A5016226641- Advanced Proteomics Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- Glycosylation and Glycoproteins Research
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- Mass Spectrometry Techniques and Applications
- Ubiquitin and proteasome pathways
- Research Data Management Practices
- Galectins and Cancer Biology
- Peptidase Inhibition and Analysis
- Medical Imaging Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Protease and Inhibitor Mechanisms
- Radiopharmaceutical Chemistry and Applications
- Carbohydrate Chemistry and Synthesis
- Histone Deacetylase Inhibitors Research
- Neuroblastoma Research and Treatments
- RNA modifications and cancer
- Biotin and Related Studies
- HIV/AIDS Impact and Responses
- Genomics and Chromatin Dynamics
- Scientific Computing and Data Management
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- Retinal Development and Disorders
National Institutes of Health
2023
National Cancer Institute
2022
Center for Cancer Research
2022
George Mason University
2019-2021
Frederick National Laboratory for Cancer Research
2019
Johns Hopkins University
2013-2018
Johns Hopkins Medicine
2013-2018
University of Alabama at Birmingham
2015
University of Mississippi Medical Center
2015
Jackson Memorial Hospital
2015
Background— After myocardial infarction, the left ventricle undergoes a wound healing response that includes robust infiltration of neutrophils and macrophages to facilitate removal dead myocytes as well turnover extracellular matrix. Matrix metalloproteinase (MMP)-9 is key enzyme regulates post-myocardial infarction ventricular remodeling. Methods Results— Infarct regions from wild-type MMP-9 null mice (n=8 per group) analyzed by glycoproteomics showed 541 N -glycosylated proteins...
The analysis of sialylated glycans is critical for understanding the role sialic acid in normal biological processes as well disease. However, labile nature typically renders routine this monosaccharide by mass spectrometric methods difficult. To overcome difficulty we pursued derivatization methodologies, extending established acetohydrazide approaches to aniline-based methods, and finally optimized p-toluidine derivatization. This new quantitative glycoform profiling method with use...
Protein glycosylation is one of the most common protein modifications, and quantitative analysis glycoproteins has potential to reveal biological functions their association with disease. However, high throughput accurate quantification technically challenging due scarcity robust assays detect quantify glycoproteins. Here we describe development multiplexed targeted MS N-linked glycosite-containing peptides in serum using parallel reaction monitoring (PRM). Each assay was characterized by...
Histone deacetylases (HDACs) have emerged as important targets for cancer treatment. HDAC-inhibitors (HDACis) are well tolerated in patients and been approved the treatment of with cutaneous T-cell lymphoma (CTCL). To improve clinical benefit HDACis solid tumors, combination strategies could be employed. In this study, we applied Analysis Functional Annotation (AFA) to provide a comprehensive list genes pathways affected upon HDACi-treatment prostate cells. This approach provides an unbiased...
Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis lung cancer. Proteins released cancer into BAL may serve as biomarkers detection. In this study, N-glycoproteins in eight cases fluid, well adenocarcinoma tissues and tumor-matched normal tissues, were analyzed using solid-phase extraction N-glycoprotein (SPEG), iTRAQ labeling, liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 80 glycoproteins found specimens, 32 identified both...
Extracellular proteins are easily accessible, which presents a subproteome of molecular targets that have high diagnostic and therapeutic potential. Efforts been made to catalog the cardiac extracellular matridome analyze topology identified for design targets. Although many bioinformatics tools developed predict protein topology, has experimentally validated only very small portion membrane proteins. The aim this study was use glycoproteomics MS approach identify glycoproteins in infarcted...
Glycoproteins secreted into plasma from T cells infected with human immunodeficiency virus (HIV) latent infection may provide insight understanding the host response to HIV in vivo. Glycoproteomics, which evaluates level of glycoproteome, remains a novel approach study this HIV. In order identify glycoproteins infection, medium cultured replication-competent was compared parental A3.01 via solid phase extraction glycopeptides (SPEG) and high-performance liquid chromatography-tandem mass...
ABSTRACT Rapid development and wide adoption of mass spectrometry-based proteomics technologies have empowered scientists to study proteins their modifications in complex samples on a large scale. This progress has also created unprecedented challenges for individual labs store, manage analyze data, both the cost proprietary software high-performance computing, long processing time that discourages on-the-fly changes data settings required explorative discovery analysis. We developed an...
Selected and multiple reaction monitoring involves a multiplexed assay of proteotypic peptides associated transitions in mass spectrometry runs. To describe peptide as stable, quantifiable, reproducible representatives proteins interest, experimental analytical validation is required. However, inadequate disparate tools methods predispose performance measures to errors inconsistencies.Implemented freely available, open-source tool the platform independent Java programing language, MRMPlus...
Although XPO5 has been characterized to have tumor-suppressor features in the miRNA biogenesis pathway, impact of altered expression cancers is unexplored. Here we report a novel "oncogenic" role advanced prostate cancer. Using cancer models, found that excess levels override inhibitory effect canoncial miRNA-mRNA regulation, resulting global increase proteins expression. Importantly, decreased could promote an proteasome degradation, whereas overexpression leads protein posttranslational...
MALDI-TOF profiling of low molecular weight peptides (peptidome) usage is limited due to the lack reproducibility from confounding inferences sample preparation, data acquisition, and processing. We applied analysis profile urine peptidome with aims to: (i) compare centrifugal ultrafiltration dialysis pretreatments, (ii) determine whether using signal LOD (sLOD), together normalization, may reduce variability. also investigated influence peaks detection on reproducibility. Dialysis allowed...
Protein glycosylation has long been recognized as one of the most common post-translational modifications. Most membrane proteins and extracellular are N-linked glycosylated, they account for majority current clinical diagnostic markers or therapeutic targets. Quantitative proteomic analysis detectable glycoproteins from cells tissues using mass spectrometry potential to provide biological basis disease development identify associated glycoproteins. However, information low abundance but...
Purpose: To identify changes in the outer retina areas without atrophy or flecks of Stargardt disease (STGD) using spectral-domain optical coherence tomography. Methods: Twenty-three STGD patients and 26 control subjects were assessed for (from border Bruch membrane [BrM] to inner segment ellipsoid zone [EZ]), BrM–retinal pigment epithelium apex, EZ thickness, apical process interdigitation zone. Results: Patients with had increased BrM–EZ thickness apparent versus at 1,000, 1,500, 2,000,...
Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites).In the bottomup approach, several factors which include but not limited to sample preparation, mass analyses, protein sequence database searches result in peptide spectrum matches (PSMs) varying lengths.Given that multiple PSMs map glycosite, we reason identified are length species unique set glycosites.Because associated spectra these...
Journal Article A FAIR Principle Data Model for Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and the Frederick National Laboratory Coordinating Center Get access Paul Aiyetan, Aiyetan Cancer Research, Frederick, MD, USAGeorge Mason University School of Systems Biology, Manassas, VA, USA Corresponding author: paul.aiyetan@nih.gov Search other works by this author on: Oxford Academic Google Scholar Kedar Narayan, Narayan USACenter Molecular Microscopy, Institute, Institutes Health,...
Abstract Background: Neuroblastoma (NB) is the 3rd most common childhood cancer and accounts for 15% of all pediatric deaths. Recently, immunotherapy using monoclonal antibodies targeting GD2 have improved survival rates some patients with NB. Unfortunately, this response not uniform, suggesting an incomplete understanding underlying immune biology. Large-scale sequencing patient tumors suggested that NB has diverse microenvironments (TMEs), which are associated MYCN-amplification (A)...