Publications

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2015
Ling C.Y, Li Q.Y, Brown M.E, Kishimoto Y., Toya Y., Devine E.E, Choi K.O, Nishimoto K., Norman I.G, Tsegyal T. et al..  2015.  Bioengineered vocal fold mucosa for voice restoration. Science Translational Medicine. 7
Shortreed M.R, Wenger C.D, Frey B.L, Sheynkman G.M, Scalf M., Keller M.P, Attie A.D, Smith L.M.  2015.  Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.
2016
Shortreed M.R, Frey B.L, Scalf M., Knoener R.A, Cesnik A.J, Smith L.M.  2016.  Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 15:1213-1221.
Guillen-Ahlers H., Rao P.K, Levenstein M.E, Kennedy-Darling J., Perumalla D.S, Jadhav A.Y, Glenn J.P, Ludwig-Kubinski A., Drigalenko E., Montoya M.J et al..  2016.  HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
2017
Buxton K.E, Kennedy-Darling J., Shortreed M.R, Zaidan N.Z, Olivier M., Scalf M., Sridharan R., Smith L.M.  2017.  Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 16:3433-3442.
Knoener R.A, Becker J.T, Scalf M., Sherer N.M, Smith L.M.  2017.  Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 7
Aguilar-Hernandez V., Kim D.Y, Stankey R.J, Scalf M., Smith L.M, Vierstra R.D.  2017.  Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Molecular Plant. 10:846-865.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith L.M.  2017.  Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. 89:7841-7846.
Proffitt J.M, Glenn J., Cesnik A.J, Jadhav A., Shortreed M.R, Smith L.M, Kavanagh K., Cox L.A, Olivier M..  2017.  Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 18
2018
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Spiniello M., Knoener R.A, Steinbrink M.I, Yang B., Cesnik A.J, Buxton K.E, Scalf M., Jarrard D.F, Smith L.M.  2018.  HyPR-MS for multiplexed discovery of MALAT1, NEAT1, and NORAD lncRNA protein interactomes. Journal of Proteome Research. 17(9):3022-3038.
Kim S.H, Stiles S.G, Feichtmeier J.M, Ramesh N., Zhan L.H, Scalf M.A, Smith L.M, Pandey U.B, Tibbetts R.S.  2018.  Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. 27:322-337.
Leduc R.D, Schwammle V., Shortreed M.R, Cesnik A.J, Solntsev S.K, Shaw J.B, Martin M.J, Vizcaino J.A, Alpi E., Danis P. et al..  2018.  ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 17:1321-1325.
Cesnik A.J, Shortreed M.R, Schaffer L.V, Knoener R.A, Frey B.L, Scalf M., Solntsev S.K, Dai Y.X, Gasch A.P, Smith L.M.  2018.  Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 17:568-578.
Smith L.M, Kelleher N.L.  2018.  Proteoforms as the next proteomics currency. Science. 359:1106-1107.
2019
Donnelly D.P, Rawlins C.M, DeHart C.J, Fornelli L, Schachner L.F, Lin Z, Lippens J.L, Aluri K.C, Sarin R, Chen B et al..  2019.  Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature methods. 16(7)
Donnelly D.P, Rawlins C.M, DeHart C.J, Fornelli L, Schachner L.F, Lin Z, Lippens J.L, Aluri K.C, Sarin R, Chen B et al..  2019.  Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature methods. 16(7)
Smith L.M, Thomas P.M, Shortreed M.R, Schaffer L.V, Fellers R.T, LeDuc R.D, Tucholski T., Ge Y., Agar J.A, Anderson L.C et al..  2019.  A five-level classification system for proteoform identifications. Nature methods. 16(10)
Schaffer L.V, Millikin R.J, Miller R.M, Anderson L.C, Fellers R.T, Ge Y., Kelleher N.L, LeDuc R.D, Liu X., Payne S.H et al..  2019.  Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics.

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