Publications

Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, et al.. 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.
Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, et al.. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 2018;90:1325-1333.
Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, et al.. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 2018;10:627-641.
Leduc RD, Schwammle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, et al.. ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 2018;17:1321-1325.
Solntsev SK, Shortreed MR, Frey BL, Smith LM. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 2018;17:1844-1851.
Cesnik AJ, Yang B, Truong A, Etheridge T, Spiniello M, Steinbrink MI, et al.. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 2018;11:808-814.
Guillen-Ahlers H, Rao PK, Perumalla DS, Montoya MJ, Jadhav AYL, Shortreed MR, et al.. Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. Jove-Journal of Visualized Experiments. 2018;.
Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, et al.. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. Journal of Proteome Research. 2018;17:3526-3536.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. 2017;89:7841-7846.
Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, et al.. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 2017;16:3433-3442.
Dai YX, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, et al.. Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 2017;16:4156-4165.
Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, et al.. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 2017;18.
Li QY, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, et al.. Global Post-Translational Modification Discovery. Journal of Proteome Research. 2017;16:1383-1390.
Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. In: Bohn PW, Pemberton JE. Palo Alto: Annual Reviews; 2016. pp. 521-545.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 2016;15:800-808.
Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 2016;15:1213-1221.
Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, et al.. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 2015;14:4714-4720.
Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM. Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences. Journal of Proteome Research. 2014;13:228-240.
Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M. Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 2014;46:441-447.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. In-Depth Identification of Protein Sequence Variants and Posttranslational Modifications in 10 Human Cell Lines. Molecular & Cellular Proteomics. 2014;13:S49-S49.
Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, et al.. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 2014;13:3810-3825.
Kennedy-Darling J, Holden MT, Shortreed MR, Smith LM. Multiplexed Programmable Release of Captured DNA. Chembiochem. 2014;15:2353-2356.
Torde RG, Therrien AJ, Shortreed MR, Smith LM, Lamos SM. Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules. 2013;18:14977-14988.
Sheynkman GM, Shortreed MR, Frey BL, Smith LM. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 2013;12:2341-2353.
Wu CH, Chen SY, Shortreed MR, Kreitinger GM, Yuan Y, Frey BL, et al.. Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification. Plos One. 2011;6.
Smith LM, Shortreed MR, Olivier M. To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation. Analyst. 2011;136:3060-3065.
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, et al.. Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis. Analytical Chemistry. 2011;83:2187-2193.
Hallows WC, Yu W, Smith BC, Devires MK, Ellinger JJ, Someya S, et al.. Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction. Molecular Cell. 2011;41:139-149.
Phillips MF, Lockett MR, Rodesch MJ, Shortreed MR, Cerrina F, Smith LM. In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication. Nucleic Acids Research. 2008;36.
Lockett MR, Weibel SC, Phillips MF, Shortreed MR, Sun B, Corn RM, et al.. Carbon-on-metal films for surface plasmon resonance detection of DNA arrays. Journal of the American Chemical Society. 2008;130:8611-8613.
Lockett MR, Shortreed MR, Smith LM. Aldehyde-terminated amorphous carbon substrates for the fabrication of biomolecule arrays. Langmuir. 2008;24:9198-9203.
Freed JK, Shortreed MR, Kleefisch CJ, Smith LM, Greene AS. Revealing the role of phosphatidylserine in shear stress-mediated protection in endothelial cells. Endothelium-Journal of Endothelial Cell Research. 2008;15:225-230.
Lockett MR, Shortreed MR, Smith LM. Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions. Analytical Chemistry. 2007;79:6031-6036.
Lamos SM, Shortreed MR, Frey BL, Belshaw PJ, Smith LM. Relative quantification of carboxylic acid metabolites by liquid chromatography - Mass spectrometry using isotopic variants of cholamine. Analytical Chemistry. 2007;79:5143-5149.
Chen SY, Zheng T, Shortreed MR, Alexander C, Smith LM. Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays. Analytical Chemistry. 2007;79:5698-5702.
Shortreed MR, Lamos SM, Frey BL, Phillips MF, Patel M, Belshaw PJ, et al.. Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. Analytical Chemistry. 2006;78:6398-6403.
Peelen D, Kodoyianni V, Lee J, Zheng T, Shortreed MR, Smith LM. Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films. Journal of Proteome Research. 2006;5:1580-1585.
Nie B, Shortreed MR, Smith LM. Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging. Analytical Chemistry. 2006;78:1528-1534.
Tulpan D, Andronescu M, Chang SB, Shortreed MR, Condon A, Hoos HH, et al.. Thermodynamically based DNA strand design. Nucleic Acids Research. 2005;33:4951-4964.
Shortreed MR, Chang SB, Hong DG, Phillips M, Campion B, Tulpan DC, et al.. A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research. 2005;33:4965-4977.
Rabaglia ME, Gray-Keller MP, Frey BL, Shortreed MR, Smith LM, Attie AD. alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice. American Journal of Physiology - Endocrinology & Metabolism. 2005;289:E218-E224.
Nie B, Shortreed MR, Smith LM. Scoring single-nucleotide polymorphisms at the single-molecule level by counting individual DNA cleavage events on surfaces. Analytical Chemistry. 2005;77:6594-6600.
Chen Y, Shortreed MR, Olivier M, Smith LM. Parallel single nucleotide polymorphism genotyping by surface invasive cleavage with universal detection. Analytical Chemistry. 2005;77:2400-2405.
Chen Y, Shortreed MR, Peelen D, Lu MC, Smith LM. Surface amplification of invasive cleavage products. Journal of the American Chemical Society. 2004;126:3016-3017.
Lu MC, Hall JG, Shortreed MR, Wang LM, Berggren WT, Stevens PW, et al.. Structure-specific DNA cleavage on surfaces. Journal of the American Chemical Society. 2002;124:7924-7931.
Lu MC, Shortreed MR, Hall JG, Wang LM, Berggren T, Stevens PW, et al.. A surface invasive cleavage assay for highly parallel SNP analysis. Human Mutation. 2002;19:416-422.