Mark A. Scalf, Ph.D. - Publications

2000 University of Wisconsin, Madison, Madison, WI 
surface chemistry, mass spectrometry

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs. Journal of Proteome Research. PMID 38043095 DOI: 10.1021/acs.jproteome.3c00506  0.463
2023 Whitworth IT, Knoener RA, Puray-Chavez M, Halfmann P, Romero S, Baddouh M, Scalf M, Kawaoka Y, Kutluay SB, Smith LM, Sherer NM. Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs. Biorxiv : the Preprint Server For Biology. PMID 37293069 DOI: 10.1101/2023.05.15.540806  0.465
2023 Whitworth IT, Henke KB, Yang B, Scalf M, Frey BL, Jarrard DF, Smith LM. Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue. Analytical Chemistry. PMID 37093976 DOI: 10.1021/acs.analchem.2c05635  0.487
2023 Kim SH, Nichols KD, Anderson EN, Liu Y, Ramesh N, Jia W, Kuerbis CJ, Scalf M, Smith LM, Pandey UB, Tibbetts RS. Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2. Elife. 12. PMID 37039476 DOI: 10.7554/eLife.84382  0.371
2022 Millikin RJ, Shortreed MR, Scalf M, Smith LM. Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ. Methods in Molecular Biology (Clifton, N.J.). 2426: 303-313. PMID 36308694 DOI: 10.1007/978-1-0716-1967-4_13  0.5
2022 Hansen SR, White DS, Scalf M, Corrêa IR, Smith LM, Hoskins AA. Multi-step recognition of potential 5' splice sites by the U1 snRNP. Elife. 11. PMID 35959885 DOI: 10.7554/eLife.70534  0.432
2022 Miller RM, Knoener RA, Benner BE, Frey BL, Scalf M, Shortreed MR, Sherer NM, Smith LM. Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1. Journal of Proteome Research. PMID 35192358 DOI: 10.1021/acs.jproteome.1c00867  0.412
2022 Carr AV, Frey BL, Scalf M, Cesnik AJ, Rolfs Z, Pike KA, Yang B, Keller MP, Jarrard DF, Shortreed MR, Smith LM. MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses. Journal of Proteome Research. PMID 35073098 DOI: 10.1021/acs.jproteome.1c00756  0.531
2022 Spiniello M, Scalf M, Casamassimi A, Abbondanza C, Smith LM. Towards an Ideal Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. International Journal of Molecular Sciences. 23. PMID 35055128 DOI: 10.3390/ijms23020942  0.474
2022 Henke KB, Miller RM, Knoener RA, Scalf M, Spiniello M, Smith LM. Identifying Protein Interactomes of Target RNAs Using HyPR-MS. Methods in Molecular Biology (Clifton, N.J.). 2404: 219-244. PMID 34694612 DOI: 10.1007/978-1-0716-1851-6_12  0.519
2021 Jia W, Kim SH, Scalf MA, Tonzi P, Millikin RJ, Guns WM, Liu L, Mastrocola AS, Smith LM, Huang TT, Tibbetts RS. Fused in sarcoma (FUS) regulates DNA replication timing and kinetics. The Journal of Biological Chemistry. 101049. PMID 34375640 DOI: 10.1016/j.jbc.2021.101049  0.444
2021 Lu L, Scalf M, Shortreed MR, Smith LM. Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. Journal of the American Society For Mass Spectrometry. PMID 33754701 DOI: 10.1021/jasms.0c00462  0.477
2021 Knoener R, Evans E, Becker JT, Scalf M, Benner B, Sherer NM, Smith LM. Identification of host proteins differentially associated with HIV-1 RNA splice variants. Elife. 10. PMID 33629952 DOI: 10.7554/eLife.62470  0.49
2020 Schaffer LV, Millikin RJ, Shortreed MR, Scalf M, Smith LM. Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. PMID 32584579 DOI: 10.1021/Acs.Jproteome.0C00332  0.611
2020 Millikin RJ, Shortreed MR, Scalf M, Smith LM. A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. Journal of Proteome Research. PMID 32243168 DOI: 10.1021/Acs.Jproteome.9B00796  0.501
2019 Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, Scalf M, Smith LM, Vierstra RD. Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in . The Journal of Biological Chemistry. PMID 31562246 DOI: 10.1074/Jbc.Ra119.010219  0.54
2019 Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM. Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global PTM Discovery Database. Journal of Proteome Research. PMID 31479276 DOI: 10.1021/Acs.Jproteome.9B00339  0.569
