Alejandro J. Brenes
YOU?
Author Swipe
View article: Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity
Hypoxia induces histone clipping and H3K4me3 loss in neutrophil progenitors resulting in long-term impairment of neutrophil immunity Open
View article: Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma
Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma Open
Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Given that neutrophils are known to display a prominent …
View article: A proteomic map of B cell activation and its shaping by mTORC1, MYC and iron
A proteomic map of B cell activation and its shaping by mTORC1, MYC and iron Open
Summary Using high resolution quantitative mass spectrometry, we have explored how immune activation and the metabolic checkpoint kinase mTORC1 (mammalian target of rapamycin complex 1) regulate the proteome of B lymphocytes. B cell activa…
View article: Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics
Calculating and Reporting Coefficients of Variation for DIA-Based Proteomics Open
The coefficient of variation (CV) is a measure that is frequently used to assess data dispersion for mass spectrometry-based proteomics. In the current era of burgeoning technical developments, there has been an increased focus on using CV…
View article: Author response: Proteomic and functional comparison between human induced and embryonic stem cells
Author response: Proteomic and functional comparison between human induced and embryonic stem cells Open
View article: PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformations
PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformations Open
The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned—ensuring precise gene expression and developmental fidelity—remains poorly understood. PROSER1, a known TET2 …
View article: Proteomic and functional comparison between human induced and embryonic stem cells
Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC an…
View article: Deep proteomic analysis of microglia reveals fundamental biological differences between model systems
Deep proteomic analysis of microglia reveals fundamental biological differences between model systems Open
Using high-resolution quantitative mass spectrometry, we present comprehensive human and mouse microglia proteomic datasets consisting of over 11,000 proteins across six microglia groups. Microglia share a core protein signature of over 5,…
View article: Proteomic and functional comparison between human induced and embryonic stem cells
Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding many of the ethical issues arising from the use …
View article: Author response: Proteomic and functional comparison between human induced and embryonic stem cells
Author response: Proteomic and functional comparison between human induced and embryonic stem cells Open
View article: Calculating and Reporting Coefficients of Variation for DIA-based Proteomics
Calculating and Reporting Coefficients of Variation for DIA-based Proteomics Open
The Coefficient of Variation (CV) is a measure that is frequently used to assess data dispersion for mass spectrometry-based proteomics. In the current era of burgeoning technical developments, there has been an increased focus on using CV…
View article: PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations
PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations Open
The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned – ensuring precise gene expression and developmental fidelity – remains poorly understood. PROSER1, a known T…
View article: Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples
Optimizing Spectronaut Search Parameters to Improve Data Quality with Minimal Proteome Coverage Reductions in DIA Analyses of Heterogeneous Samples Open
Data-independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spe…
View article: Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures
Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures Open
View article: Reviewer #3 (Public Review): Proteomic and functional comparison between human induced and embryonic stem cells
Reviewer #3 (Public Review): Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding ethical issues arising from the use of embryo-de…
View article: None: Proteomic and functional comparison between human induced and embryonic stem cells
None: Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding ethical issues arising from the use of embryo-de…
View article: Proteomic and functional comparison between human induced and embryonic stem cells
Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding ethical issues arising from the use of embryo-de…
View article: Reviewer #2 (Public Review): Proteomic and functional comparison between human induced and embryonic stem cells
Reviewer #2 (Public Review): Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding ethical issues arising from the use of embryo-de…
View article: Proteomic and functional comparison between human induced and embryonic stem cells
Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling. In this study, we characterise the proteomes of multiple hiPSC an…
View article: proteomicsCV: Calculates the Percentage CV for Mass Spectrometry-Based Proteomics Data
proteomicsCV: Calculates the Percentage CV for Mass Spectrometry-Based Proteomics Data Open
Calculates the percentage coefficient of variation (CV) for mass spectrometry-based proteomic data. The CV can be calculated with the traditional formula for raw (non log transformed) intensity data, or log transformed data. This package c…
View article: Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection
Extensive acute and sustained changes to neutrophil proteomes post-SARS-CoV-2 infection Open
Background Neutrophils are important in the pathophysiology of coronavirus disease 2019 (COVID-19), but the molecular changes contributing to altered neutrophil phenotypes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV…
View article: Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples
Optimising Spectronaut search parameters to improve data quality with minimal proteome coverage reductions in DIA analyses of heterogeneous samples Open
Data independent acquisition has seen breakthroughs that enable comprehensive proteome profiling using short gradients. As the proteome coverage continues to increase, the quality of the data generated becomes much more relevant. Using Spe…
View article: Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures
Quantitative proteomics reveals tissue-specific, infection-induced and species-specific neutrophil protein signatures Open
Summary Neutrophils are one of the first responders to infection and are a key component of the innate immune system through their ability to phagocytose and kill invading pathogens, secrete antimicrobial molecules and produce extracellula…
View article: DIA label-free proteomic analysis of murine bone-marrow-derived macrophages
DIA label-free proteomic analysis of murine bone-marrow-derived macrophages Open
View article: The Immunological Proteome Resource
The Immunological Proteome Resource Open
The Immunological Proteome Resource (ImmPRes ; http://immpres.co.uk/ ) is an open access public resource integrating proteomic data generated by large-scale mass-spectrometry analysis of murine hematopoietic populations. The initial focus …
View article: Neutrophil proteomics identifies temporal changes and hallmarks of delayed recovery in COVID19
Neutrophil proteomics identifies temporal changes and hallmarks of delayed recovery in COVID19 Open
Rationale Neutrophils are important in the pathophysiology of COVID19 but the molecular changes contributing to altered neutrophil phenotypes following SARS-CoV-2 infection are not fully understood. Objectives To use quantitative mass spec…
View article: Deep proteomic analysis of microglia reveals fundamental biological differences between model systems
Deep proteomic analysis of microglia reveals fundamental biological differences between model systems Open
Using high resolution quantitative mass spectrometry, we have generated the most comprehensive human and mouse microglia proteomic datasets to date, consisting of over 11,000 proteins across all six microglia groups. Microglia from differe…
View article: Nrf2 activation reprograms macrophage intermediary metabolism and suppresses the type I interferon response
Nrf2 activation reprograms macrophage intermediary metabolism and suppresses the type I interferon response Open
To overcome oxidative, inflammatory, and metabolic stress, cells have evolved cytoprotective protein networks controlled by nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) and its negative regulator, Kelch-like ECH associated protei…
View article: Proteomic and functional comparison between human induced and embryonic stem cells
Proteomic and functional comparison between human induced and embryonic stem cells Open
Human induced pluripotent stem cells (hiPSCs) have great potential to be used as alternatives to embryonic stem cells (hESCs) in regenerative medicine and disease modelling, thereby avoiding many of the ethical issues arising from the use …
View article: Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes
Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes Open
Tissue-resident intestinal intraepithelial T lymphocytes (T-IEL) patrol the gut and have important roles in regulating intestinal homeostasis. T-IEL include both induced T-IEL, derived from systemic antigen-experienced lymphocytes, and nat…