Publications: Michael Shortreed

Yau, B.; Naghiloo, S.; Diaz-Vegas, A.; Carr, A. V.; Van Gerwen, J.; Needham, E. J.; Jevon, D.; Chen, S. Y.; Hoehn, K. L.; Brandon, A. E.; Macia, L.; Cooney, G. J.; Shortreed, M. R.; Smith, L. M.; Keller, M. P.; Thorn, P.; Larance, M.; James, D. E.; Humphrey, S. J.; Kebede, M. A., Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. Iscience 2021, 24 (10). 10.1016/j.isci.2021.103099

Weisbrod, C. R.; Anderson, L. C.; Hendrickson, C. L.; Schaffer, L. V.; Shortreed, M. R.; Smith, L. M.; Shabanowitz, J.; Hunt, D. F., Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal. Chem. 2021, 93 (26), 9119-9128. 10.1021/acs.analchem.1c00847

Shortreed, M. R.; Millikin, R. J.; Liu, L.; Rolfs, Z.; Miller, R. M.; Schaffer, L. V.; Frey, B. L.; Smith, L. M., Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. J. Proteome Res 2021, 20 (4), 1997-2004. 10.1021/acs.jproteome.0c00838

Schaffer, L. V.; Anderson, L. C.; Butcher, D. S.; Shortreed, M. R.; Miller, R. M.; Pavelec, C.; Smith, L. M., Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. J. Proteome Res 2021, 20 (1), 317-325. 10.1021/acs.jproteome.0c00403

Lu, L.; Scalf, M.; Shortreed, M. R.; Smith, L. M., Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics. Journal of the American Society for Mass Spectrometry 2021, 32 (6), 1319-1325. 10.1021/jasms.0c00462

Cesnik, A. J.; Miller, R. M.; Ibrahim, K.; Lu, L.; Millikin, R. J.; Shortreed, M. R.; Frey, B. L.; Smith, L. M., Spritz: A Proteogenomic Database Engine. J. Proteome Res 2021, 20 (4), 1826-1834. 10.1021/acs.jproteome.0c00407

Schaffer, L. V.; Millikin, R. J.; Shortreed, M. R.; Scalf, M.; Smith, L. M., Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. J. Proteome Res 2020, 19 (8), 3510-3517. 10.1021/acs.jproteome.0c00332

Millikin, R. J.; Shortreed, M. R.; Scalf, M.; Smith, L. M., A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. J. Proteome Res 2020, 19 (5), 1975-1981. 10.1021/acs.jproteome.9b00796

Lu, L.; Riley, N. M.; Shortreed, M. R.; Bertozzi, C. R.; Smith, L. M., O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nature Methods 2020, 17 (11), 1133-+. 10.1038/s41592-020-00985-5

Spiniello, M.; Steinbrink, M. I.; Cesnik, A. J.; Miller, R. M.; Scalf, M.; Shortreed, M. R.; Smith, L. M., Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA 2019, 25 (10), 1337-1352. 10.1261/rna.072157.119

Smith, L. M.; Thomas, P. M.; Shortreed, M. R.; Schaffer, L. V.; Fellers, R. T.; Leduc, R. D.; Tucholski, T.; Ge, Y.; Agar, J. N.; Anderson, L. C.; Chamot-Rooke, J.; Gault, J.; Loo, J. A.; Pasa-Tolic, L.; Robinson, C. V.; Schluter, H.; Tsybin, Y. O.; Vilaseca, M.; Vizcaino, J. A.; Danis, P. O.; Kelleher, N. L., A five-level classification system for proteoform identifications. Nature Methods 2019, 16 (10), 939-940. 10.1038/s41592-019-0573-x

Schaffer, L. V.; Tucholski, T.; Shortreed, M. R.; Ge, Y.; Smith, L. M., Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Anal. Chem. 2019, 91 (17), 10937-10942. 10.1021/acs.analchem.9b02343

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. W.; Payne, S. H.; Sun, L. L.; Thomas, P. M.; Tucholski, T.; Wang, Z.; Wu, S.; Wu, Z. J.; Yu, D. H.; Shortreed, M. R.; Smith, L. M., Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019, 19 (10). 10.1002/pmic.201800361

Rolfs, Z.; Solntsev, S. K.; Shortreed, M. R.; Frey, B. L.; Smith, L. M., Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. J. Proteome Res 2019, 18 (1), 349-358. 10.1021/acs.jproteome.8b00651

