%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 eLife %D 2022 %T Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP %A Hansen, S. R. %A White, D. S. %A Scalf, M. %A Correa, I. R. %A Smith, L. M. %A Hoskins, A. A. %A Staley, J. P. %B eLife %V 11 %8 Aug %@ 2050-084X %G eng %M WOS:000849185900001 %] e70534 %R 10.7554/eLife.70534 %0 Journal Article %J International Journal of Molecular Sciences %D 2022 %T Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules %A Spiniello, M. %A Scalf, M. %A Casamassimi, A. %A Abbondanza, C. %A Smith, L. M. %B International Journal of Molecular Sciences %V 23 %8 Jan %G eng %M WOS:000747189800001 %] 942 %R 10.3390/ijms23020942 %0 Journal Article %J eLife %D 2021 %T Identification of host proteins differentially associated with HIV-1 RNA splice variants %A Knoener, R. %A Evans, E. %A Becker, J. T. %A Scalf, M. %A Benner, B. %A Sherer, N. M. %A Smith, L. M. %B eLife %V 10 %8 Feb %@ 2050-084X %G eng %M WOS:000624344600001 %] e62470 %R 10.7554/eLife.62470 %0 Journal Article %D 2021 %T Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics %A Lu, L. %A Scalf, M. %A Shortreed, M. R. %A Smith, L. M. %V 32 %P 1319-1325 %8 Jun %@ 1044-0305 %G eng %M WOS:000714641000006 %R 10.1021/jasms.0c00462 %0 Journal Article %J Journal of Proteome Research %D 2020 %T A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics %A Millikin, R. J. %A Shortreed, M. R. %A Scalf, M. %A Smith, L. M. %B Journal of Proteome Research %V 19 %P 1975-1981 %8 May %@ 1535-3893 %G eng %M WOS:000530084700009 %R 10.1021/acs.jproteome.9b00796 %0 Journal Article %J Journal of Proteome Research %D 2020 %T Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data %A Schaffer, L. V. %A Millikin, R. J. %A Shortreed, M. R. %A Scalf, M. %A Smith, L. M. %B Journal of Proteome Research %V 19 %P 3510-3517 %8 Aug %@ 1535-3893 %G eng %M WOS:000562081000055 %R 10.1021/acs.jproteome.0c00332 %0 Journal Article %J Journal of Biological Chemistry %D 2019 %T Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis %A Gemperline, D. C. %A Marshall, R. S. %A Lee, K. H. %A Zhao, Q. Z. %A Hu, W. M. %A McLoughlin, F. %A Scalf, M. %A Smith, L. M. %A Vierstra, R. D. %B Journal of Biological Chemistry %V 294 %P 17570-17592 %8 Nov %@ 0021-9258 %G eng %M WOS:000503173500032 %R 10.1074/jbc.RA119.010219 %0 Journal Article %J Plant Cell %D 2018 %T Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing %A Chen, X. S. %A Lu, L. %A Qian, S. M. %A Scalf, M. %A Smith, L. M. %A Zhong, X. H. %B Plant Cell %V 30 %P 134-152 %8 Jan %@ 1040-4651 %G eng %R 10.1105/tpc.17.00626 %0 Journal Article %J Stem Cell Reports %D 2018 %T Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance %A Zaidan, N. Z. %A Walker, K. J. %A Brown, J. E. %A Schaffer, L. V. %A Scalf, M. %A Shortreed, M. R. %A Iyer, G. %A Smith, L. M. %A Sridharan, R. %B Stem Cell Reports %V 10 %P 627-641 %8 Feb %@ 2213-6711 %G eng %R 10.1016/j.stemcr.2017.12.016 %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 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 Plant Cell %D 2018 %T SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress %A Rytz, T. C. %A Miller, M. J. %A McLoughlin, F. %A Augustine, R. C. %A Marshall, R. S. %A Juan, Y. T. %A Charng, Y. Y. %A Scalf, M. %A Smith, L. M. %A Vierstra, R. D. %B Plant Cell %V 30 %P 1077-1099 %8 May %@ 1040-4651 %G eng %R 10.1105/tpc.17.00993 %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 Journal of Proteome Research %D 2017 %T Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry %A