Proteins, biomarker discovery

BACTERIAL PROTEIN BIOMARKER DISCOVERY A FOCUSED APPROACH TO DEVELOPING MOLECULAR-BASED IDENTIFICATION SYSTEMS... 

Rifai, N., Gillette, M. and Carr, S.A. (2006) Protein biomarker discovery and validation the long and rmcertain path to clinical utility. Nature Biotechnology, 24 (8), 971-983. 

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R. Aebersold, L. Anderson, R. Caprioli, B. Druker, L. Hartwell, R. Smith, Perspective A program to improve protein biomarker discovery for cancer, J. Proteome Res., 4 (2005) 1104. 

Protein biomarker discovery is an important field that can aid in clinical diagnosis of a range of diseases. A defective gene can be translated into an abnormal protein... 

Listgarten J, et al. Difference detection in LC-MS data for protein biomarker discovery. 

Additionally it has been our experience that mass spectrometry as a routine detection/identification technique for bacteria is not well received by microbiologists and clinicians who prefer less expensive, less complicated approaches to bacterial typing and identification, such as methods based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). For that reason we have adapted our MS approach to serve as a means of biomarker discovery that feeds candidate proteins or leads into development as PCR targets or other immunoassay techniques. 

It is therefore not surprising that the interest in PyMS as a typing tool diminished at the turn of the twenty-first century and hence why taxonomists have turned to MS-based methods that use soft ionization methods such as electrospray ionization (ESI-MS) and matrix-assisted laser desorption ionization (MALDI MS). These methods generate information-rich spectra of metabolites and proteins, and because the molecular ion is seen, the potential for biomarker discovery is being realized. The analyses of ESI-MS and MALDI-MS data will still need chemometric methods, and it is hoped that researchers in these areas can look back and learn from the many PyMS studies where machine learning was absolutely necessary to turn the complex pyrolysis MS data into knowledge of bacterial identities. 

High-throughput proteomic methods hold great promise for the discovery of novel protein biomarkers that can be translated into practical interventions for the diagnosis, treatment, and prevention of disease. These approaches may also facilitate the development of therapeutic agents that are targeted to specific molecular alterations in diseases such as cancer. In many cases, malignant cells yield unique protein profiles when total protein extracts from such cells are analyzed by 2-D gel electrophoresis or mass spectrometry (MS) methods. Such proteomic studies have the potential to provide an important complement to the analysis of DNA and mRNA extracts from these tissues.1... 

The previous chapters have dealt mainly with LC/MS analysis involving short run times, many samples, and relatively small numbers of compounds in samples. What about samples containing very complex compound mixtures, for example, natural products, samples from biomarker discovery, protein digests, and QA/QC method development or metabolite identification samples requiring detection of every component Such workflows often require several analysis steps with different columns and different mobile phases and pH values to increase the separation probability by changing the selectivities of individual runs. 

Surface enhanced laser desorption/ionization (SELDI) is a distinctive form of laser desorption ionization where the target plays an active role in the sample preparation procedure and ionization process [49]. Depending on the chemical or biochemical treatment, the SELDI surface acts as solid phase extraction or an affinity probe. Chromatographic surface is used for sample fractionation and purification of biological samples prior to direct analysis by laser desorption/ ionization. SELDI is mainly applied for protein profiling and in biomarker discovery by comparing protein profiles from control and patient groups. 

A final caveat in the RPAIA field that limits biomarker discovery as well as other uses in drug development is the somewhat limited panel of antibodies that have been validated to date for the platform. Many antibodies that work on western blots have the potential to work with RPMAs as well, because in both platforms proteins are in a denatured state. However, because the molecular weight of analytes detected by RPMA cannot be known, it is imperative to demonstrate the specificity of antibodies, usually measured by the absence of nonspecific reactive bands on western blots developed under similar blocking conditions. A second requirement for antibody validation is proof of principle that an antibody detects quantitative changes in the expected target on an... 

Microarrays have become robust, reliable research tools that enable researchers to screen for a multitude of parameters using minimal amounts of sample material. The acceptance of protein microarrays is growing constantly they have already been demonstrated to be useful tools in disease-related biomarker discovery. In addition, protein microarrays have been introduced into clinical trials in order to investigate the potential adverse effects of drug candidates. Depending on the number of validated disease-specific biomarkers, as well as on their therapeutic relevance, such assays are performed either on a protein microarray or a bead-based platform. 

Food fingerprint can be defined as a specific molecular marker diagnostic for a characteristic food/nutritional state or condition. These biological markers also referred as biomarkers are specific indicators that can be objectively measured and evaluated (1). They can be genes, proteins, or metabolites. Biomarker discovery and validation is still a current hot topic for nutrition and food science. Emerging omics technologies provide a good discovery-based approach for... 

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