Miller, R. M.; Millikin, R. J.; Hoffmann, C. V.; Solntsev, S. K.; Sheynkman, G. M.; Shortreed, M. R.; Smith, L. M., Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. J. Proteome Res 2019, 18 (9), 3429-3438. 10.1021/acs.jproteome.9b00330

Dai, Y. X.; Buxton, K. E.; Schaffer, L. V.; Miller, R. M.; Millikin, R. J.; Scalf, M.; Frey, B. L.; Shortreed, M. R.; Smith, L. M., Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. J. Proteome Res 2019, 18 (10), 3671-3680. 10.1021/acs.jproteome.9b00339

Zaidan, N. Z.; Walker, K. J.; Brown, J. E.; Schaffer, L. V.; Scalf, M.; Shortreed, M. R.; Iyer, G.; Smith, L. M.; Sridharan, R., Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports 2018, 10 (2), 627-641. 10.1016/j.stemcr.2017.12.016

Solntsev, S. K.; Shortreed, M. R.; Frey, B. L.; Smith, L. M., Enhanced Global Post-translational Modification Discovery with MetaMorpheus. J. Proteome Res 2018, 17 (5), 1844-1851. 10.1021/acs.jproteome.7b00873

Schaffer, L. V.; Shortreed, M. R.; Cesnik, A. J.; Frey, B. L.; Solntsev, S. K.; Scalf, M.; Smith, L. M., Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Anal. Chem. 2018, 90 (2), 1325-1333. 10.1021/acs.analchem.7b04221

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., Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. J. Proteome Res 2018, 17 (10), 3526-3536. 10.1021/acs.jproteome.8b00469

Millikin, R. J.; Solntsev, S. K.; Shortreed, M. R.; Smith, L. M., Ultrafast Peptide Label-Free Quantification with FlashLFQ. J. Proteome Res 2018, 17 (1), 386-391. 10.1021/acs.jproteome.7b00608

Leduc, R. D.; Schwammle, V.; Shortreed, M. R.; Cesnik, A. J.; Solntsev, S. K.; Shaw, J. B.; Martin, M. J.; Vizcaino, J. A.; Alpi, E.; Danis, P.; Kelleher, N. L.; Smith, L. M.; Ge, Y.; Agar, J. N.; Chamot-Rooke, J.; Loo, J. A.; Pasa-Tolic, L.; Tsybin, Y. O., ProForma: A Standard Proteoform Notation. J. Proteome Res 2018, 17 (3), 1321-1325. 10.1021/acs.jproteome.7b00851

Guillen-Ahlers, H.; Rao, P. K.; Perumalla, D. S.; Montoya, M. J.; Jadhav, A. Y. L.; Shortreed, M. R.; Smith, L. M.; Olivier, M., Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. JoVE-Journal of Visualized Experiments 2018, (136). 10.3791/57140

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., Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Translational oncology 2018, 11 (3), 808-814. 10.1016/j.tranon.2018.04.002

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., Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. J. Proteome Res 2018, 17 (1), 568-578. 10.1021/acs.jproteome.7b00685

Proffitt, J. M.; Glenn, J.; Cesnik, A. J.; Jadhav, A.; Shortreed, M. R.; Smith, L. M.; Kavanagh, K.; Cox, L. A.; Olivier, M., Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. BMC Genomics 2017, 18. 10.1186/s12864-017-4279-0

Li, Q. Y.; Shortreed, M. R.; Wenger, C. D.; Frey, B. L.; Schaffer, L. V.; Scalf, M.; Smith, L. M., Global Post-Translational Modification Discovery. J. Proteome Res 2017, 16 (4), 1383-1390. 10.1021/acs.jproteome.6b00034

Dai, Y. X.; Shortreed, M. R.; Scalf, M.; Frey, B. L.; Cesnik, A. J.; Solntsev, S.; Schaffer, L. V.; Smith, L. M., Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. J. Proteome Res 2017, 16 (11), 4156-4165. 10.1021/acs.jproteome.7b00516

Dai, Y.; Kennedy-Darling, J.; Shortreed, M. R.; Scalf, M.; Gasch, A. P.; Smith, L. M., Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Anal. Chem. 2017, 89 (15), 7841-7846. 10.1021/acs.analchem.7b01784

Buxton, K. E.; Kennedy-Darling, J.; Shortreed, M. R.; Zaidan, N. Z.; Olivier, M.; Scalf, M.; Sridharan, R.; Smith, L. M., Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. J. Proteome Res 2017, 16 (9), 3433-3442. 10.1021/acs.jproteome.7b00448