Buxton, K. E. %A Kennedy-Darling, J. %A Shortreed, M. R. %A Zaidan, N. Z. %A Olivier, M. %A Scalf, M. %A Sridharan, R. %A Smith, L. M. %B Journal of Proteome Research %V 16 %P 3433-3442 %8 Sep %@ 1535-3893 %G eng %R 10.1021/acs.jproteome.7b00448 %0 Journal Article %J Scientific Reports %D 2017 %T Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry %A Knoener, R. A. %A Becker, J. T. %A Scalf, M. %A Sherer, N. M. %A Smith, L. M. %K cooperative binding %K gene-expression %K genomic rna %K hnrnp a1 %K immunodeficiency-virus type-1 %K pre-messenger-rna %K saccharomyces-cerevisiae %K t-cells %K unexpected roles %K viral protein expression %X HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells. One hundred eighty-nine proteins were identified to interact with unspliced HIV RNA including Rev and Gag/Gag-Pol, 24 host proteins previously shown to bind segments of HIV RNA, and over 90 proteins previously shown to impact HIV replication. Further analysis using siRNA knockdown techniques against several of these proteins revealed significant changes to HIV expression. These results demonstrate the utility of the approach for the discovery of host proteins involved in HIV replication. Additionally, because this strategy only requires availability of 30 nucleotides of the HIV-RNA for hybridization with a capture oligonucleotide, it is readily applicable to any HIV system of interest regardless of cell type, HIV-1 virus strain, or experimental perturbation. %B Scientific Reports %V 7 %8 Dec 5 %@ 2045-2322 %G English %M WOS:000417051000015 %R ARTN 16965
10.1038/s41598-017-16793-5 %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 Molecular Plant %D 2017 %T Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis %A Aguilar-Hernandez, V. %A Kim, D. Y. %A Stankey, R. J. %A Scalf, M. %A Smith, L. M. %A Vierstra, R. D. %B Molecular Plant %V 10 %P 846-865 %8 Jun %@ 1674-2052 %G eng %R 10.1016/j.molp.2017.04.008 %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 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 Proteomics %D 2016 %T Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine %A Gemperline, D. C. %A Scalf, M. %A Smith, L. M. %A Vierstra, R. D. %B Proteomics %V 16 %P 920-924 %G eng %9 Article %R 10.1002/pmic.201500420 %0 Journal Article %J Elife %D 2016 %T POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis %A Chen, X. %A Lu, L. %A Mayer, K. S. %A Scalf, M. %A Qian, S. %A Lomax, A. %A Smith, L. M. %A Zhong, X. %B Elife %V 5 %G eng %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 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 Plant Cell %D 2013 %T Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis %A Kim, D. Y. %A Scalf, M. %A L. M. Smith %A Vierstra, R. D. %B Plant Cell %V 25 %P 1523-1540 %8 May %@ 1040-4651 %G English %9 Article %2 PMC3694690 %R 10.1105/tpc.112.108613 %0 Journal Article %J Plos One %D 2013 %T Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry %A Russell, J. D. %A Scalf, M. %A Book, A. J. %A Ladror, D. T. %A Vierstra, R. D. %A L. M. Smith %A Coon, J. J. %B Plos One %V 8 %8 Mar %@ 1932-6203 %G eng %2 PMC3594244 %] e58157 %R 10.1371/journal.pone.0058157 %0 Journal Article %J Molecular & Cellular Proteomics %D 2013 %T Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis %A Miller, M. J. %A Scalf, M. %A Rytz, T. C. %A Hubler, S. L. %A L. M. Smith %A Vierstra, R. D. %B Molecular & Cellular Proteomics %V 12 %P 449-463 %8 Feb %@ 1535-9476 %G eng %2 PMC3567865 %R 10.1074/mcp.M112.025056 %0 Journal Article %J Journal of