hallows, William C. %A Yu, Wei %A Smith, Brian C. %A Devires, Mark K. %A Ellinger, James J. %A Someya, Shinichi %A Shortreed, Michael R. %A Prolla, Tomas %A Markley, John L. %A L. M. Smith %A Zhao, Shimin %A Guan, Kun-Liang %A Denu, John M. %B Molecular Cell %V 41 %P 139-149 %8 Jan %G eng %2 PMC3101115 %R 10.1016/j.molcel.2011.01.002 %F ISI 2011 03 18 %0 Journal Article %J Analytical Chemistry %D 2008 %T Identification of Cell Surface Markers to Differentiate Rat Endothelial and Fibroblast Cells Using Lectin Arrays and LC-ESI-MS/MS %A Lee, J. E. %A Mirza, S. P. %A Didier, D. N. %A Scalf, M. %A Olivier, M. %A Greene, A. S. %A L. M. Smith %B Analytical Chemistry %V 80 %P 8269-8275 %8 Nov %G eng %2 PMC2950091 %R 10.1021/ac801390b %F ISI 2008 11 27 %0 Journal Article %J Analytical Biochemistry %D 2007 %T Characterization of vascular endothelial growth factor receptors on the endothelial cell surface during hypoxia using whole cell binding arrays %A Lee, Ji Eun %A Didier, Damela N. %A Lockett, Matthew R. %A Scalf, Mark %A Greene, Andrew S. %A Olivier, Michael %A L. M. Smith %B Analytical Biochemistry %V 369 %P 241-247 %8 Oct %G eng %2 PMC2706495 %R 10.1016/j.ab.2007.06.010 %F ISI 2007 10 19 %0 Journal Article %J International Journal of Mass Spectrometry %D 2002 %T Collision cross sections of gas phase DNA ions %A Moradian, A. %A Scalf, M. %A Westphall, M. S. %A L. M. Smith %A Douglas, D. J. %B International Journal of Mass Spectrometry %V 219 %P 161-170 %8 Aug 1 %G eng %R 10.1016/S1387-3806(02)00546-8 %0 Journal Article %J Analytical Chemistry %D 1997 %T DNA analysis using an electrospray scanning mobility particle sizer %A Mouradian, S. %A Skogen, J. W. %A Dorman, F. D. %A Zarrin, F. %A Kaufman, S. L. %A L. M. Smith %B Analytical Chemistry %V 69 %P 919-925 %8 Mar %@ 0003-2700 %G eng %R 10.1021/ac960785k %0 Journal Article %J Biochemica %D 1996 %T The Cleavase Fragment Length Polymorphism (CFLP) assay %A Brow, M. A. D. %A Oldenburg, M. C. %A Lyamichev, V. %A Heisler, L. M. %A Grotelueschen, J. %A Lyamicheva, N. %A Kozyavkin, S. %A Fors, L. %A Dahlberg, J. E. %A L. M. Smith %A Olive, D. M. %B Biochemica %V 1 %P 14-15 %G eng %0 Journal Article %J Journal of Clinical Microbiology %D 1996 %T Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage %A Brow, M. A. D. %A Oldenburg, M. C. %A Lyamichev, V. %A Heisler, L. M. %A Lyamicheva, N. %A Hall, J. G. %A Eagan, N. J. %A Olive, D. M. %A L. M. Smith %A Fors, L. %A Dahlberg, J. E. %B Journal of Clinical Microbiology %V 34 %P 3129-3137 %8 Dec %@ 0095-1137 %G eng %2 PMC229470 %0 Journal Article %J Focus %D 1996 %T Mutation detection by cleavase fragment length polymorphism %A Brow, M. A. D. %A Oldenburg, M. C. %A Lyamichev, V. %A Heisler, L. M. %A Grotelueschen, J. %A Lyamicheva, N. %A Kozyavkin, S. %A Fors, L., %A Dahlberg, J. %A L. M. Smith %A Olive, D. M. %B Focus %V 18 %P 2-5 %G eng %0 Journal Article %J Proceedings - Electrochemical Society %D 1994 %T Fabrication of microstructures for use in biological and optical applications %A Denton, D. D. %A Thiel, A. J. %A L. M. Smith %A Bajikar, S. %A White, V. %A Ghodssi, R. %A