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I

Schaffer L.V, Millikin R.J, Shortreed M.R, Scalf M., Smith L.M. 2020. Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. Journal of Proteome Research. 19:3510-3517.

H

Guillen-Ahlers H., Rao P.K, Levenstein M.E, Kennedy-Darling J., Perumalla D.S, Jadhav A.Y, Glenn J.P, Ludwig-Kubinski A., Drigalenko E., Montoya M.J et al.. 2016. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.

Dai Y.L, Millikin R.J, Rolfs Z., Shortreed M.R, Smith L.M. 2022. 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.

Cesnik A.J, Shortreed M.R, Sheynkman G.M, Frey B.L, Smith L.M. 2016. 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.

G

Li Q., Shortreed M.R, Wenger C.D, Frey B.L, Schaffer L.V, Scalf M., Smith L.M. 2017. Global Post-Translational Modification Discovery. J Proteome Res.

Shortreed M.R, Wenger C.D, Frey B.L, Sheynkman G.M, Scalf M., Keller M.P, Attie A.D, Smith L.M. 2015. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.

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.

E

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.

Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al.. 2022. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23

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.

Shortreed M.R, Frey B.L, Scalf M., Knoener R.A, Cesnik A.J, Smith L.M. 2016. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 15:1213-1221.

Buxton K.E, Kennedy-Darling J., Shortreed M.R, Zaidan N.Z, Olivier M., Scalf M., Sridharan R., Smith L.M. 2017. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 16:3433-3442.

Dai Y.X, Shortreed M.R, Scalf M., Frey B.L, Cesnik A.J, Solntsev S., Schaffer L.V, Smith L.M. 2017. Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 16:4156-4165.

D

Miller R.M, Knoener R.A, Benner B.E, Frey B.L, Scalf M., Shortreed M.R, Sherer N.M, Smith L.M. 2022. Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br. Journal of Proteome Research. 21:993-1001.

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

Sheynkman G.M, Shortreed M.R, Frey B.L, Smith L.M. 2013. Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 12:2341-2353.

C

Schaffer L.V, Anderson L.C, Butcher D.S, Shortreed M.R, Miller R.M, Pavelec C., Smith L.M. 2021. 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.

Zaidan N.Z, Walker K.J, Brown J.E, Schaffer L.V, Scalf M., Shortreed M.R, Iyer G., Smith L.M, Sridharan R.. 2018. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 10:627-641.

B

Shortreed M.R, Millikin R.J, Liu L., Rolfs Z., Miller R.M, Schaffer L.V, Frey B.L, Smith L.M. 2021. Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. Journal of Proteome Research. 20:1997-2004.

Millikin R.J, Shortreed M.R, Scalf M., Smith L.M. 2020. 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.

A

Chen S.Y, Zheng T., Shortreed M.R, Alexander C., Smith L.M. 2007. Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays. Analytical Chemistry. 79:5698-5702.

Rabaglia M.E, Gray-Keller M.P, Frey B.L, Shortreed M.R, Smith L.M, Attie A.D. 2005. alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice. American Journal of Physiology - Endocrinology & Metabolism. 289:E218-E224.

Weisbrod C.R, Anderson L.C, Hendrickson C.L, Schaffer L.V, Shortreed M.R, Smith L.M, Shabanowitz J., Hunt D.F. 2021. 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.

Guillen-Ahlers H., Shortreed M.R, Smith L.M, Olivier M.. 2014. Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 46:441-447.

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