A5038367294- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Trypanosoma species research and implications
- Venomous Animal Envenomation and Studies
- Biochemical and Molecular Research
- Bioinformatics and Genomic Networks
- Mosquito-borne diseases and control
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Research on Leishmaniasis Studies
- Antimicrobial Peptides and Activities
- Chemical Synthesis and Analysis
- Cardiomyopathy and Myosin Studies
- Rabies epidemiology and control
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Biochemical and Structural Characterization
- Monoclonal and Polyclonal Antibodies Research
- Peptidase Inhibition and Analysis
- S100 Proteins and Annexins
- RNA Research and Splicing
- Insect Resistance and Genetics
- Photosynthetic Processes and Mechanisms
Fundação Carlos Chagas
2016-2025
Instituto de Investigaciones Biológicas Clemente Estable
2025
Institut Pasteur de Montevideo
2025
Fundação Oswaldo Cruz
2014-2024
Instituto de Biologia Molecular do Paraná
2019-2020
Universidade Federal do Rio Grande do Norte
2015
Centro Universitário Curitiba
2014
Universidade Federal do Rio de Janeiro
2005-2013
Centro de Ingeniería Genética y Biotecnología
2013
European Bioinformatics Institute
2013
Abscisic acid (ABA) mediates resistance to abiotic stress and controls developmental processes in plants. The group-A PP2Cs, of which ABI1 is the prototypical member, are protein phosphatases that play critical roles as negative regulators very early ABA signal transduction. Because redundancy thought limit genetic dissection signalling, identify redundant signalling proteins, we pursued a proteomics approach. We generated YFP-tagged Arabidopsis expression lines identified vivo...
A goal of proteomics is to distinguish between states a biological system by identifying protein expression differences. Liu et al. demonstrated method perform semi-relative quantitation in shotgun data correlating the number tandem mass spectra obtained for each protein, or "spectral count", with its abundance mixture; however, two issues have remained open: how normalize spectral counting and efficiently pinpoint differences profiles. Moreover, Chen recently showed increase identified...
The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs novel three-tier Bayesian approach that uses layers of spectrum, peptide, protein logic to lead the data converge single list reliable identifications. SEPro integrated into PatternLab proteomics environment, where an arsenal tools analyzing shotgun proteomic provided. By using semi-labeled decoy benchmarking, we show significantly outperforms commercially...
Dengue is the most prevalent human arbovirus disease worldwide. virus (DENV) infection causes syndromes varying from self-limiting febrile illness to severe dengue. Although dengue pathophysiology not completely understood, it widely accepted that increased inflammation plays important roles in pathogenesis. Platelets are blood cells classically known as effectors of hemostasis which have been increasingly recognized major immune and inflammatory activities. Nevertheless, phenotype effector...
Abstract Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS comprising hundreds of recombinant proteins are systematically mixed cross-linking. We use one standard dataset to guide the development Scout, a search engine with MS-cleavable cross-linkers. Using other, independent datasets and published datasets, benchmark performance Scout existing...
Ideally, shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, large dynamic range and complexity cellular proteomes results in oversampling abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested equalization technology, ProteoMiner, conjunction Multidimensional Protein Identification Technology (MudPIT) to determine how could improve methods for analysis proteomes....
Abstract Summary: XDIA is a computational strategy for analyzing multiplexed spectra acquired using electron transfer dissociation and collision-activated dissociation; it significantly increases identified (∼250%) unique peptides (∼30%) when compared with the data-dependent ETCaD analysis on middle-down, single-phase shotgun proteomic analysis. Increasing improves quantitation statistics confidence protein coverage, respectively. Availability: The software data produced in this work are...
OPINION article Front. Genet., 02 July 2014Sec. Computational Genomics https://doi.org/10.3389/fgene.2014.00199
Differential proteomics by spectral counting nation.The results showed that Z-normalization combined with SVM-F correctly identified which and how many protein markers were added to the yeast lysates for all different concentrations.The software we used is available at http://pcarvalho.com/patternlab.
Abstract Summary: We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given FDR bound, approach uses a theoretical estimator to maximize number identifications that satisfy both fold-change cutoff varies with t-test P-value as power law and stringency criterion aims detect lowly abundant proteins. The new has yielded significant improvements sensitivity over previous one. Availability: Freely available...
Abstract Summary: YADA can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to corresponding tandem spectrum, account for different co-fragmenting ion species (multiplexed spectra). We describe how enables a pipeline consisting of ProLuCID DTASelect analyzing large-scale middle-down proteomics data. Availability: http://fields.scripps.edu/yada Contact: paulo@pcarvalho.com Supplementary information: data are...
PatternLab for proteomics is a self-contained computational environment analyzing shotgun proteomic data. Recent improvements incorporate modules to facilitate the analysis, such as FastaDBXtractor sequence database preparation and ProLuCID runner simplifying managing protein identification search engine; pushing limits on standards, SEPro, which relies semi-labeled decoy approach increasing confidence in filtering organizing peptide spectrum matches; with novel features, SEProQ enabling...
Coronavirus disease 2019 (COVID-19) has affected over 400 million people worldwide, leading to 6 deaths. Among the complex symptomatology of COVID-19, hypercoagulation and thrombosis have been described directly contribute lethality, pointing out platelets as an important SARS-CoV-2 target. In this work, we explored platelet proteome COVID-19 patients through a label-free shotgun proteomics approach identify responses infection, well validation experiments in larger patient cohort....
Herein we report the characterization and optimization of single-step inline enrichment phosphopeptides directly from small amounts whole cell tissue lysates (100–500 μg) using a hydroxyapatite (HAP) microcolumn Multidimensional Protein Identification Technology (MudPIT). In comparison to triplicate HILIC-IMAC phosphopeptide study, ∼80% identified HAP-MudPIT were unique. Similarly, analysis consensus phosphorylation motifs between two methods illustrates complementarity calcium- iron-based...
Toxoplasma gondii infects a wide range of hosts worldwide, including humans and domesticated animals causing toxoplasmosis disease. Recently, exosomes, small extracellular vesicles (EV) that contain nucleic acids, proteins, lipids derived from their original cells were linked with disease protection. The effect EVs T. on the immune response its relevance in physiological context is unknown. Here we disclose first proteomic profiling compared to isolated human foreskin fibroblast infected...
SUMMARY PTK2, a non-receptor tyrosine kinase, is essential for regulating pivotal cellular functions, including survival by reducing p53 levels and activating PI3K/AKT pathway. However, the mechanism underlying PTK2 stabilization during stress remained unclear. Here, we identified Bclaf1, multifunctional protein known to stabilize partners, as interactor. Using advanced microscopy techniques, nuclear Bclaf1 biomolecular condensates containing in cardiomyocytes under oxidative stress. While...
Abstract Professional drivers represent an ideal cohort for investigating the effects of solar radiation on skin due to their unique, asymmetric exposure sun, a consequence vehicle window orientations. Consequently, one side face is naturally subjected more radiation, resulting in uneven sunlight exposure. This scenario supports paired experimental design precise within-individual comparisons, crucial assessing sun exposure’s impact health, including signs aging. Leveraging this approach,...