Publications

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2022
Carr A.V, Frey B.L, Scalf M., Cesnik A.J, Rolfs Z., Pike K.A, Yang B., Keller M.P, Jarrard D.F, Shortreed M.R et al..  2022.  MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses. Journal of Proteome Research. 21:410-419.
Plubell D.L, Kall L., Webb-Robertson B.J, Bramer L.M, Ives A., Kelleher N.L, Smith L.M, Montine T.J, Wu C.C, MacCoss M.J.  2022.  Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? br Journal of Proteome Research. 21:891-898.
2021
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.
2019
Donnelly D.P, Rawlins C.M, DeHart C.J, Fornelli L, Schachner L.F, Lin Z, Lippens J.L, Aluri K.C, Sarin R, Chen B et al..  2019.  Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature methods. 16(7)
Smith L.M, Thomas P.M, Shortreed M.R, Schaffer L.V, Fellers R.T, LeDuc R.D, Tucholski T., Ge Y., Agar J.A, Anderson L.C et al..  2019.  A five-level classification system for proteoform identifications. Nature methods. 16(10)
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., Payne S.H et al..  2019.  Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics.
2018
Guillen-Ahlers H, Rao P.K, Perumalla D.S, Montoya M.J, Jadhav A.YL, Shortreed M.R, Smith L.M, Olivier M.  2018.  Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. Journal of Visualized Experiments. (136)
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
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.  2018.  Identification and quantification of murine mitochondrial proteoforms using an integrated top-down and intact-mass strategy. Journal of Proteome Research. 17(10):3526-3536.
Kim S.H, Stiles S.G, Feichtmeier J.M, Ramesh N., Zhan L.H, Scalf M.A, Smith L.M, Pandey U.B, Tibbetts R.S.  2018.  Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. 27:322-337.
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. et al..  2018.  ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 17:1321-1325.
2017
Proffitt J.M, Glenn J., Cesnik A.J, Jadhav A., Shortreed M.R, Smith L.M, Kavanagh K., Cox L.A, Olivier M..  2017.  Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 18
2016
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.
Sheynkman G.M, Shortreed M.R, Cesnik A.J, Smith L.M.  2016.  Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. 9:521-545.
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
2014
Rhoads T.W, Rose C.M, Bailey D.J, Riley N.M, Molden R.C, Nestler A.J, Merrill A.E, Smith L.M, Hebert A.S, Westphall M.S et al..  2014.  Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 86:2314-2319.
2012
Sturm R., Sheynkman G., Booth C., Smith L.M, Pedersen J.A, Li L.J.  2012.  Absolute Quantification of Prion Protein (90-231) Using Stable Isotope-Labeled Chymotryptic Peptide Standards in a LC-MRM AQUA Workflow. Journal of the American Society for Mass Spectrometry. 23:1522-1533.
2011
Park J, Qin H, Scalf M, Hilger RT, Westphall MS, Smith L.M, Blick RH.  2011.  A Mechanical Nanomembrane Detector for Time-of-Flight Mass Spectrometry. Nano Letters. 11:3681-3684.
Pellitteri-Hahn M.C, Halligan B.D, Scalf M., Smith L.M, Hickey W.J.  2011.  Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells. Journal of Proteomics. 74:411-419.
Hallows WC, Yu W, Smith BC, Devires MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith L.M et al..  2011.  Sirt3 Promotes the Urea Cycle and Fatty Acid Oxidation during Dietary Restriction. Molecular Cell. 41:139-149.
2009
Chen S., Phillips M.F, Cerrina F., Smith L.M.  2009.  Controlling Oligonucleotide Surface Density in Light-Directed DNA Array Fabrication. Langmuir. 25:6570-6575.
Mandir JB, Lockett MR, Phillips MF, Allawi HT, Lyamichev VI, Smith L.M.  2009.  Rapid Determination of RNA Accessible Sites by Surface Plasmon Resonance Detection of Hybridization to DNA Arrays. Analytical Chemistry. 81:8949-8956.

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