All Faculty and Research Staff Publications

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2019
Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA. 2019 ;25:1337-1352.
Dai YX, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM. 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. 2019 ;18:3671-3680.
Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, Leduc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, et al. A five-level classification system for proteoform identifications. Nature MethodsNat Methods. 2019 ;16:939-940.
Rolfs Z, Solntsev SK, Shortreed MR, Frey BL, Smith LM. Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 2019 ;18:349-358.
Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, Leduc RD, Liu XW, Payne SH, et al. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics. 2019 ;19.
Miller RM, Millikin RJ, Hoffmann CV, Solntsev SK, Sheynkman GM, Shortreed MR, Smith LM. Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. Journal of Proteome Research. 2019 ;18:3429-3438.
Schaffer LV, Tucholski T, Shortreed MR, Ge Y, Smith LM. Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Analytical Chemistry. 2019 ;91:10937-10942.
2018
Guillen-Ahlers H, Rao PK, Perumalla DS, Montoya MJ, Jadhav AYL, Shortreed MR, Smith LM, Olivier M. Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. Jove-Journal of Visualized Experiments. 2018 .
Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 2018 ;10:627-641.
Solntsev SK, Shortreed MR, Frey BL, Smith LM. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 2018 ;17:1844-1851.
Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 2018 ;90:1325-1333.
Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. Journal of Proteome Research. 2018 ;17:3526-3536.
Cesnik AJ, Yang B, Truong A, Etheridge T, Spiniello M, Steinbrink MI, Shortreed MR, Frey BL, Jarrard DF, Smith LM. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 2018 ;11:808-814.
Leduc RD, Schwammle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, et al. ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 2018 ;17:1321-1325.
Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai YX, Gasch AP, Smith LM. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 2018 ;17:568-578.
Millikin RJ, Solntsev SK, Shortreed MR, Smith LM. Ultrafast Peptide Label-Free Quantification with FlashLFQ. Journal of Proteome Research. 2018 ;17:386-391.

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