2019 Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA interactome using HyPR-MS. Rna (New York, N.Y.). PMID 31296583 DOI: 10.1261/Rna.072157.119  0.582
2019 Mayer KS, Chen X, Sanders D, Chen J, Jiang J, Nguyen P, Scalf M, Smith LM, Zhong X. HDA9-PWR-HOS15 is a core histone deacetylase complex regulating transcription and development. Plant Physiology. PMID 30765479 DOI: 10.1104/Pp.18.01156  0.501
2018 Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. Journal of Proteome Research. PMID 30180576 DOI: 10.1021/Acs.Jproteome.8B00469  0.589
2018 Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nature Genetics. PMID 30082787 DOI: 10.1038/S41588-018-0187-8  0.488
2018 Spiniello M, Knoener RA, Steinbrink MI, Yang B, Cesnik AJ, Buxton KE, Scalf M, Jarrard DF, Smith LM. HyPR-MS for multiplexed discovery of MALAT1, NEAT1, and NORAD lncRNA protein interactomes. Journal of Proteome Research. PMID 29972301 DOI: 10.1021/Acs.Jproteome.8B00189  0.572
2018 Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM. Identification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus. Journal of Proteome Research. PMID 29793340 DOI: 10.1021/Acs.Jproteome.8B00141  0.596
2018 Rytz TC, Miller MJ, McLoughlin F, Augustine RC, Marshall RS, Juan YT, Charng YY, Scalf M, Smith LM, Vierstra RD. SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 During Heat Stress. The Plant Cell. PMID 29588388 DOI: 10.1105/Tpc.17.00993  0.55
2018 Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. PMID 29358085 DOI: 10.1016/J.Stemcr.2017.12.016  0.534
2018 Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X. Canonical and Non-canonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. The Plant Cell. PMID 29343504 DOI: 10.1105/Tpc.17.00626  0.506
2017 Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. PMID 29227670 DOI: 10.1021/Acs.Analchem.7B04221  0.603
2017 Knoener RA, Becker JT, Scalf M, Sherer NM, Smith LM. Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 7: 16965. PMID 29208937 DOI: 10.1038/S41598-017-16793-5  0.502
2017 Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. PMID 29195273 DOI: 10.1021/Acs.Jproteome.7B00685  0.479
2017 Kim SH, Stiles SG, Feichtmeier JM, Ramesh N, Zhan L, Scalf MA, Smith LM, Pandey UB, Tibbetts RS. Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. PMID 29161404 DOI: 10.1093/Hmg/Ddx403  0.441
2017 Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM. Elucidating E. coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. PMID 28968100 DOI: 10.1021/Acs.Jproteome.7B00516  0.585
2017 Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. PMID 28704058 DOI: 10.1021/Acs.Jproteome.7B00448  0.791
2017 Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. PMID 28654248 DOI: 10.1021/Acs.Analchem.7B01784  0.811
2017 Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. Correction to "Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements". Journal of Proteome Research. PMID 28608680 DOI: 10.1021/Acs.Jproteome.7B00333  0.491
2017 Aguilar-Hernández V, Kim DY, Stankey RJ, Scalf M, Smith LM, Vierstra RD. Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome During Photomorphogenesis. Molecular Plant. PMID 28461270 DOI: 10.1016/J.Molp.2017.04.008  0.563
2017 Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM. Global Post-Translational Modification Discovery. Journal of Proteome Research. PMID 28248113 DOI: 10.1021/Acs.Jproteome.6B00034  0.55
2016 Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife. 5. PMID 27873573 DOI: 10.7554/Elife.17214  0.516
2016 Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AY, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HI, Cole R, et al. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. PMID 27184763 DOI: 10.1016/J.Ygeno.2016.05.002  0.788
