JOURNAL OF PROTEOME RESEARCHProteomic analysisTranscriptomeProteinAnalyze the proteomeMass spectrometry based quantitativeAnalysisProteomics dataBacterialProteinsDynamicsPhosphoproteomics2016PhosphoproteomeCharacterization2019TissuesPhosphorylationBiologicalResearchAlterationsComplexVivoDataStagesProfilingStudyGeneticConditionsCellLarge-scaleModelGroupTags
JOURNAL OF PROTEOME RESEARCH3
Proteomic analysis2
- High-throughput quantitative proteomic analysis has previously been used to identify differentially expressed proteins and pathways associated with breast tumor phenotypes [ 12 ]. (biomedcentral.com)
- an iTRAQ-based quantitative proteomic analysis. (bvsalud.org)
Transcriptome4
- In conclusion, the proteome and transcriptome correlation results from this study indicate that ion transport plays a critical role in the adaptation of S. paramamosain to sudden reduction in salinity. (hindawi.com)
- Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. (rsc.org)
- In this study, the transcriptome and proteome were integrated and analyzed. (techscience.com)
- In this study, we present integrated quantitative proteome, transcriptome, and methylome analyses of hematopoietic stem cells (HSCs) and four multipotent progenitor (MPP) populations. (lu.se)
Protein12
- These factors can limit the reproducibility of peptide identification and quantification as well as the comprehensiveness, robustness and throughput of proteome analysis, particularly when analyzing samples of high complexity or wide dynamic range of protein concentrations as represented by tissues and body fluids 7 . (nature.com)
- Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. (elifesciences.org)
- Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. (elifesciences.org)
- Lamin A/C cumulative protein expression of all variants is reported by semi-quantitative Western blotting. (mdpi.com)
- Among several quantitation techniques, isobaric labeling-based quantitative proteomics has gained increasing attention because of its multiplexed capability, allowing for absolute and relative protein quantitation in multiple samples within a single run 2 , 3 . (springer.com)
- We describe the design and synthesis of a novel set of iso-baric tags for quantitative glycan profiling, which will have broad applications in carbohydrate based biomarker dis-covery, therapeutic protein characterization, and vaccine development. (nist.gov)
- Quantitative Site-specific Phosphorylation Dynamics of Human Protein Kinases during Mitotic Progression. (mpg.de)
- Major research interests are cancer proteomics, focusing on the secretome, tumoral dynamics, quantitative proteomics, protein phosphorylation, and the stoichiometry of ubiquitination and acetylation. (hupo.org)
- By using in-depth mass spectrometry-based quantitative proteomics to monitor protein levels in a comprehensive and quantitative manner, our ongoing research aims at defining the fetal- and adult-specific proteomic programs that regulate normal and malignant hematopoiesis. (lu.se)
- Two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry (MS) based quantitative proteomics were used to study differential protein abundance in various B cell types during B cell maturation. (lu.se)
- A particular focus is development of new proteomics techniques to investigate protein interactions between host and pathogen and to investigate systemic proteome changes during sepsis. (lu.se)
- The group uses quantitative imaging, protein engineering and various single cell techniques to accomplish their goals. (lu.se)
Analyze the proteome1
- Quantitative multiplexed proteomics has become a powerful tool to analyze the proteome across various conditions. (biorxiv.org)
Mass spectrometry based quantitative1
- MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics. (mpg.de)
Analysis11
- Similar to QTL analysis [ 11 ], differences in proteomic patterns across biological systems that exhibit quantitative differences in traits provide an unbiased perspective to identify molecular mechanism that underpin these differences in phenotype. (biomedcentral.com)
- Here, we coupled LCM with a proteomics workflow that provides fully automated analysis of proteomes from microdissected tissues. (nih.gov)
- Quantitative analysis of NAD synthesis-breakdown fluxes. (springer.com)
- In addition motif redundancy can affect quantitative and statistical analysis and prevent a realistic comparison of peptide numbers between datasets. (biorxiv.org)
- The msCompare tool has previously demonstrated quantitative-proteomics analysis within Galaxy [ 6 ]. (biorxiv.org)
- Quantitative Mass Spectrometry Analysis Reveals Similar Substrate Consensus Motif for Human Mps1 Kinase and Plk1. (mpg.de)
- From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets. (mpg.de)
- Quantitative Analysis of the Human Spindle Phosphoproteome at Distinct Mitotic Stages. (mpg.de)
- This approach used the stable heavy isotope-based labeling of the unmodified lysine residues with acetyl groups, followed by deep proteomic profiling and the use of a novel in-house-developed software program for quantitative analysis for stoichiometry determination. (genengnews.com)
- The relatively young research field of proteome analysis has rapidly become a key technology in biological research. (unibas.ch)
- To view our previous 2DE proteomic results, click on Proteome analysis of B cell maturation. (lu.se)
Proteomics data1
- Standards for quantitative proteomics data formats are still in the early adoption phase and formats like MzQuantML [ 7 ] are not yet widely supported. (biorxiv.org)
Bacterial3
