Alejandro J. Brenes

This study evaluates DIA search engines, high-load libraries, and instrumentation platforms for single-cell proteomics across different cell types.

The paper introduces a pipeline for single-cell proteomics analysis that addresses challenges in data processing and annotation using context-aware methods and large language models.

The paper uses single cell proteomic analysis to identify distinct functional states of neutrophils in human glioblastoma, revealing clusters with pathogenic and anti-tumorigenic properties not detectable by scRNA-seq.

This study maps the proteomic changes in B cells during activation and shows how mTORC1, MYC, and iron regulate protein production and growth.

This paper discusses the calculation and reporting of coefficients of variation in DIA-based proteomics and proposes guidelines and an R package for accurate benchmarking.

This study shows PROSER1 regulates DNA demethylation through dual mechanisms, balancing gene expression and preventing developmental malformations.

This study compares the proteomes of human induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs), finding quantitative differences in protein expression affecting growth, metabolism, and secreted factors.

The paper compares proteomic profiles of human and mouse microglia from different sources, revealing significant differences between in vitro and ex vivo cultures.

The paper characterizes proteome variation across 202 human iPSC lines, identifies 700 pQTLs, and links pQTLs to disease-associated GWAS variants.

The paper shows that erosion of X chromosome inactivation in human iPSCs leads to increased protein expression from X-linked and autosomal genes, altering protein-RNA correlations and increasing protein content.

The paper evaluates the impact of integrating multiple TMT batches in proteomic analysis and proposes solutions to reduce missing values, false positives, and inter-batch accuracy issues.

The paper presents a proteomic analysis of 217 HipSci iPSC lines, identifying >16,000 protein groups and their roles in iPSC biology.