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Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis.

Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, Scalf M, Smith LM, Vierstra RD.

J Biol Chem. 2019 Nov 15;294(46):17570-17592. doi: 10.1074/jbc.RA119.010219. Epub 2019 Sep 27.


Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database.

Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM.

J Proteome Res. 2019 Oct 4;18(10):3671-3680. doi: 10.1021/acs.jproteome.9b00339. Epub 2019 Sep 18.


Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS.

Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM.

RNA. 2019 Oct;25(10):1337-1352. doi: 10.1261/rna.072157.119. Epub 2019 Jul 11.


HDA9-PWR-HOS15 Is a Core Histone Deacetylase Complex Regulating Transcription and Development.

Mayer KS, Chen X, Sanders D, Chen J, Jiang J, Nguyen P, Scalf M, Smith LM, Zhong X.

Plant Physiol. 2019 May;180(1):342-355. doi: 10.1104/pp.18.01156. Epub 2019 Feb 14.


Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.

Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM.

J Proteome Res. 2018 Oct 5;17(10):3526-3536. doi: 10.1021/acs.jproteome.8b00469. Epub 2018 Sep 18.


EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.

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.

Nat Genet. 2018 Sep;50(9):1247-1253. doi: 10.1038/s41588-018-0187-8. Epub 2018 Aug 6.


HyPR-MS for Multiplexed Discovery of MALAT1, NEAT1, and NORAD lncRNA Protein Interactomes.

Spiniello M, Knoener RA, Steinbrink MI, Yang B, Cesnik AJ, Buxton KE, Scalf M, Jarrard DF, Smith LM.

J Proteome Res. 2018 Sep 7;17(9):3022-3038. doi: 10.1021/acs.jproteome.8b00189. Epub 2018 Jul 31.


Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.

Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM.

J Proteome Res. 2018 Jul 6;17(7):2370-2376. doi: 10.1021/acs.jproteome.8b00141. Epub 2018 Jun 11.


SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress.

Rytz TC, Miller MJ, McLoughlin F, Augustine RC, Marshall RS, Juan YT, Charng YY, Scalf M, Smith LM, Vierstra RD.

Plant Cell. 2018 May;30(5):1077-1099. doi: 10.1105/tpc.17.00993. Epub 2018 Mar 27.


Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance.

Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R.

Stem Cell Reports. 2018 Feb 13;10(2):627-641. doi: 10.1016/j.stemcr.2017.12.016.


Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing.

Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X.

Plant Cell. 2018 Jan;30(1):134-152. doi: 10.1105/tpc.17.00626. Epub 2018 Jan 17.


Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.

Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM.

Anal Chem. 2018 Jan 16;90(2):1325-1333. doi: 10.1021/acs.analchem.7b04221. Epub 2017 Dec 22.


Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry.

Knoener RA, Becker JT, Scalf M, Sherer NM, Smith LM.

Sci Rep. 2017 Dec 5;7(1):16965. doi: 10.1038/s41598-017-16793-5.


Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM.

J Proteome Res. 2018 Jan 5;17(1):568-578. doi: 10.1021/acs.jproteome.7b00685. Epub 2017 Dec 15.


Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS.

Kim SH, Stiles SG, Feichtmeier JM, Ramesh N, Zhan L, Scalf MA, Smith LM, Pandey UB, Tibbetts RS.

Hum Mol Genet. 2018 Jan 15;27(2):322-337. doi: 10.1093/hmg/ddx403.


Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.

Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM.

J Proteome Res. 2017 Nov 3;16(11):4156-4165. doi: 10.1021/acs.jproteome.7b00516.


Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.

Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM.

J Proteome Res. 2017 Sep 1;16(9):3433-3442. doi: 10.1021/acs.jproteome.7b00448. Epub 2017 Aug 4.


Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.

Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM.

Anal Chem. 2017 Aug 1;89(15):7841-7846. doi: 10.1021/acs.analchem.7b01784. Epub 2017 Jul 11.


Correction to "Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements".

Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM.

