Alvaro Sebastian Vaca Jácome

Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity

Ronald R. Cutler, Laura Corveleyn, Claudia Ctortecka, Francesca LiCausi et autres

Single-cell proteomics confidently quantifies cellular heterogeneity, however quantification of post-translational modifications, such as those deposited on histone proteins, remains elusive. Here, we develop a robust mass spectrometry-based method for the unbiased analysis of single-cell histone post-translational modifications (sc-hPTM). sc-hPTM identifies both single- …

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Longitudinal Plasma Multiomics Characterization of Nephrotoxicity in Beagles Following Repeated Dosing of Enteric-Coated Propyl Gallate Tablets

Nathaly Reyes‐Garcés, Weiwen Sun, B. Timothy Hummer, Xuejun Peng et autres

Permeation enhancers (PEs) are excipients used in oral biotherapeutic formulations to facilitate the transport of bioactive compounds across the intestinal barrier and prevent their degradation. Concerns associated with the chronic use of PEs demand comprehensive approaches to elucidate their potential toxicity mechanisms. …

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Corrigendum to “Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data”

D. Vidović, Behrouz Shamsaei, Stephan C. Schürer, Phillip Kogan et autres

Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

D. Vidović, Behrouz Shamsaei, Stephan C. Schürer, Phillip Kogan et autres

The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function and molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive to cells. Because of the importance of proteins and …

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High-Throughput Determination of Exchange Rates of Unmodified and PTM-Containing Peptides Using HX-MS

Jamie A. Moroco, Alvaro Sebastian Vaca Jácome, Pierre Michel Jean Beltran, Andrew H. Reiter et autres

Despite the widespread use of MS for hydrogen/deuterium exchange measurements, no systematic, large-scale study has been conducted to compare the observed exchange rates in protein-derived, unstructured peptides measured by MS to the predicted exchange rates calculated from NMR-derived values and how neighboring …

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Disrupted uromodulin trafficking is rescued by targeting TMED cargo receptors

Silvana Bazúa‐Valenti, Matthew Brown, Jason Zavras, Magdalena Riedl Khursigara et autres

The trafficking dynamics of uromodulin (UMOD), the most abundant protein in human urine, play a critical role in the pathogenesis of kidney disease. Monoallelic mutations in the UMOD gene cause autosomal dominant tubulointerstitial kidney disease (ADTKD-UMOD), an incurable genetic disorder that leads …

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Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry

Kshiti Meera Phulphagar, Claudia Ctortecka, Alvaro Sebastian Vaca Jácome, Susan Klaeger et autres

Comprehensive and in-depth identification of the human leukocyte antigen class I (HLA-I) and class II (HLA-II) tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is a powerful technology for direct identification of HLA peptides from patient-derived tumor samples …

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Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry

Kshiti Meera Phulphagar, Claudia Ctortecka, Alvaro Sebastian Vaca Jácome, Susan Klaeger et autres

Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving …

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Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks

Ilse Delint‐Ramírez, Lahiri Konada, Lance Heady, Richard Rueda et autres

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Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

Deborah O. Dele-Oni, Karen E. Christianson, Shawn B. Egri, Alvaro Sebastian Vaca Jácome et autres

While gene expression profiling has traditionally been the method of choice for large-scale perturbational profiling studies, proteomics has emerged as an effective tool in this context for directly monitoring cellular responses to perturbations. We previously reported a pilot library containing 3400 profiles …

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Cloud-based DIA data analysis module for signal refinement improves accuracy and throughput of large datasets

Karen E. Christianson, Jacob D. Jaffe, Steven A. Carr, Alvaro Sebastian Vaca Jácome

Abstract Data-independent acquisition (DIA) is a powerful mass spectrometry method that promises higher coverage, reproducibility, and throughput than traditional quantitative proteomics approaches. However, the complexity of DIA data caused by fragmentation of co-isolating peptides presents significant challenges for confident assignment of identity …

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Causal interactions from proteomic profiles: Molecular data meet pathway knowledge

Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupınar et autres

We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. The method mimics a biologist's traditional approach of explaining changes in …

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