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Filters: Author is Shortreed, M. R. [Clear All Filters]
Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. 19:3510-3517.. 2020.
HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.. 2016.
A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis. Journal of Proteome Research. 21:2609-2618.. 2022.
Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 15:800-808.. 2016.
Global Post-Translational Modification Discovery. J Proteome Res.. 2017.
Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.. 2015.
Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. Journal of Proteome Research. 18:349-358.. 2019.
Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 90:1325-1333.. 2018.
Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23. 2022.
Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 17:1844-1851.. 2018.
Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 15:1213-1221.. 2016.
Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 16:3433-3442.. 2017.
Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 16:4156-4165.. 2017.
Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br. Journal of Proteome Research. 21:993-1001.. 2022.
Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 13:3810-3825.. 2014.
Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 12:2341-2353.. 2013.
Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. Journal of Proteome Research. 20:317-325.. 2021.
Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 10:627-641.. 2018.
Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. Journal of Proteome Research. 20:1997-2004.. 2021.
A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics. Journal of Proteome Research. 19:1975-1981.. 2020.
Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays. Analytical Chemistry. 79:5698-5702.. 2007.
alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice. American Journal of Physiology - Endocrinology & Metabolism. 289:E218-E224.. 2005.
Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Analytical Chemistry. 93:9119-9128.. 2021.
Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 46:441-447.. 2014.