- While previous studies have characterized bacterial growth physiology at steady-state, a quantitative understanding of bacterial physiology in time-varying environments is lacking. (nature.com)
- Here we develop a quantitative theory connecting bacterial growth and division rates to proteome allocation in time-varying nutrient environments. (nature.com)
- To understand the dynamics of bacterial growth physiology and size control in dynamic nutrient environments, we have developed a coarse-grained proteome sector model which connects gene expression to growth rate and division control, and accurately predicts the cell-level E. coli response to nutrient perturbations in both exponential and stationary phase seen in experimental data 5 , 25 . (nature.com)
Proteins3
- A breakthrough for the identification of the proteome of the presynaptic active zone was the successful employment of antibodies directed against a cytosolic epitope of membrane integral synaptic vesicle proteins for the immunopurification of synaptic vesicles docked to the presynaptic plasma membrane. (mdpi.com)
- We used iTRAQ quantitative proteomics to study the dynamic changes in salivary gland proteins in female Haemaphysalis longicornis at four feeding stages: unfed, partially fed, semi-engorged and engorged. (biomedcentral.com)
- Proteomics analyzes the full complement of proteins in an organism (the proteome), at a particular moment in time, by means of mass spectrometry. (unibas.ch)
Dynamics4
- When subjected to pulsatile nutrient concentration, we find that bacteria exhibit a transient memory of previous metabolic states due to the slow dynamics of proteome reallocation. (nature.com)
- The proteome of the presynaptic active zone controls neurotransmitter release and the short- and long-term structural and functional dynamics of the nerve terminal. (mdpi.com)
- Many of the published analyses of quantitative proteomics datasets use complete software packages like Progenesis (Nonlinear Dynamics), PEAKS [ 1 ] or MaxQuant [ 2 ] to name few. (biorxiv.org)
- Quantitative proteomics strategies such as SILAC and iTRAQ have been widely applied to study the dynamics of proteome. (genengnews.com)
Phosphoproteomics3
- Quantitative Phosphoproteomics Dissection of Seven-transmembrane Receptor Signaling Using Full and Biased Agonists. (mpg.de)
- Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis. (mpg.de)
- Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics. (mpg.de)
20161
- Nature Biotechnology , 2016), we show that proteomes can be linked to and reconstructed from cellular Raman spectra. (aps.org)
Phosphoproteome1
Characterization1
- A comprehensive characterization of brain and retina synaptic vesicle proteome by quantitative mass spectrometry. (mpg.de)
20191
- Recently, he was Vice-Chair of the 6th Symposium of the Mexican Proteomic Society (2015) and Chair of the organizing committees of the 8th Symposium of the Mexican Proteomic Society, the 2nd Ibero -American Symposium on Mass Spectrometry and the 3rd PanAmerican-Human Proteome Organization (Pan-HuPO) meeting, held in 2019. (hupo.org)
Tissues1
- Developing top down proteomics to maximize proteome and sequence coverage from cells and tissues. (chicagobiomedicalconsortium.org)
Phosphorylation1
- Finally, by combining the sequence recognition model with the quantitative changes in phosphorylation measured in the two drug perturbation experiments, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 previously known substrates. (nih.gov)
Biological1
- Quantitative data is increasingly used to describe complex biological processes and is called on for mathematical modeling. (unibas.ch)
Research1
- Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC-MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. (nature.com)
Alterations1
- These massive rearrangements suggest that there might not be single driver mutations, but that the quantitative alterations in cellular traits associated with malignant transformation is distributed among multiple genetic loci. (biomedcentral.com)
Complex1
- As a proof of principle, we applied this technique to yeast alcohol dehydrogenase-1 exposed in vitro to H 2 O 2 and also in vivo to the complex proteome of the Gram-negative bacterium Bacillus subtilis . (hindawi.com)
Vivo1
- 2011) A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles. (phosphosite.org)
Data1
- Using quantitative proteome data of E. coli cultured under various conditions (Schmidt et al. (aps.org)
Stages1
- Here you can compare interactive 2D-DIGE images representing B cell proteomes for different maturation stages. (lu.se)
Profiling3
- A novel strategy for quantitative profiling of serum or plasma proteomes is described. (nist.gov)
- Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers. (mpg.de)
- 2021. "Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells. (pnnl.gov)
Study1
- In a recent study, Dr. Chen and colleagues developed a quantitative proteomics strategy to stoichiometrically identify site-specific lysine acetylation in mammalian cells. (genengnews.com)
Genetic1
- The dynamic nature of the proteome ensures that the cell is able to respond to perturbation of environmental, genetic, biochemical, and pathological conditions. (hindawi.com)
Conditions1
Cell1
Large-scale1
- 2021. "Assessment of TMT labeling efficiency in large-scale quantitative proteomics: the critical effect of sample pH. (pnnl.gov)
Model1
- We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. (elifesciences.org)
Group1
- Pontus Nordenfelt is Assistant Professor and principal investigator of the Quantitative Infection Biology group at Lund University. (lu.se)
Tags1
- 120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. (nature.com)