2016 Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. Elucidating Proteoform Families from Proteoform Intact Mass and Lysine Count Measurements. Journal of Proteome Research. PMID 26941048 DOI: 10.1021/Acs.Jproteome.5B01090  0.611
2016 Gemperline DC, Scalf M, Smith LM, Vierstra RD. Morpheus spectral counter: a computational tool for label-free quantitative mass spectrometry using the morpheus search engine. Proteomics. PMID 26791624 DOI: 10.1002/Pmic.201500420  0.578
2016 Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X. Author response: POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis Elife. DOI: 10.7554/Elife.17214.028  0.45
2015 Li Q, Uygun BE, Geerts S, Ozer S, Scalf M, Gilpin SE, Ott HC, Yarmush ML, Smith LM, Welham NV, Frey BL. Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 75: 37-46. PMID 26476196 DOI: 10.1016/J.Biomaterials.2015.10.011  0.555
2015 Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, Attie AD, Smith LM. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14: 4714-20. PMID 26418581 DOI: 10.1021/Acs.Jproteome.5B00599  0.756
2014 Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. PMID 24999558 DOI: 10.1021/Pr5004938  0.804
2014 Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochemical and Biophysical Research Communications. 445: 535-41. PMID 24486316 DOI: 10.1016/J.Bbrc.2014.01.040  0.787
2014 Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM. Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. Journal of Proteome Research. 13: 228-40. PMID 24175627 DOI: 10.1021/Pr4009207  0.748
2014 Hansen S, Rodgers M, Laurent R, Sun Y, Scalf M, Smith L, Hoskins A. Reconstitution and Single Molecule Characterization of Yeast Spliceosomal E Complex Biophysical Journal. 106: 496a. DOI: 10.1016/J.Bpj.2013.11.2775  0.528
2013 Kim DY, Scalf M, Smith LM, Vierstra RD. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. The Plant Cell. 25: 1523-40. PMID 23667124 DOI: 10.1105/Tpc.112.108613  0.571
2013 Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, Coon JJ. Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry. Plos One. 8: e58157. PMID 23536786 DOI: 10.1371/Journal.Pone.0058157  0.814
2013 Miller MJ, Scalf M, Rytz TC, Hubler SL, Smith LM, Vierstra RD. Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Molecular & Cellular Proteomics : McP. 12: 449-63. PMID 23197790 DOI: 10.1074/Mcp.M112.025056  0.507
2011 Park J, Qin H, Scalf M, Hilger RT, Westphall MS, Smith LM, Blick RH. A mechanical nanomembrane detector for time-of-flight mass spectrometry. Nano Letters. 11: 3681-4. PMID 21806063 DOI: 10.1021/Nl201645U  0.762
2011 Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM. Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis. Analytical Chemistry. 83: 2187-93. PMID 21314137 DOI: 10.1021/Ac103023Q  0.768
2011 Pellitteri-Hahn MC, Halligan BD, Scalf M, Smith L, Hickey WJ. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells Journal of Proteomics. 74: 411-419. PMID 21172464 DOI: 10.1016/J.Jprot.2010.12.003  0.573
2010 Book AJ, Gladman NP, Lee SS, Scalf M, Smith LM, Vierstra RD. Affinity purification of the Arabidopsis 26 S proteasome reveals a diverse array of plant proteolytic complexes. The Journal of Biological Chemistry. 285: 25554-69. PMID 20516081 DOI: 10.1074/Jbc.M110.136622  0.455
2009 Saracco SA, Hansson M, Scalf M, Walker JM, Smith LM, Vierstra RD. Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. 59: 344-58. PMID 19292762 DOI: 10.1111/J.1365-313X.2009.03862.X  0.602
2008 Lee JE, Mirza SP, Didier DN, Scalf M, Olivier M, Greene AS, Smith LM. Identification of cell surface markers to differentiate rat endothelial and fibroblast cells using lectin arrays and LC-ESI-MS/MS. Analytical Chemistry. 80: 8269-75. PMID 18821777 DOI: 10.1021/Ac801390B  0.48