J Proteome Res. 2017 Jul 7;16(7):2660. doi: 10.1021/acs.jproteome.7b00333. Epub 2017 Jun 13. No abstract available.


Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis.

Aguilar-Hernández V, Kim DY, Stankey RJ, Scalf M, Smith LM, Vierstra RD.

Mol Plant. 2017 Jun 5;10(6):846-865. doi: 10.1016/j.molp.2017.04.008. Epub 2017 Apr 28.


Global Post-Translational Modification Discovery.

Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM.

J Proteome Res. 2017 Apr 7;16(4):1383-1390. doi: 10.1021/acs.jproteome.6b00034. Epub 2017 Mar 1.


POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis.

Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, Smith LM, Zhong X.

Elife. 2016 Nov 22;5. pii: e17214. doi: 10.7554/eLife.17214.


HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

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, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M.

Genomics. 2016 Jun;107(6):267-73. doi: 10.1016/j.ygeno.2016.05.002. Epub 2016 May 13.


Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.

Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM.

J Proteome Res. 2016 Apr 1;15(4):1213-21. doi: 10.1021/acs.jproteome.5b01090. Epub 2016 Mar 16. Erratum in: J Proteome Res. 2017 Jul 7;16(7):2660.


Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine.

Gemperline DC, Scalf M, Smith LM, Vierstra RD.

Proteomics. 2016 Mar;16(6):920-4. doi: 10.1002/pmic.201500420.


Proteomic analysis of naturally-sourced biological scaffolds.

Li Q, Uygun BE, Geerts S, Ozer S, Scalf M, Gilpin SE, Ott HC, Yarmush ML, Smith LM, Welham NV, Frey BL.

Biomaterials. 2016 Jan;75:37-46. doi: 10.1016/j.biomaterials.2015.10.011. Epub 2015 Oct 8.


Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.

Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, Attie AD, Smith LM.

J Proteome Res. 2015 Nov 6;14(11):4714-20. doi: 10.1021/acs.jproteome.5b00599. Epub 2015 Sep 29.


Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.

Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM.

J Proteome Res. 2014 Aug 1;13(8):3810-25. doi: 10.1021/pr5004938. Epub 2014 Jul 17.


Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions.

Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM.

Biochem Biophys Res Commun. 2014 Mar 14;445(3):535-41. doi: 10.1016/j.bbrc.2014.01.040. Epub 2014 Jan 30.


Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.

Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM.

J Proteome Res. 2014 Jan 3;13(1):228-40. doi: 10.1021/pr4009207. Epub 2013 Nov 11.


Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis.

Kim DY, Scalf M, Smith LM, Vierstra RD.

Plant Cell. 2013 May;25(5):1523-40. doi: 10.1105/tpc.112.108613. Epub 2013 May 10.


Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry.

Russell JD, Scalf M, Book AJ, Ladror DT, Vierstra RD, Smith LM, Coon JJ.

PLoS One. 2013;8(3):e58157. doi: 10.1371/journal.pone.0058157. Epub 2013 Mar 11.


Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis.

Miller MJ, Scalf M, Rytz TC, Hubler SL, Smith LM, Vierstra RD.

Mol Cell Proteomics. 2013 Feb;12(2):449-63. doi: 10.1074/mcp.M112.025056. Epub 2012 Nov 29.


A mechanical nanomembrane detector for time-of-flight mass spectrometry.

Park J, Qin H, Scalf M, Hilger RT, Westphall MS, Smith LM, Blick RH.

Nano Lett. 2011 Sep 14;11(9):3681-4. doi: 10.1021/nl201645u. Epub 2011 Aug 3.


Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis.

Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM.

Anal Chem. 2011 Mar 15;83(6):2187-93. doi: 10.1021/ac103023q. Epub 2011 Feb 11.


Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: comparison of growing- and energy-starved cells.

Pellitteri-Hahn MC, Halligan BD, Scalf M, Smith L, Hickey WJ.

J Proteomics. 2011 Apr 1;74(4):411-9. doi: 10.1016/j.jprot.2010.12.003. Epub 2010 Dec 21.


