Devin K. Schweppe
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View article: Direct cell reprogramming by a designed agonist inducing HER2-FGFR proximity
Direct cell reprogramming by a designed agonist inducing HER2-FGFR proximity Open
Growth factor induced receptor dimerization and activation of downstream pathways can modulate cell fate decisions. Here, we investigate the potential of de novo designed synthetic ligands, termed Novokines, to reprogram cell identity by i…
View article: Nova: A library for rapid development of mass spectrometry software applications
Nova: A library for rapid development of mass spectrometry software applications Open
Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously used in application development for C++, Python, and Java. Fe…
View article: Designed NGF mimetics with reduced nociceptive signatures in neurons
Designed NGF mimetics with reduced nociceptive signatures in neurons Open
The clinical use of Nerve Growth Factor (NGF) for neuronal regeneration has been hampered by pain sensitization side effects. NGF signals through the receptor tyrosine kinase TrkA and the co-receptor p75 NTR ; pain sensitization is thought…
View article: Author response: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Author response: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
View article: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent chang…
View article: Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the<i>TTN</i>RNA
Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the<i>TTN</i>RNA Open
Eukaryotic nuclei adopt a highly compartmentalized architecture that influences nearly all genomic processes. Understanding how this architecture impacts gene expression has been hindered by a lack of tools for elucidating the molecular in…
View article: Author response: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
Author response: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci Open
View article: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci Open
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the leve…
View article: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci Open
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the leve…
View article: High-throughput identification of calcium-regulated proteins across diverse proteomes
High-throughput identification of calcium-regulated proteins across diverse proteomes Open
View article: Comet fragment-ion indexing for enhanced peptide sequencing
Comet fragment-ion indexing for enhanced peptide sequencing Open
Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment ion indexing in Comet, a widely-used, open-source search engine. We demonstrate that this enhancement mainta…
View article: Author response: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Author response: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
View article: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent chang…
View article: The proteomic landscape and temporal dynamics of mammalian gastruloid development
The proteomic landscape and temporal dynamics of mammalian gastruloid development Open
Gastrulation is the process by which the early embryo establishes a body plan and primes itself for organogenesis. As gastrulation is challenging to study in vivo , stem cell-derived “gastruloids” have emerged as powerful surrogates. Altho…
View article: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci Open
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the leve…
View article: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies Open
Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cas…
View article: Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition
Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition Open
Summary Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metab…
View article: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent chang…
View article: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to characterize compound-dependent chan…
View article: Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays
Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays Open
In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent chang…
View article: High-Throughput Identification of Calcium Regulated Proteins Across Diverse Proteomes
High-Throughput Identification of Calcium Regulated Proteins Across Diverse Proteomes Open
Summary Calcium ions play important roles in nearly every biological process, yet whole-proteome analysis of calcium effectors has been hindered by lack of high-throughput, unbiased, and quantitative methods to identify proteins-calcium en…
View article: Comparing peptide identifications by FAIMS versus quadrupole gas-phase fractionation
Comparing peptide identifications by FAIMS versus quadrupole gas-phase fractionation Open
High-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to liquid chromatography-mass spectrometry (LC-MS) has been shown to increase peptide and protein detections compared to LC-MS/MS alone. However, FAIMS has not been c…
View article: Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics
Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics Open
Sample multiplexed quantitative proteomics assays have proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquis…
View article: Global and tissue-specific aging effects on murine proteomes
Global and tissue-specific aging effects on murine proteomes Open
View article: CysDB: a human cysteine database based on experimental quantitative chemoproteomics
CysDB: a human cysteine database based on experimental quantitative chemoproteomics Open
View article: CysDB: A Human Cysteine Database based on Experimental Quantitative Chemoproteomics
CysDB: A Human Cysteine Database based on Experimental Quantitative Chemoproteomics Open
Cysteine chemoproteomics studies provide proteome-wide portraits of the ligandability or potential ‘druggability’ of thousands of cysteine residues. Consequently, these studies are enabling resources for closing the druggability gap, namel…
View article: Real-time spectral library matching for sample multiplexed quantitative proteomics
Real-time spectral library matching for sample multiplexed quantitative proteomics Open
Sample multiplexed quantitative proteomics has proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor co-isolation can dramatically reduce the efficiency of data acquisition a…
View article: Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression
Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression Open
View article: Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci<i>in situ</i>
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci<i>in situ</i> Open
Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP),…
View article: A proteome-wide atlas of drug mechanism of action
A proteome-wide atlas of drug mechanism of action Open