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T

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)

Spiniello M., Scalf M., Casamassimi A., Abbondanza C., Smith L.M. 2022. Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. International Journal of Molecular Sciences. 23

Tulpan D., Andronescu M., Chang S.B, Shortreed M.R, Condon A., Hoos H.H, Smith L.M. 2005. Thermodynamically based DNA strand design. Nucleic Acids Research. 33:4951-4964.

Shortreed M.R, Chang S.B, Hong D.G, Phillips M., Campion B., Tulpan D.C, Andronescu M., Condon A., Hoos H.H, Smith L.M. 2005. A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research. 33:4965-4977.

S

Rytz T.C, Miller M.J, McLoughlin F., Augustine R.C, Marshall R.S, Juan Y.T, Charng Y.Y, Scalf M., Smith L.M, Vierstra R.D. 2018. SUMOylome Profiling Reveals a Diverse Array of Nuclear Targets Modified by the SUMO Ligase SIZ1 during Heat Stress. Plant Cell. 30:1077-1099.

R

Mandir JB, Lockett MR, Phillips MF, Allawi HT, Lyamichev VI, Smith L.M. 2009. Rapid Determination of RNA Accessible Sites by Surface Plasmon Resonance Detection of Hybridization to DNA Arrays. Analytical Chemistry. 81:8949-8956.

P

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.

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.

Yang W, Auciello O, Butler JE, Cai W, Carlisle JA, Gerbi JE, Gruen DM, Knickerbocker T, Lasseter TL, Russell, Jr. JN et al.. 2002. Preparation and electrochemical characterization of DNA-modified nanocrystalline diamond films. Materials Research Society Symposium Proceedings. 737

M

Ladror D.T, Frey B.L, Scalf M., Levenstein M.E, Artymiuk J.M, Smith L.M. 2014. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochemical and Biophysical Research Communications. 445:535-541.

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.

L

Zheng T, Yu H, Alexander CM, Beebe DJ, Smith L.M. 2007. Lectin-modified microchannels for mammalian cell capture and purification. Biomedical Microdevices. 9:611-617.

I

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.

H

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.

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.

G

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.

F

Hoffman E.A, Frey B.L, Smith L.M, Auble D.T. 2015. Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes. Journal of Biological Chemistry. 290:26404-26411.

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)

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)

E

Mehdi S.Q, Recktenwald D.J, Smith L.M, Li G.C, Armour E.P, Hahn G.M. 1984. Effect of hyperthermia on murine cell surface histocompatibility antigens. Cancer Research. 44:3394-3397.

D

Yang W.S, Auciello O., Butler J.E, Cai W., Carlisle J.A, Gerbi J., Gruen D.M, Knickerbocker T., Lasseter T.L, Russell J.N et al.. 2002. DNA-modified nanocrystalline diamond thin-films as stable, biologically active substrates. Nature Materials. 1:253-257.

C

Schaffer L.V, Anderson L.C, Butcher D.S, Shortreed M.R, Miller R.M, Pavelec C., Smith L.M. 2021. Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. Journal of Proteome Research. 20:317-325.

B

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)

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