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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.

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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.

Lu L., Scalf M., Shortreed M.R, Smith L.M. 2021. Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. 32:1319-1325.

Carr A.V, Frey B.L, Scalf M., Cesnik A.J, Rolfs Z., Pike K.A, Yang B., Keller M.P, Jarrard D.F, Shortreed M.R et al.. 2022. MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses. Journal of Proteome Research. 21:410-419.

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.

Lamos S.M, Krusemark C.J, McGee C.J, Scalf M., Smith L.M, Belshaw P.J. 2006. Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry. Angewandte Chemie-International Edition. 45:4329-4333.

Gemperline D.C, Scalf M., Smith L.M, Vierstra R.D. 2016. Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. Proteomics. 16:920-924.

Hansen S.R, White D.S, Scalf M., Correa I.R, Smith L.M, Hoskins A.A, Staley J.P. 2022. Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife. 11

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Chen X., Lu L., Mayer K.S, Scalf M., Qian S., Lomax A., Smith L.M, Zhong X.. 2016. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife. 5

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.

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.

Li Q.Y, Uygun B.E, Geerts S., Ozer S., Scalf M., Gilpin S.E, Ott H.C, Yarmush M.L, Smith L.M, Welham N.V et al.. 2016. Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 75:37-46.

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Pellitteri-Hahn M.C, Halligan B.D, Scalf M., Smith L.M, Hickey W.J. 2011. Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. Journal of Proteomics. 74:411-419.

Miller M.J, Scalf M., Rytz T.C, Hubler S.L, Smith L.M, Vierstra R.D. 2013. Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis. Molecular & Cellular Proteomics. 12:449-463.

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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.

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Saracco S.A, Hansson M., Scalf M., Walker J.M, Smith L.M, Vierstra R.D. 2009. Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis. Plant Journal. 59:344-358.

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

Book A.J, Yang P.Z, Scalf M., Smith L.M, Vierstra R.D. 2005. Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis. Plant Physiology. 138:1046-1057.

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