Omics
Ionizing Radiation-induced Proteomic Oxidation in Escherichia coliMeasurement of ionizing radiation induced proteome-wide oxidative modification in both E. coli and the highly radiation resistant D. radiodurans. Although E. coli has several IR-induced oxidation events, D. radiodurans is virtually unaffected by IR treatment. An active site cysteine in the enzyme GAPDH within the glycolytic pathway was the largest IR-induced change in E coli, a result that replicated in human cells, suggesting GAPDH is partially responsible for IR response in higher organisms.
Organellar Maps Through Proteomic Profiling – A Conceptual GuideProtein subcellular localization is highly regulated and critical for protein function. Spatial proteomics aims at capturing the localization dynamics of all proteins expressed in a given cell type. Among different approaches, organellar mapping through proteomic profiling stands out as the only method capable of determining the subcellular localizations of thousands of proteins in a single experiment. Importantly, it can also detect movements of proteins between subcellular compartments, providing an unbiased systems analysis tool for investigating physiological and pathological cellular processes.
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell ProteomicsThrough evaluating and optimizing boosting ratio and MS acquisition conditions (automatic gain control and ion injection time), the improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy allows for precise and robust quantitative single-cell proteomics. A total of 2,622 proteins were identified and 1,452 proteins (58%) were quantified in more than 70% of the sample channels in the analysis of 104 FACS-isolated AML single cells, which recapitulates the key biological differences amongst three AML cell lines.
Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular ClassificationAnal squamous cell carcinoma is a rare tumor and the treatment standards have not suffered any improvement since 1970s. For this reason, a molecular characterization of the disease is still necessary. In this work, two molecular groups with a different protein and genetic profile were described. Additionally, some of these differences suggested biological processes that may be therapeutic targets.
Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine PhosphoproteomeThere are clear advantages to experimental approaches that reduce the amount of necessary cellular material for wide-scale quantitative profiling of the tyrosine phosphoproteome, particularly in biological systems where material is limited. The incorporation of boost channels in a multiplexed tandem mass tag experiment containing cells treated with the broad-spectrum tyrosine phosphatase inhibitor pervanadate enabled up to 6.3-fold deeper quantification of the tyrosine phosphoproteome while maintaining accuracy and precision.
The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and Their Cerebral Metastasis from Patient Derived Mouse XenograftsProteome profiling data of eight xenografted cutaneous and cerebellar metastasis of human melanoma cells were combined with eicosanoid and glutathione measurements as well as multiparametric morphologic analyses and immunofluorescence. The analyses revealed significant differences in the expression of molecules associated with metastatic properties, while lacking any commonalties when comparing the metastatic variants from four different donors. Apparently we lack appropriate meta-analysis strategies making use of the large number of presently identified metastasis-associated molecules for successful classification of cells.
Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and ValidationMultiple reaction monitoring with isotope dilution assays were developed for quantification of 200 proteins in dried blood spots, with median inter-day CV of 8%. Developed assays were used to measure the concentration ranges of these 200 proteins in twenty same sex, same race and age matched individuals. These, precise, sensitive, and multiplexed assays can be applied for de novo biomarker discovery and for biomarker quantification or verification experiments.
Functional Characterization and Comparison of Plasmodium falciparum Proteins as Targets of Transmission-blocking AntibodiesThe malaria agent Plasmodium falciparum continues to evade control efforts. Despite multiple datasets for the Plasmodium sexual-stage transcriptome and proteome, there have been no rational screens to identify candidate antigens for transmission-blocking vaccine (TBV) development. We demonstrate the use of rational screens and comparative functional assessments in identifying proteins of the P. falciparum transmission pathway and establishing a robust pre-clinical TBV pipeline.
Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated PeptidesThe citrullinome of P. gingivalis outer membrane vesicles (OMV) has been explored by a novel two-dimensional separation system combined with high resolution mass spectrometry and in-house build software. Analysis of OMVs from wild-type and two PPAD mutants resulted in confident discrimination based on citrullinated peptides. In the wild-type citrullinome 78 proteins were identified having a total of 161 validated citrullination sites. A single citrullination was identified in the C351A mutant and none in the ΔPPAD mutant.