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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.

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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

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.

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Miller R.M, Knoener R.A, Benner B.E, Frey B.L, Scalf M., Shortreed M.R, Sherer N.M, Smith L.M. 2022. Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br. Journal of Proteome Research. 21:993-1001.