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Author Details

Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
1964
281
55
Leah V Schaffer (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38043095Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.J Proteome Res2024
36383138Overview and considerations in bottom-up proteomics.Analyst2023
37039476Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2.Elife2023
37130807Newly synthesized glycoprotein profiling to identify molecular signatures of warm ischemic injury in donor lungs.Am J Physiol Lung Cell Mol Physiol2023
37093976Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue.Anal Chem2023
37293069Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs.bioRxiv2023
36308694Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ.Methods Mol Biol2023
36308684Enhanced Proteomic Data Analysis with MetaMorpheus.Methods Mol Biol2023
34694612Identifying Protein Interactomes of Target RNAs Using HyPR-MS.Methods Mol Biol2022
35657588Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite.Methods Mol Biol2022
35657582Proteoforms and Proteoform Families: Past, Present, and Future.Methods Mol Biol2022
36206157A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis.J Proteome Res2022
35192358Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1.J Proteome Res2022
35073098MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses.J Proteome Res2022
35220718Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?J Proteome Res2022
35241129Enhanced protein isoform characterization through long-read proteogenomics.Genome Biol2022
35055128Towards an Ideal <i>In Cell</i> Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules.Int J Mol Sci2022
32967423Spritz: A Proteogenomic Database Engine.J Proteome Res2021
33629952Identification of host proteins differentially associated with HIV-1 RNA splice variants.Elife2021
33683901Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.J Proteome Res2021
33754701Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics.J Am Soc Mass Spectrom2021
33661641ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics.J Proteome Res2021
34738820Internal Fragment Ions Disambiguate and Increase Identifications in Top-Down Proteomics.J Proteome Res2021
34375640Fused in sarcoma regulates DNA replication timing and kinetics.J Biol Chem2021
34836951An atlas of protein turnover rates in mouse tissues.Nat Commun2021
34622154Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet.iScience2021
34767442The Human Proteoform Project: Defining the human proteome.Sci Adv2021
34181432Automated Assignment of Proteoform Classification Levels.J Proteome Res2021
34165955Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis.Anal Chem2021
33074679Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data.J Proteome Res2021
32243168A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics.J Proteome Res2020
33692656An Algorithm to Improve the Speed of Semi and Non-Specific Enzyme Searches in Proteomics.Curr Bioinform2020
33106676O-Pair Search with MetaMorpheus for O-glycopeptide characterization.Nat Methods2020
32650610Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.Proteomes2020
32812765Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry.J Am Soc Mass Spectrom2020
32584579Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data.J Proteome Res2020
30346791Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion.J Proteome Res2019
31562246Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in <i>Arabidopsis</i>.J Biol Chem2019
31296583Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS.RNA2019
31378069Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data.J Proteome Res2019
31451767A five-level classification system for proteoform identifications.Nat Methods2019
31479276Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database.J Proteome Res2019
31420320Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".Sci Immunol2019
31393705Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms.Anal Chem2019
31276622Encrypted Oligonucleotide Arrays for Molecular Authentication.ACS Comb Sci2019
31249407Best practices and benchmarks for intact protein analysis for top-down mass spectrometry.Nat Methods2019
30765479HDA9-PWR-HOS15 Is a Core Histone Deacetylase Complex Regulating Transcription and Development.Plant Physiol2019
31086819Differentiated fibrocytes assume a functional mesenchymal phenotype with regenerative potential.Sci Adv2019
31050378Identification and Quantification of Proteoforms by Mass Spectrometry.Proteomics2019
29161404Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS.Hum Mol Genet2018
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Collaborators

Michael R Shortreed
University of Wisconsin-Madison
Co-authored papers 75
Mark Scalf
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 65
Brian L Frey
University of Wisconsin-Madison, 1101 University Ave
Co-authored papers 42
Robert J Millikin
Morgridge Institute for Research
Co-authored papers 17
Anthony J Cesnik
University of Wisconsin-Madison
Co-authored papers 16
Leah V Schaffer (CM4AI)
University of California San Diego
Co-authored papers 15
Zach Rolfs
University of Wisconsin-Madison
Co-authored papers 12
Michael Olivier
Co-authored papers 11
Neil L Kelleher
Northwestern University
Co-authored papers 10
Rachel A Knoener
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 10
Gloria M Sheynkman (CM4AI)
University of Virginia
Co-authored papers 10
Stefan K Solntsev
University of Wisconsin-Madison
Co-authored papers 9
Timothy J Griffin
University of Minnesota
Co-authored papers 8
Ying Ge
University of Wisconsin-Madison
Co-authored papers 7
Joseph A Loo
University of California los angeles
Co-authored papers 6
Yunxiang Dai
University of Wisconsin-Madison
Co-authored papers 5
Yury O Tsybin
EPFL Innovation Park
Co-authored papers 5
Jeffrey N Agar
Northeastern University
Co-authored papers 5
Ljiljana Pa??a-Toli??
Pacific Northwest National Laboratory
Co-authored papers 5
Lissa C Anderson
Florida State University
Co-authored papers 5
Qiyao Li
The Second Hospital of Hebei Medical University
Co-authored papers 5
Julia Chamot-Rooke
Institut Pasteur, Universite Paris Cite, CNRS UAR4
Co-authored papers 5
Paul O Danis
Co-authored papers 5
Ji Eun Lee
Soonchunhyang University College of Medicine, Bucheon Hospital
Co-authored papers 4
Leroy Hood
Center for Phenomic Health, The Buck Institute for Research on Aging
Co-authored papers 4
Audrey P Gasch
University of Wisconsin-Madison
Co-authored papers 4
Pratik D Jagtap
University of Minnesota
Co-authored papers 3
Paul M Thomas
Northwestern University
Co-authored papers 3
Jessica Severin
Center for Integrative Medical Sciences
Co-authored papers 3
Katherine E Buxton
University of Wisconsin , 1101 University Avenue
Co-authored papers 3
Release 1.2