Fish, G. %A McCaughan, L. %B Proceedings - Electrochemical Society %V 94-14 %P 103-14 %@ 0161-6374 %G English %0 Journal Article %J JAMA %D 1994 %T Statement on use of DNA testing for presymptomatic identification of cancer risk %A Collins, F. S. %A Benjamin, L. J. %A Botstein, D. %A Cox, J. R. %A Davidson, N. %A Gray, J. W. %A Holtzman, N. %A Housman, D. E. %A Jamison, K. R. %A Nelkin, D. %A Rothstein, R. %A Smith, D. C. %A L. M. Smith %A Spence, M. A. %A Tilghman, S. M. %B JAMA %V 271 %P 785-785 %8 Mar %@ 0098-7484 %G eng %R 10.1001/jama.1994.03510340075038 %0 Journal Article %J Methods in Enzymology %D 1993 %T High-speed DNA sequencing by capillary gel electrophoresis %A Luckey, John A. %A Drossman, Howard %A Kostichka, Tony %A L. M. Smith %B Methods in Enzymology %V 218 %P 154-72 %@ 0076-6879 %G English %R 10.1016/0076-6879(93)18014-4 %0 Journal Article %J Bio/Technology %D 1992 %T High speed automated DNA sequencing in ultrathin slab gels %A Kostichka, Anthony J. %A Marchbanks, Michael L. %A Brumley, Robert L., Jr. %A Drossman, Howard %A L. M. Smith %B Bio/Technology %V 10 %P 78-81 %@ 0733-222X %G English %R 10.1038/nbt0192-78 %0 Journal Article %J BioTechniques %D 1990 %T An automated instrument for the performance of enzymatic DNA sequencing reactions %A D'Cunha, J. %A Berson, B. J. %A Brumley, R. L., Jr. %A Wagner, P. R. %A L. M. Smith %B BioTechniques %V 9 %P 80-5, 88-90 %@ 0736-6205 %G English %0 Journal Article %J Nucleic Acids Research %D 1990 %T High speed DNA sequencing by capillary electrophoresis %A Luckey, J. A. %A Drossman, H. %A Kostichka, A. J. %A Mead, D. A. %A Dcunha, J. %A Norris, T. B. %A L. M. Smith %B Nucleic Acids Research %V 18 %P 4417-4421 %8 Aug %@ 0305-1048 %G eng %2 PMC331259 %R 10.1093/nar/18.15.4417 %0 Journal Article %J Analytical Chemistry %D 1990 %T High-speed separations of DNA sequencing reactions by capillary electrophoresis %A Drossman, H. %A Luckey, J. A. %A Kostichka, A. J. %A Dcunha, J. %A L. M. Smith %B Analytical Chemistry %V 62 %P 900-903 %8 May %@ 0003-2700 %G eng %R 10.1021/ac00208a003 %0 Journal Article %J Struct. Methods, Proc. Conversation Discip. Biomol. Stereodyn., 6th %D 1990 %T Peak height variability and accuracy in automated DNA sequencing %A Sanders, Jane Z. %A MacKellar, Sara L. %A Otto, Barbara J. %A Dodd, Christopher T. %A Heiner, Cheryl %A Hood, Leroy E. %A L. M. Smith %B Struct. Methods, Proc. Conversation Discip. Biomol. Stereodyn., 6th %V 1 %P 89-102 %G English %0 Journal Article %J BioTechniques %D 1987 %T Approaches to subpicomole protein sequencing %A Kent, S. %A Hood, L. %A Aebersold, R. %A Teplow, D. %A L. M. Smith %A Farnsworth, V. %A Cartier, P. %A Hines, W. %A Hughes, P. %A Dodd, C. %B BioTechniques %V 5 %P 314-321 %8 May-Jun %@ 0736-6205 %G eng %0 Journal Article %J Nature %D 1986 %T Fluorescence detection in automated DNA sequence analysis %A L. M. Smith %A Sanders, Jane Z. %A Kaiser, Robert J. %A Hughes, Peter %A Dodd, Chris %A Connell, Charles R. %A Heiner, Cheryl %A Kent, Stephen B. H. %A Hood, Leroy E. %B Nature %V 321 %P 674-9 %@ 0028-0836 %G English %R 10.1038/321674a0