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Author Details

Michael R Shortreed
University of Wisconsin-Madison
1996
85
29
Leah V Schaffer (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36308684Enhanced Proteomic Data Analysis with MetaMorpheus.Methods Mol Biol2023
36308694Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ.Methods Mol Biol2023
35241129Enhanced protein isoform characterization through long-read proteogenomics.Genome Biol2022
35657588Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite.Methods Mol Biol2022
36108102Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.J Proteome Res2022
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
32967423Spritz: A Proteogenomic Database Engine.J Proteome Res2021
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
34622154Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet.iScience2021
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
32058723Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line.J Proteome Res2020
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
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
31050378Identification and Quantification of Proteoforms by Mass Spectrometry.Proteomics2019
29195273Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.J Proteome Res2018
29912191Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells.J Vis Exp2018
30180576Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.J Proteome Res2018
29578715Enhanced Global Post-translational Modification Discovery with MetaMorpheus.J Proteome Res2018
29358085Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance.Stem Cell Reports2018
29723810Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers.Transl Oncol2018
29793340Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.J Proteome Res2018
29397739ProForma: A Standard Proteoform Notation.J Proteome Res2018
29083185Ultrafast Peptide Label-Free Quantification with FlashLFQ.J Proteome Res2018
29227670Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.Anal Chem2018
28654248Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.Anal Chem2017
28248113Global Post-Translational Modification Discovery.J Proteome Res2017
29132314Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.BMC Genomics2017
28968100Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.J Proteome Res2017
28704058Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.J Proteome Res2017
28608680Correction to "Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements".J Proteome Res2017
27049631Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annu Rev Anal Chem (Palo Alto Calif)2016
27184763HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.Genomics2016
26941048Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.J Proteome Res2016
26704769Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.J Proteome Res2016
26418581Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.J Proteome Res2015
24175627Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.J Proteome Res2014
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Collaborators

Lloyd M Smith
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 75
Brian L Frey
University of Wisconsin-Madison, 1101 University Ave
Co-authored papers 25
Mark Scalf
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 24
Anthony J Cesnik
University of Wisconsin-Madison
Co-authored papers 16
Leah V Schaffer (CM4AI)
University of California San Diego
Co-authored papers 15
Robert J Millikin
Morgridge Institute for Research
Co-authored papers 15
Michael Olivier
Co-authored papers 9
Stefan K Solntsev
University of Wisconsin-Madison
Co-authored papers 9
Gloria M Sheynkman (CM4AI)
University of Virginia
Co-authored papers 8
Zach Rolfs
University of Wisconsin-Madison
Co-authored papers 7
Yunxiang Dai
University of Wisconsin-Madison
Co-authored papers 5
Ying Ge
University of Wisconsin-Madison
Co-authored papers 5
Lissa C Anderson
Florida State University
Co-authored papers 5
Neil L Kelleher
Northwestern University
Co-authored papers 4
Rachel A Knoener
University of Wisconsin-Madison College of Letters and Sciences
Co-authored papers 4
Audrey P Gasch
University of Wisconsin-Madison
Co-authored papers 4
Julia Chamot-Rooke
Institut Pasteur, Universite Paris Cite, CNRS UAR4
Co-authored papers 3
Yury O Tsybin
EPFL Innovation Park
Co-authored papers 3
Jeffrey N Agar
Northeastern University
Co-authored papers 3
Richard D LeDuc
Northwestern University
Co-authored papers 3
Trisha Tucholski
University of Wisconsin-Madison, 1101 University Ave.
Co-authored papers 3
Joseph A Loo
University of California los angeles
Co-authored papers 3
Ljiljana Pa??a-Toli??
Pacific Northwest National Laboratory
Co-authored papers 3
Paul O Danis
Co-authored papers 3
Christopher L Hendrickson
Florida State University
Co-authored papers 2
Katherine E Buxton
University of Wisconsin , 1101 University Avenue
Co-authored papers 2
Rupa Sridharan
Wisconsin Institute for Discovery, University of Wisconsin-Madison
Co-authored papers 2
Juan Antonio Vizca??no
EMBL-European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Pratik D Jagtap
University of Minnesota
Co-authored papers 2
Timothy J Griffin
University of Minnesota
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Release 1.2