2008 Zhang X, Scalf M, Westphall MS, Smith LM. Membrane protein separation and analysis by supercritical fluid chromatography-mass spectrometry. Analytical Chemistry. 80: 2590-8. PMID 18303916 DOI: 10.1021/Ac702319U  0.541
2008 Murray JK, Sadowsky JD, Scalf M, Smith LM, Tomita Y, Gellman SH. Exploration of structure--activity relationships among foldamer ligands for a specific protein binding site via parallel and split-and-mix library synthesis. Journal of Combinatorial Chemistry. 10: 204-15. PMID 18275161 DOI: 10.1021/Cc700153Z  0.448
2007 Lee JE, Didier DN, Lockett MR, Scalf M, Greene AS, Olivier M, Smith LM. Characterization of vascular endothelial growth factor receptors on the endothelial cell surface during hypoxia using whole cell binding arrays. Analytical Biochemistry. 369: 241-7. PMID 17624292 DOI: 10.1016/J.Ab.2007.06.010  0.629
2006 Lamos SM, Krusemark CJ, McGee CJ, Scalf M, Smith LM, Belshaw PJ. Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry. Angewandte Chemie (International Ed. in English). 45: 4329-33. PMID 16733838 DOI: 10.1002/Anie.200600743  0.751
2006 Zhang X, Scalf M, Berggren TW, Westphall MS, Smith LM. Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/MS mass spectrometry. Journal of the American Society For Mass Spectrometry. 17: 490-9. PMID 16488154 DOI: 10.1016/J.Jasms.2005.12.007  0.594
2005 Murray JK, Farooqi B, Sadowsky JD, Scalf M, Freund WA, Smith LM, Chen J, Gellman SH. Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation. Journal of the American Chemical Society. 127: 13271-80. PMID 16173757 DOI: 10.1021/Ja052733V  0.477
2005 Book AJ, Yang P, Scalf M, Smith LM, Vierstra RD. Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis. Plant Physiology. 138: 1046-57. PMID 15908606 DOI: 10.1104/Pp.104.057406  0.522
2003 Sydor JR, Scalf M, Sideris S, Mao GD, Pandey Y, Tan M, Mariano M, Moran MF, Nock S, Wagner P. Chip-based analysis of protein-protein interactions by fluorescence detection and on-chip immunoprecipitation combined with microLC-MS/MS analysis. Analytical Chemistry. 75: 6163-70. PMID 14615996 DOI: 10.1021/Ac034258U  0.435
2002 Moradian A, Scalf M, Westphall MS, Smith LM, Douglas D. Collision cross sections of gas phase DNA ions International Journal of Mass Spectrometry. 219: 161-170. DOI: 10.1016/S1387-3806(02)00546-8  0.512
2001 Ebeling DD, Westphall MS, Scalf M, Smith LM. A cylindrical capacitor ionization source: droplet generation and controlled charge reduction for mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 15: 401-5. PMID 11291117 DOI: 10.1002/Rcm.245  0.696
2000 Ebeling DD, Westphall MS, Scalf M, Smith LM. Corona discharge in charge reduction electrospray mass spectrometry. Analytical Chemistry. 72: 5158-61. PMID 11080858 DOI: 10.1021/Ac000559H  0.697
2000 Scalf M, Westphall MS, Smith LM. Charge reduction electrospray mass spectrometry. Analytical Chemistry. 72: 52-60. PMID 10655634 DOI: 10.1021/Ac990878C  0.538
1999 Scalf M, Westphall MS, Krause J, Kaufman SL, Smith LM. Controlling charge states of large ions. Science (New York, N.Y.). 283: 194-7. PMID 9880246 DOI: 10.1126/Science.283.5399.194  0.524
1999 Krause J, Scalf M, Smith LM. High resolution characterization of DNA fragment ions produced by ultraviolet matrix-assisted laser desorption/ionization using linear and reflecting time-of-flight mass spectrometry Journal of the American Society For Mass Spectrometry. 10: 423-429. DOI: 10.1016/S1044-0305(99)00009-4  0.486
1998 Ono T, Scalf M, Smith LM. 2'-Fluoro modified nucleic acids: polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionization mass spectrometry. Nucleic Acids Research. 25: 4581-8. PMID 9358169 DOI: 10.1093/Nar/25.22.4581  0.523
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