Shortreed, M. R.; Frey, B. L.; Scalf, M.; Knoener, R. A.; Cesnik, A. J.; Smith, L. M., Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. J. Proteome Res 2016, 15 (4), 1213-1221. 10.1021/acs.jproteome.5b01090

Sheynkman, G. M.; Shortreed, M. R.; Cesnik, A. J.; Smith, L. M., Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. In Annual Review of Analytical Chemistry, Vol 9, Bohn, P. W.; Pemberton, J. E., Eds. Annual Reviews: Palo Alto, 2016; Vol. 9, pp 521-545. 10.1146/annurev-anchem-071015-041722

Cesnik, A. J.; Shortreed, M. R.; Sheynkman, G. M.; Frey, B. L.; Smith, L. M., Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. J. Proteome Res 2016, 15 (3), 800-808. 10.1021/acs.jproteome.5b00817

Shortreed, M. R.; Wenger, C. D.; Frey, B. L.; Sheynkman, G. M.; Scalf, M.; Keller, M. P.; Attie, A. D.; Smith, L. M., Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. J. Proteome Res 2015, 14 (11), 4714-4720. 10.1021/acs.jproteome.5b00599

Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Scalf, M.; Smith, L. M., Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences. J. Proteome Res 2014, 13 (1), 228-240. 10.1021/pr4009207

Kennedy-Darling, J.; Holden, M. T.; Shortreed, M. R.; Smith, L. M., Multiplexed Programmable Release of Captured DNA. Chembiochem 2014, 15 (16), 2353-2356. 10.1002/cbic.201402343

Kennedy-Darling, J.; Guillen-Ahlers, H.; Shortreed, M. R.; Scalf, M.; Frey, B. L.; Kendziorski, C.; Olivier, M.; Gasch, A. P.; Smith, L. M., Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. J. Proteome Res 2014, 13 (8), 3810-3825. 10.1021/pr5004938

Guillen-Ahlers, H.; Shortreed, M. R.; Smith, L. M.; Olivier, M., Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics 2014, 46 (13), 441-447. 10.1152/physiolgenomics.00041.2014

Torde, R. G.; Therrien, A. J.; Shortreed, M. R.; Smith, L. M.; Lamos, S. M., Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules 2013, 18 (12), 14977-14988. 10.3390/molecules181214977

Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Smith, L. M., Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics 2013, 12 (8), 2341-2353. 10.1074/mcp.O113.028142

Wu, C. H.; Chen, S. Y.; Shortreed, M. R.; Kreitinger, G. M.; Yuan, Y.; Frey, B. L.; Zhang, Y.; Mirza, S.; Cirillo, L. A.; Olivier, M.; Smith, L. M., Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification. PLoS One 2011, 6 (10). 10.1371/journal.pone.0026217

Smith, L. M.; Shortreed, M. R.; Olivier, M., To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation. Analyst 2011, 136 (15), 3060-3065. 10.1039/c1an15037e

Russell, J. D.; Hilger, R. T.; Ladror, D. T.; Tervo, M. A.; Scalf, M.; Shortreed, M. R.; Coon, J. J.; Smith, L. M., Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis. Anal. Chem. 2011, 83 (6), 2187-2193. 10.1021/ac103023q

Hallows, W. C.; Yu, W.; Smith, B. C.; Devires, M. K.; Ellinger, J. J.; Someya, S.; Shortreed, M. R.; Prolla, T.; Markley, J. L.; Smith, L. M.; Zhao, S.; Guan, K.-L.; Denu, J. M., Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction. Mol. Cell 2011, 41 (2), 139-149. 10.1016/j.molcel.2011.01.002

Phillips, M. F.; Lockett, M. R.; Rodesch, M. J.; Shortreed, M. R.; Cerrina, F.; Smith, L. M., In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication. Nucleic Acids Res. 2008, 36 (1). 10.1093/nar/gkm1103

Lockett, M. R.; Weibel, S. C.; Phillips, M. F.; Shortreed, M. R.; Sun, B.; Corn, R. M.; Hamers, R. J.; Cerrina, F.; Smith, L. M., Carbon-on-metal films for surface plasmon resonance detection of DNA arrays. Journal of the American Chemical Society 2008, 130 (27), 8611-8613. 10.1021/ja802454c

