%0 Journal Article %J Journal of Proteome Research %D 2022 %T Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br %A Miller, R. M. %A Knoener, R. A. %A Benner, B. E. %A Frey, B. L. %A Scalf, M. %A Shortreed, M. R. %A Sherer, N. M. %A Smith, L. M. %B Journal of Proteome Research %V 21 %P 993-1001 %8 Apr %@ 1535-3893 %G eng %M WOS:000784194300013 %R 10.1021/acs.jproteome.1c00867 %0 Journal Article %J Journal of Proteome Research %D 2022 %T MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses %A Carr, A. V. %A Frey, B. L. %A Scalf, M. %A Cesnik, A. J. %A Rolfs, Z. %A Pike, K. A. %A Yang, B. %A Keller, M. P. %A Jarrard, D. F. %A Shortreed, M. R. %A Smith, L. M. %B Journal of Proteome Research %V 21 %P 410-419 %8 Feb %@ 1535-3893 %G eng %M WOS:000752365700010 %R 10.1021/acs.jproteome.1c00756 %0 Journal Article %J Nature Communications %D 2021 %T An atlas of protein turnover rates in mouse tissues %A Rolfs, Z. %A Frey, B. L. %A Shi, X. D. %A Kawai, Y. %A Smith, L. M. %A Welham, N. V. %B Nature Communications %V 12 %8 Nov %G eng %M WOS:000722939600026 %] 6778 %R 10.1038/s41467-021-26842-3 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus %A Shortreed, M. R. %A Millikin, R. J. %A Liu, L. %A Rolfs, Z. %A Miller, R. M. %A Schaffer, L. V. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1997-2004 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900021 %R 10.1021/acs.jproteome.0c00838 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Spritz: A Proteogenomic Database Engine %A Cesnik, A. J. %A Miller, R. M. %A Ibrahim, K. %A Lu, L. %A Millikin, R. J. %A Shortreed, M. R. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1826-1834 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900003 %R 10.1021/acs.jproteome.0c00407 %0 Journal Article %J Journal of Proteome Research %D 2019 %T Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion %A Rolfs, Z. %A Solntsev, S. K. %A Shortreed, M. R. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 18 %P 349-358 %8 Jan %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.8b00651 %0 Journal Article %J Journal of Proteome Research %D 2018 %T Enhanced Global Post-translational Modification Discovery with MetaMorpheus %A Solntsev, S. K. %A Shortreed, M. R. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 17 %P 1844-1851 %8 May %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00873 %0 Journal Article %J Analytical Chemistry %D 2018 %T Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families %A Schaffer, L. V. %A Shortreed, M. R. %A Cesnik, A. J. %A Frey, B. L. %A Solntsev, S. K. %A Scalf, M. %A Smith, L. M. %B Analytical Chemistry %V 90 %P 1325-1333 %8 Jan %@ 0003-2700 %G eng %R 10.1021/acs.analchem.7b04221 %0 Journal Article %J Transl Oncol %D 2018 %T Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers %A Cesnik, A. J. %A Yang, B. %A Truong, A. %A Etheridge, T. %A Spiniello, M. %A Steinbrink, M. I. %A Shortreed, M. R. %A Frey, B. L. %A Jarrard, D. F. %A Smith, L. M. %B Transl Oncol %V 11 %P 808-814 %8 Jun %@ 1936-5233 %G eng %R 10.1016/j.tranon.2018.04.002 %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 J Proteome Res %D 2017 %T Global Post-Translational Modification Discovery %A Li, Q. %A Shortreed, M. R. %A Wenger, C. D. %A Frey, B. L. %A Schaffer, L. V. %A Scalf, M. %A Smith, L. M. %B J Proteome Res %G eng %0 Journal Article %J Journal of Proteome Research %D 2016 %T Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements %A Shortreed, M. R. %A Frey, B. L. %A Scalf, M. %A Knoener, R. A. %A Cesnik, A. J. %A L. M. Smith %B Journal of Proteome Research %V 15 %P 1213-1221 %8 Apr %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.5b01090 %0 Journal Article %J Journal of Proteome Research %D 2016 %T Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy %A Cesnik, A. J. %A Shortreed, M. R. %A Sheynkman, G. M. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 15 %P 800-808 %8 Mar %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.5b00817 %0 Journal Article %J Biomaterials %D 2016 %T Protein turnover during in vitro tissue engineering %A Li, Q. Y. %A Chang, Z. %A Oliveira, G. %A Xiong, M. %A L. M. Smith %A Frey, B. L. %A Welham, N. V. %B Biomaterials %V 81 %P 104-113 %8 Mar %@ 0142-9612 %G eng %R 10.1016/j.biomaterials.2015.12.004 %0 Journal Article %J Biomaterials %D 2016 %T Proteomic analysis of naturally-sourced biological scaffolds %A Li, Q. Y. %A Uygun, B. E. %A Geerts, S. %A Ozer, S. %A Scalf, M. %A Gilpin, S. E. %A Ott, H. C. %A Yarmush, M. L. %A L. M. Smith %A Welham, N. V. %A Frey, B. L. %B Biomaterials %V 75 %P 37-46 %8 Jan %@ 0142-9612 %G eng %] Ber s, 1995, journal of cell biology, v131, p1083 %R 10.1016/j.biomaterials.2015.10.011 %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 Journal of