Affinity purification of the Arabidopsis 26 S proteasome reveals a diverse array of plant proteolytic complexes.

Book AJ, Gladman NP, Lee SS, Scalf M, Smith LM, Vierstra RD.

J Biol Chem. 2010 Aug 13;285(33):25554-69. doi: 10.1074/jbc.M110.136622. Epub 2010 Jun 1.


Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis.

Saracco SA, Hansson M, Scalf M, Walker JM, Smith LM, Vierstra RD.

Plant J. 2009 Jul;59(2):344-58. doi: 10.1111/j.1365-313X.2009.03862.x. Epub 2009 Mar 9.


Identification of cell surface markers to differentiate rat endothelial and fibroblast cells using lectin arrays and LC-ESI-MS/MS.

Lee JE, Mirza SP, Didier DN, Scalf M, Olivier M, Greene AS, Smith LM.

Anal Chem. 2008 Nov 1;80(21):8269-75. doi: 10.1021/ac801390b. Epub 2008 Sep 27.


Membrane protein separation and analysis by supercritical fluid chromatography-mass spectrometry.

Zhang X, Scalf M, Westphall MS, Smith LM.

Anal Chem. 2008 Apr 1;80(7):2590-8. doi: 10.1021/ac702319u. Epub 2008 Feb 28.


Exploration of structure--activity relationships among foldamer ligands for a specific protein binding site via parallel and split-and-mix library synthesis.

Murray JK, Sadowsky JD, Scalf M, Smith LM, Tomita Y, Gellman SH.

J Comb Chem. 2008 Mar-Apr;10(2):204-15. doi: 10.1021/cc700153z. Epub 2008 Feb 15.


Characterization of vascular endothelial growth factor receptors on the endothelial cell surface during hypoxia using whole cell binding arrays.

Lee JE, Didier DN, Lockett MR, Scalf M, Greene AS, Olivier M, Smith LM.

Anal Biochem. 2007 Oct 15;369(2):241-7. Epub 2007 Jun 12.


Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry.

Lamos SM, Krusemark CJ, McGee CJ, Scalf M, Smith LM, Belshaw PJ.

Angew Chem Int Ed Engl. 2006 Jun 26;45(26):4329-33. No abstract available.


Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/MS mass spectrometry.

Zhang X, Scalf M, Berggren TW, Westphall MS, Smith LM.

J Am Soc Mass Spectrom. 2006 Apr;17(4):490-499. doi: 10.1016/j.jasms.2005.12.007. Epub 2006 Feb 17.


Efficient synthesis of a beta-peptide combinatorial library with microwave irradiation.

Murray JK, Farooqi B, Sadowsky JD, Scalf M, Freund WA, Smith LM, Chen J, Gellman SH.

J Am Chem Soc. 2005 Sep 28;127(38):13271-80.


Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis.

Book AJ, Yang P, Scalf M, Smith LM, Vierstra RD.

Plant Physiol. 2005 Jun;138(2):1046-57. Epub 2005 May 20.


Chip-based analysis of protein-protein interactions by fluorescence detection and on-chip immunoprecipitation combined with microLC-MS/MS analysis.

Sydor JR, Scalf M, Sideris S, Mao GD, Pandey Y, Tan M, Mariano M, Moran MF, Nock S, Wagner P.

Anal Chem. 2003 Nov 15;75(22):6163-70.


A cylindrical capacitor ionization source: droplet generation and controlled charge reduction for mass spectrometry.

Ebeling DD, Westphall MS, Scalf M, Smith LM.

Rapid Commun Mass Spectrom. 2001;15(6):401-5.


Corona discharge in charge reduction electrospray mass spectrometry.

Ebeling DD, Westphall MS, Scalf M, Smith LM.

Anal Chem. 2000 Nov 1;72(21):5158-61.


Charge reduction electrospray mass spectrometry.

Scalf M, Westphall MS, Smith LM.

Anal Chem. 2000 Jan 1;72(1):52-60.


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