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Robert J. Chalkley

University of California, San Francisco · US
Area of research
Spectroscopy · Molecular Biology
Research interest
Research interests include Advanced Proteomics Techniques and Applications, Mass Spectrometry Techniques and Applications, Glycosylation and Glycoproteins Research, and Metabolomics and Mass Spectrometry Studies.
h-index
49
citations
10,495
works
155
NIH funding
primary concept
email

Recent publications

Comparative analysis of glycoproteomic software using a tailored glycan database
Analytical and Bioanalytical Chemistry 2025cited by 12position: lastdoi
Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila
Neuron 2025cited by 1position: middledoi
Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation
Nature Communications 2024cited by 26position: middledoi
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response
Nature Cell Biology 2023cited by 31position: middledoi
Chemical Genetic Identification of PKC Epsilon Substrates in Mouse Brain
Molecular & Cellular Proteomics 2023cited by 3position: middledoi
15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector
Frontiers in Plant Science 2022cited by 31position: middledoi
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
Nature Methods 2021cited by 146position: middledoi
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry
Structure 2020cited by 57position: middledoi
Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites
Molecular & Cellular Proteomics 2020cited by 46position: lastdoi
Revealing nascent proteomics in signaling pathways and cell differentiation
Proceedings of the National Academy of Sciences 2018cited by 70position: middledoi
Expanding the Use of Spectral Libraries in Proteomics
Journal of Proteome Research 2018cited by 62position: middledoi
PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3
Nature Communications 2017cited by 176position: middledoi
Peripheral Elevation of a Klotho Fragment Enhances Brain Function and Resilience in Young, Aging, and α-Synuclein Transgenic Mice
Cell Reports 2017cited by 123position: middledoi
Proteomic analysis reveals O-GlcNAc modification on proteins with key regulatory functions in <i>Arabidopsis</i>
Proceedings of the National Academy of Sciences 2017cited by 122position: middledoi
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
Molecular & Cellular Proteomics 2017cited by 74position: middledoi
Hyper-O-GlcNAcylation activates nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling through interplay with phosphorylation and acetylation
Journal of Biological Chemistry 2017cited by 74position: middledoi
Tissue-Specific Glycosylation at the Glycopeptide Level
Molecular & Cellular Proteomics 2015cited by 123position: lastdoi
Characterizing Sialic Acid Variants at the Glycopeptide Level
Analytical Chemistry 2015cited by 72position: lastdoi
Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis
Molecular & Cellular Proteomics 2015cited by 66position: middledoi
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
Nature Biotechnology 2014cited by 2,864position: middledoi
MS-Viewer: A Web-based Spectral Viewer for Proteomics Results
Molecular & Cellular Proteomics 2014cited by 148position: lastdoi
NGF and ProNGF: Regulation of neuronal and neoplastic responses through receptor signaling
Advances in Biological Regulation 2014cited by 114position: middledoi
Glucose Sensor O-GlcNAcylation Coordinates with Phosphorylation to Regulate Circadian Clock
Cell Metabolism 2013cited by 249position: middledoi
Lessons in <i>de novo</i> peptide sequencing by tandem mass spectrometry
Mass Spectrometry Reviews 2013cited by 210position: lastdoi
Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification
Molecular & Cellular Proteomics 2013cited by 185position: lastdoi
Multisite Light-Induced Phosphorylation of the Transcription Factor PIF3 Is Necessary for Both Its Rapid Degradation and Concomitant Negative Feedback Modulation of Photoreceptor phyB Levels in <i>Arabidopsis</i>  
The Plant Cell 2013cited by 156position: middledoi
O-Linked β-N-Acetylglucosamine (O-GlcNAc) Site Thr-87 Regulates Synapsin I Localization to Synapses and Size of the Reserve Pool of Synaptic Vesicles
Journal of Biological Chemistry 2013cited by 59position: middledoi
Proteome Informatics Research Group (iPRG)_2012: A Study on Detecting Modified Peptides in a Complex Mixture
Molecular & Cellular Proteomics 2013cited by 30position: firstdoi
The DegraBase: A Database of Proteolysis in Healthy and Apoptotic Human Cells
Molecular & Cellular Proteomics 2012cited by 146position: middledoi
Modification Site Localization Scoring: Strategies and Performance
Molecular & Cellular Proteomics 2012cited by 113position: firstdoi

Grants

Collaborative Research: RUI: RESEARCH-PGR Meeting Future Food Demands: Phosphoproteomics to Unravel Signaling Pathways in Soybean's Response to Phosphate and Iron Deficiency
NSF2329894$115,1722024–2027PIRePORTER

Frequent collaborators

Alma L. Burlingame · University of California, San Francisco10 papers (2013–2025)Shou‐Ling Xu · Carnegie Institution for Science4 papers (2013–2022)Zhiyong Wang · Carnegie Institution for Science4 papers (2013–2022)Peter R. Baker · University of California, San Francisco3 papers (2013–2022)Eric W. Deutsch · European Bioinformatics Institute3 papers (2013–2017)Katalin F. Medzihradszky · University of California, San Francisco3 papers (2013–2015)Weimin Ni · University of California, Berkeley3 papers (2013–2017)Krista Kaasik · University of California, San Francisco3 papers (2013–2015)Juan Antonio Vizcaíno · European Bioinformatics Institute2 papers (2014–2017)Hubert Hondermarck · University of Newcastle Australia2 papers (2014–2015)Gerhard Mayer · European Bioinformatics Institute2 papers (2014–2017)Peter H. Quail · University of California, Berkeley2 papers (2013–2017)Andrew R. Jones · University of Liverpool2 papers (2014–2017)Kathy H. Li · University of California, San Francisco2 papers (2023–2025)Kevan M. Shokat · Howard Hughes Medical Institute2 papers (2013–2023)Keith Vosseller · Drexel University2 papers (2013–2017)Nuno Bandeira · University of California San Diego2 papers (2013–2014)Martin Eisenacher · Johannes Gutenberg University Mainz2 papers (2014–2017)Ralph Bradshaw · University of California, Irvine2 papers (2014–2015)Jason C. Maynard · University of California, San Francisco2 papers (2017–2020)