Sampling and Analytical Strategies for Biomarker Discovery Using Mass Spectrometry

There is an often unspoken truth behind the course of scientific investigation that involves not what is necessarily academically worthy of study, but rather what is scientifically worthy in the eyes of funding agencies. The perception of worthy research is, as cost is driven in the simplest sense in economics, often driven by demand. Presently, the demand for novel diagnostic and therapeutic protein biomarkers that possess high sensitivity and specificity is placing major impact on the field of proteomics. The focal discovery technology that is being relied on is mass spectrometry (MS), whereas the challenge of biomarker discovery often lies not in the application of MS but in the underlying proteome sampling and bioinformatic processing strategies. Although biomarker discovery research has been historically technology-driven, it is clear from the meager success in generating validated biomarkers that increasing attention must be placed at the pre-analytic stage, such as sample retrieval and preparation. As diseases vary, so do the combinations of sampling and sample analyses necessary to discover novel biomarkers. In this review, we highlight different strategies used toward biomarker discovery and discuss them in terms of their reliance on technology and methodology

Analyzing the Effects of the Saluda Dam on the Surface-Water Hydrology of the Congaree National Park Floodplain, South Carolina

2008 S.C. Water Resources Conference - Addressing Water Challenges Facing the State and Regio

Advanced Mass Spectrometric Methods for the Rapid and Quantitative Characterization of Proteomes

Progress is reviewed towards the development of a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of high performance separations and mass spectrometry. The approach uses high accuracy mass measurements from Fourier transform ion cyclotron resonance mass spectrometry (FTICR) to validate peptide ‘accurate mass tags’ (AMTs) produced by global protein enzymatic digestions for a specific organism, tissue or cell type from ‘potential mass tags’ tentatively identified using conventional tandem mass spectrometry (MS/MS). This provides the basis for subsequent measurements without the need for MS/ MS. High resolution capillary liquid chromatography separations combined with high sensitivity, and high resolution accurate FTICR measurements are shown to be capable of characterizing peptide mixtures of more than 105 components. The strategy has been initially demonstrated using the microorganisms Saccharomyces cerevisiae and Deinococcus radiodurans. Advantages of the approach include the high confidence of protein identification, its broad proteome coverage, high sensitivity, and the capability for stableisotope labeling methods for precise relative protein abundance measurements

Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers

The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease-specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, proteomic pattern analysis has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer

Fully automated synthesis of (phospho)peptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization

BACKGROUND: Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60(c-src). RESULTS: The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR) autophosphorylation site (pY1173) antibody ELISA (9H2) was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phospho)peptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of enzyme. CONCLUSIONS: The ability of this method to interface with various robotics and instrumentation is highly flexible since the microtiter plate is an industry standard. It is highly scalable by increasing the surface area within the well or the number of wells and does not require specialized robotics. The microtiter plate array system is well suited to the study of protein kinase substrates, antigens, binding molecules, and inhibitors since these all can be quantitatively studied at a single uniform, reproducible interface

The Application of Topmodel to Assess Mercury Fluxes in the McTier Creek Watershed

2008 S.C. Water Resources Conference - Addressing Water Challenges Facing the State and Regio

South Carolina Digital Flood Inundation Mapping Pilot Investigation

2012 S.C. Water Resources Conference - Exploring Opportunities for Collaborative Water Research, Policy and Managemen

An insight into the sialome of the oriental rat flea, Xenopsylla cheopis (Rots)

<p>Abstract</p> <p>Background</p> <p>The salivary glands of hematophagous animals contain a complex cocktail that interferes with the host hemostasis and inflammation pathways, thus increasing feeding success. Fleas represent a relatively recent group of insects that evolved hematophagy independently of other insect orders.</p> <p>Results</p> <p>Analysis of the salivary transcriptome of the flea <it>Xenopsylla cheopis</it>, the vector of human plague, indicates that gene duplication events have led to a large expansion of a family of acidic phosphatases that are probably inactive, and to the expansion of the FS family of peptides that are unique to fleas. Several other unique polypeptides were also uncovered. Additionally, an apyrase-coding transcript of the CD39 family appears as the candidate for the salivary nucleotide hydrolysing activity in <it>X.cheopis</it>, the first time this family of proteins is found in any arthropod salivary transcriptome.</p> <p>Conclusion</p> <p>Analysis of the salivary transcriptome of the flea <it>X. cheopis </it>revealed the unique pathways taken in the evolution of the salivary cocktail of fleas. Gene duplication events appear as an important driving force in the creation of salivary cocktails of blood feeding arthropods, as was observed with ticks and mosquitoes. Only five other flea salivary sequences exist at this time at NCBI, all from the cat flea <it>C. felis</it>. This work accordingly represents the only relatively extensive sialome description of any flea species. Sialotranscriptomes of additional flea genera will reveal the extent that these novel polypeptide families are common throughout the Siphonaptera.</p

Experimental Observation of ABCB Stacked Tetralayer Graphene

In tetralayer graphene, three inequivalent layer stackings should exist; however, only rhombohedral (ABCA) and Bernal (ABAB) stacking have so far been observed. The three stacking sequences differ in their electronic structure, with the elusive third stacking (ABCB) being unique as it is predicted to exhibit an intrinsic bandgap as well as locally flat bands around the K points. Here, we use scattering-type scanning near-field optical microscopy and confocal Raman microscopy to identify and characterize domains of ABCB stacked tetralayer graphene. We differentiate between the three stacking sequences by addressing characteristic interband contributions in the optical conductivity between 0.28 and 0.56 eV with amplitude and phase-resolved near-field nanospectroscopy. By normalizing adjacent flakes to each other, we achieve good agreement between theory and experiment, allowing for the unambiguous assignment of ABCB domains in tetralayer graphene. These results establish near-field spectroscopy at the interband transitions as a semiquantitative tool, enabling the recognition of ABCB domains in tetralayer graphene flakes and, therefore, providing a basis to study correlation physics of this exciting phase

Разработка Генеральной схемы санитарной очистки территории Тегульдетского района Томской области

Выпускная квалификационная работа объемом 86 страницы, содержит 6 рисунков, 15 таблиц, 34 источника.Final qualification work with a volume of 86 pages, includes 6 figures, 15 tables, 34 source