Biological Chemistry %D 2015 %T Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes %A Hoffman, E. A. %A Frey, B. L. %A L. M. Smith %A Auble, D. T. %B Journal of Biological Chemistry %V 290 %P 26404-26411 %8 Oct %@ 0021-9258 %G eng %R 10.1074/jbc.R115.651679 %0 Journal Article %J Journal of Proteome Research %D 2015 %T Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search %A Shortreed, M. R. %A Wenger, C. D. %A Frey, B. L. %A Sheynkman, G. M. %A Scalf, M. %A Keller, M. P. %A Attie, A. D. %A L. M. Smith %B Journal of Proteome Research %V 14 %P 4714-4720 %8 Nov %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.5b00599 %0 Journal Article %J Journal of Proteome Research %D 2014 %T Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae %A Kennedy-Darling, J. %A Guillen-Ahlers, H. %A Shortreed, M. R. %A Scalf, M. %A Frey, B. L. %A Kendziorski, C. %A Olivier, M. %A Gasch, A. P. %A L. M. Smith %B Journal of Proteome Research %V 13 %P 3810-3825 %8 Aug %@ 1535-3893 %G eng %2 PMC4123949 %R 10.1021/pr5004938 %0 Journal Article %J Biochemical and Biophysical Research Communications %D 2014 %T Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions %A Ladror, D. T. %A Frey, B. L. %A Scalf, M. %A Levenstein, M. E. %A Artymiuk, J. M. %A L. M. Smith %B Biochemical and Biophysical Research Communications %V 445 %P 535-541 %8 Mar %@ 0006-291X %G English %9 Article %R 10.1016/j.bbrc.2014.01.040 %0 Journal Article %J Journal of the American Society for Mass Spectrometry %D 2013 %T Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation %A Frey, B. L. %A Ladror, D. T. %A Sondalle, S. B. %A Krusemark, C. J. %A Jue, A. L. %A Coon, J. J. %A L. M. Smith %B Journal of the American Society for Mass Spectrometry %V 24 %P 1710-1721 %8 Nov %@ 1044-0305 %G English %9 Article %2 PMC3827969 %R 10.1007/s13361-013-0701-2 %0 Journal Article %J Molecular & Cellular Proteomics %D 2013 %T Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq %A Sheynkman, G. M. %A Shortreed, M. R. %A Frey, B. L. %A L. M. Smith %B Molecular & Cellular Proteomics %V 12 %P 2341-2353 %8 Aug %@ 1535-9476 %G English %9 Article %R 10.1074/mcp.O113.028142 %0 Journal Article %J Biomaterials %D 2013 %T Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry %A Welham, N. V. %A Chang, Z. %A L. M. Smith %A Frey, B. L. %B Biomaterials %V 34 %P 669-676 %8 Jan %@ 0142-9612 %G eng %2 PMC3496020 %R 10.1016/j.biomaterials.2012.09.050 %0 Journal Article %J Plos One %D 2011 %T Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification %A Wu, C. H. %A Chen, S. Y. %A Shortreed, M. R. %A Kreitinger, G. M. %A Yuan, Y. %A Frey, B. L. %A Zhang, Y. %A Mirza, S. %A Cirillo, L. A. %A Olivier, M. %A L. M. Smith %B Plos One %V 6 %8 Oct %@ 1932-6203 %G eng %2 PMC3197616 %] e26217 %R 10.1371/journal.pone.0026217 %0 Journal Article %J Journal of the American Society for Mass Spectrometry %D 2009 %T Modifying the Charge State Distribution of Proteins in Electrospray Ionization Mass Spectrometry by Chemical Derivatization %A Krusemark, C. J. %A Frey, B. L. %A Belshaw, P. J. %A L. M. Smith %B Journal of the American Society for Mass Spectrometry %V 20 %P 1617-1625 %8 Sep %G eng %2 PMC2776692 %R 10.1016/j.jasms.2009.04.017 %F ISI 2009 10 29 %0 Journal Article %J International Journal of Mass Spectrometry %D 2008 %T Ion-ion reactions with fixed-charge modified proteins to produce ions in a single, very high charge state %A Frey, B. L. %A Krusemark, C. J. %A Ledvina, A. R. %A Coon, J. J. %A Belshaw, P. J. %A L. M. Smith %B International Journal of Mass Spectrometry %V 276 %P 136-143 %8 Oct %G eng %2 PMC2598753 %R 10.1016/j.ijms.2008.07.029 %F ISI 2008 11 06 %0 Journal Article %J Analytical Chemistry %D 2006 %T Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry %A Shortreed, M. R. %A Lamos, S. M. %A Frey, B. L. %A Phillips, M. F. %A Patel, M. %A Belshaw, P. J. %A L. M. Smith %B Analytical Chemistry %V 78 %P 6398-6403 %8 Sep %G eng %R 10.1021/ac0607008 %F ISI 2006 09 29 %0 Journal Article %J American Journal of Physiology - Endocrinology & Metabolism %D 2005 %T alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice %A Rabaglia, M. E. %A Gray-Keller, M. P. %A Frey, B. L. %A Shortreed, M. R. %A L. M. Smith %A Attie, A. D. %B American Journal of Physiology - Endocrinology & Metabolism %V 289 %P E218-E224 %8 Aug %G eng %R 10.1152/ajpendo.00573.2004 %F ISI 2005 week 32 %0 Journal Article %J Journal of the American Society for Mass Spectrometry %D 2005 %T Controlling gas-phase reactions for efficient charge reduction electrospray mass spectrometry of intact proteins %A Frey, B. L. %A Lin, Y. %A Westphall, M. S. %A L. M. Smith %B Journal of the American Society for Mass Spectrometry %V 16 %P 1876-1887 %8 Nov %G eng %2 PMC1489883 %R 10.1016/j.jasms.2005.07.019 %F ISI 2005 week 49