Proteomics %D 2011 %T Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells %A Pellitteri-Hahn, M. C. %A Halligan, B. D. %A Scalf, M. %A L. M. Smith %A Hickey, W. J. %B Journal of Proteomics %V 74 %P 411-419 %8 Apr %@ 1874-3919 %G eng %R 10.1016/j.jprot.2010.12.003 %0 Journal Article %J Plant Journal %D 2009 %T Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis %A Saracco, S. A. %A Hansson, M. %A Scalf, M. %A Walker, J. M. %A L. M. Smith %A Vierstra, R. D. %B Plant Journal %V 59 %P 344-358 %8 Jul %G eng %2 PMC3639010 %R 10.1111/j.1365-313X.2009.03862.x %F ISI 2009 07 17 %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 Journal of the American Society for Mass Spectrometry %D 2006 %T Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/MS mass spectrometry %A Zhang, X. %A Scalf, M. %A Berggren, T. W. %A Westphall, M. S. %A L. M. Smith %B Journal of the American Society for Mass Spectrometry %V 17 %P 490-499 %8 Apr %G eng %R 10.1016/j.jasms.2005.12.007 %F ISI 2006 week 19 %0 Journal Article %J Angewandte Chemie-International Edition %D 2006 %T Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry %A Lamos, S. M. %A Krusemark, C. J. %A McGee, C. J. %A Scalf, M. %A L. M. Smith %A Belshaw, P. J. %B Angewandte Chemie-International Edition %V 45 %P 4329-4333 %@ 1433-7851 %G eng %R 10.1002/anie.200600743 %0 Journal Article %J Journal of the American Chemical Society %D 2005 %T Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation %A Murray, J. K. %A Farooqi, B. %A Sadowsky, J. D. %A Scalf, M. %A Freund, W. A. %A L. M. Smith %A Chen, J. D. %A Gellman, S. H. %B Journal of the American Chemical Society %V 127 %P 13271-13280 %8 Sep 28 %G eng %R 10.1021/ja052733v %F ISI 2005 week 43 %0 Journal Article %J Plant Physiology %D 2005 %T Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis %A Book, A. J. %A Yang, P. Z. %A Scalf, M. %A L. M. Smith %A Vierstra, R. D. %B Plant Physiology %V 138 %P 1046-1057 %8 Jun %G eng %2 PMC1150419 %R 10.1104/pp.104.057406 %F ISI 2005 week 28 %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 Rapid Communications in Mass Spectrometry %D 2001 %T A cylindrical capacitor ionization source: droplet generation and controlled charge reduction for mass spectrometry %A Ebeling, D. D. %A Westphall, M. S. %A Scalf, M. %A L. M. Smith %B Rapid Communications in Mass Spectrometry %V 15 %P 401-5 %@ 0951-4198 (Print)
0951-4198 (Linking) %G English %9 Article %R 10.1002/rcm.245 %0 Journal Article %J Analytical Chemistry %D 2000 %T Charge reduction electrospray mass spectrometry %A Scalf, M. %A Westphall, M. S. %A L. M. Smith %B Analytical Chemistry %V 72 %P 52-60 %8 Jan %@ 0003-2700 %G eng %R 10.1021/ac990878c %0 Journal Article %J Analytical Chemistry %D 2000 %T Corona discharge in charge reduction electrospray mass spectrometry %A Ebeling, D. D. %A Westphall, M. S. %A Scalf, M. %A L. M. Smith %B Analytical Chemistry %V 72 %P 5158-5161 %8 Nov %@ 0003-2700 %G eng %R 10.1021/ac000559h %0 Journal Article %J Science %D 1999 %T Controlling charge states of large ions %A Scalf, M. %A Westphall, M. S. %A Krause, J. %A Kaufman, S. L. %A L. M. Smith %B Science %V 283 %P 194-197 %8 Jan %@ 0036-8075 %G eng %R 10.1126/science.283.5399.194 %0 Journal Article %J Nucleic Acids Research %D 1997 %T 2'-fluoro modified nucleic acids: polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionization mass spectrometry %A Ono, T. %A Scalf, M. %A L. M. Smith %B Nucleic Acids Research %V 25 %P 4581-4588 %8 Nov %@ 0305-1048 %G eng %2 PMC147098 %R 10.1093/nar/25.22.4581