Lockett, M. R.; Shortreed, M. R.; Smith, L. M., Aldehyde-terminated amorphous carbon substrates for the fabrication of biomolecule arrays. Langmuir 2008, 24 (17), 9198-9203. 10.1021/la800991t

Freed, J. K.; Shortreed, M. R.; Kleefisch, C. J.; Smith, L. M.; Greene, A. S., Revealing the role of phosphatidylserine in shear stress-mediated protection in endothelial cells. Endothelium-Journal of Endothelial Cell Research 2008, 15 (4), 225-230. 10.1080/10623320802228849

Lockett, M. R.; Shortreed, M. R.; Smith, L. M., Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions. Anal. Chem. 2007, 79 (15), 6031-6036. 10.1021/ac070424c

Lamos, S. M.; Shortreed, M. R.; Frey, B. L.; Belshaw, P. J.; Smith, L. M., Relative quantification of carboxylic acid metabolites by liquid chromatography – Mass spectrometry using isotopic variants of cholamine. Anal. Chem. 2007, 79 (14), 5143-5149. 10.1021/ac062416m

Chen, S. Y.; Zheng, T.; Shortreed, M. R.; Alexander, C.; Smith, L. M., Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays. Anal. Chem. 2007, 79 (15), 5698-5702. 10.1021/ac070423k

Shortreed, M. R.; Lamos, S. M.; Frey, B. L.; Phillips, M. F.; Patel, M.; Belshaw, P. J.; Smith, L. M., Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. Anal. Chem. 2006, 78 (18), 6398-6403. 10.1021/ac0607008

Peelen, D.; Kodoyianni, V.; Lee, J.; Zheng, T.; Shortreed, M. R.; Smith, L. M., Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films. J. Proteome Res 2006, 5 (7), 1580-1585. 10.1021/pr050467e

Nie, B.; Shortreed, M. R.; Smith, L. M., Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging. Anal. Chem. 2006, 78 (5), 1528-1534. 10.1021/ac052067g

Tulpan, D.; Andronescu, M.; Chang, S. B.; Shortreed, M. R.; Condon, A.; Hoos, H. H.; Smith, L. M., Thermodynamically based DNA strand design. Nucleic Acids Res. 2005, 33 (15), 4951-4964. 10.1093/nar/gki773

Shortreed, M. R.; Chang, S. B.; Hong, D. G.; Phillips, M.; Campion, B.; Tulpan, D. C.; Andronescu, M.; Condon, A.; Hoos, H. H.; Smith, L. M., A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Res. 2005, 33 (15), 4965-4977. 10.1093/nar/gki812

Rabaglia, M. E.; Gray-Keller, M. P.; Frey, B. L.; Shortreed, M. R.; Smith, L. M.; Attie, A. D., alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice. Am. J. Physiol.-Endocrinol. Metab 2005, 289 (2), E218-E224. 10.1152/ajpendo.00573.2004

Nie, B.; Shortreed, M. R.; Smith, L. M., Scoring single-nucleotide polymorphisms at the single-molecule level by counting individual DNA cleavage events on surfaces. Anal. Chem. 2005, 77 (20), 6594-6600. 10.1021/ac051025p

Chen, Y.; Shortreed, M. R.; Olivier, M.; Smith, L. M., Parallel single nucleotide polymorphism genotyping by surface invasive cleavage with universal detection. Anal. Chem. 2005, 77 (8), 2400-2405. 10.1021/ac0483825

Chen, Y.; Shortreed, M. R.; Peelen, D.; Lu, M. C.; Smith, L. M., Surface amplification of invasive cleavage products. Journal of the American Chemical Society 2004, 126 (10), 3016-3017. 10.1021/ja039355j

Lu, M. C.; Shortreed, M. R.; Hall, J. G.; Wang, L. M.; Berggren, T.; Stevens, P. W.; Kelso, D. M.; Lyamichev, V.; Neri, B.; Smith, L. M., A surface invasive cleavage assay for highly parallel SNP analysis. Human Mutation 2002, 19 (4), 416-422. 10.1002/humu.10071

Lu, M. C.; Hall, J. G.; Shortreed, M. R.; Wang, L. M.; Berggren, W. T.; Stevens, P. W.; Kelso, D. M.; Lyamichev, V.; Neri, B.; Skinner, J. L.; Smith, L. M., Structure-specific DNA cleavage on surfaces. Journal of the American Chemical Society 2002, 124 (27), 7924-7931. 10.1021/ja012082c