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2018
Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM.  2018.  Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus. Journal of Proteome Research. 17(7):2370-2376.
Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.L, Frey B.L, Jarrard D.F, Smith L.M.  2018.  Long noncoding RNAs AC009014. 3 and newly discovered XPLAID differentiate aggressive and indolent prostate cancers. Translational Oncology. 11(3):808-814.
Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.R, Frey B.L, Jarrard D.F, Smith L.M.  2018.  Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 11:808-814.
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.
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.
Millikin R.J, Solntsev S.K, Shortreed M.R, Smith L.M.  2018.  Ultrafast Peptide Label-Free Quantification with FlashLFQ. Journal of Proteome Research. 17:386-391.
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)
Spiniello M., Steinbrink M.I, Cesnik A.J, Miller R.M, Scalf M., Shortreed M.R, Smith L.M.  2019.  Comprehensive in vivo identification of the c-Myc mRNA interactome using HyPR-MS. Cold Spring Harbor Laboratory Press.
Dai Y., Buxton K.E, Schaffer L.V, Miller R.M, Millikin R.J, Scalf M., Frey B.L, Shortreed M.R, Smith L.M.  2019.  Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. Journal of Proteome Research. 18(10)
Ling C., Nishimoto K., Rolfs Z., Smith L.M, Frey B.L, Wellham N.V.  2019.  Differentiated fibrocytes assume a functional mesenchymal phenotype with regenerative potential. Science advances. 5(5)
Holden M.T, Smith L.M.  2019.  Encrypted Oligonucleotide Arrays for Molecular Authentication. ACS Combinatorial Science.
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)
Rolfs Z., Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2019.  Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 18:349-358.
Mayer K.S, Chen X., Sanders D., Chen J., Jiang J., N P., Scalf M., Smith L.M, Zhong X..  2019.  HDA9-PWR-HOS15 is a core histone deacetylase complex regulating transcription and development. Plant Physiology. 180(1):342-355.
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.
Miller R.M, Millikin R.J, Hoffman C.V, Solntsev S.K, Sheynkman G.M, Shortreed M.R, Smith L.M.  2019.  Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. Journal of Proteome Research. 18(9)
Schaffer L.V, Tucholski T., Shortreed M.R, Ge Y., Smith L.M.  2019.  Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Analytical Chemistry. 91(17)
Gemperline D.C, Marshall R.S, Lee K.H, Zhao Q.Z, Hu W.M, McLoughlin F., Scalf M., Smith L.M, Vierstra R.D.  2019.  Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. Journal of Biological Chemistry. 294:17570-17592.
2020
Rolfs Z., Millikin R.J, Smith L.M.  2020.  An Algorithm to Improve the Speed of Semi and Non-specific Enzyme Searches in Proteomics. Current Bioinformatics. 15:1065-1074.
Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. Journal of Proteome Research. 19:1975-1981.
Schaffer L.V, Millikin R.J, Shortreed M.R, Scalf M., Smith L.M.  2020.  Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. 19:3510-3517.
Lu L., Riley N.M, Shortreed M.R, Bertozzi C.R, Smith L.M.  2020.  O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nature Methods. 17:1133-+.

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