Publications

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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)
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)
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.
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.
2018
Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2018.  Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 17:1844-1851.
Schaffer L.V, Shortreed M.R, Cesnik A.J, Frey B.L, Solntsev S.K, Scalf M., Smith L.M.  2018.  Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 90:1325-1333.
Rolfs Z., Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2018.  Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 18(1):349-358.
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.
Schaffer L.V, Rensvold J.W, Shortreed M.R, Cesnik A.J, Jochem A., Scalf M., Frey B.L, Pagliarini D.J, Smith L.M.  2018.  Identification and quantification of murine mitochondrial proteoforms using an integrated top-down and intact-mass strategy. Journal of Proteome Research. 17(10):3526-3536.
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.
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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