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There are many implications of biomedical informatics for proteomics, including multiple platform technologies (for example, two-dimensional.
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- Informatics In Proteomics - CRC Press Book
- Proteome informatics I: bioinformatics tools for processing experimental data.
Please accept our apologies for any inconvenience this may cause. Add to Wish List. Toggle navigation Additional Book Information. Description Table of Contents Reviews. Summary The handling and analysis of data generated by proteomics investigations represent a challenge for computer scientists, biostatisticians, and biologists to develop tools for storing, retrieving, visualizing, and analyzing genomic data. Informatics in Proteomics examines the ongoing advances in the application of bioinformatics to proteomics research and analysis.
Through computer simulations, scientists can determine more about how diseases affect cells, predict how various drug interventions would work, and ultimately use proteins as therapeutic targets. This book first addresses the infrastructure needed for public protein databases. It discusses information management systems and user interfaces for storage, retrieval, and visualization of the data as well as issues surrounding data standardization and integration of protein sequences recorded in the last two decades. The authors subsequently examine the application of statistical and bioinformatic tools to data analysis, data presentation, and data mining.
They discuss the implementation of algorithms, statistical methods, and computer applications that facilitate pattern recognition and biomarker discovery by integrating data from multiple sources. This book offers a well-rounded resource of informatic approaches to data storage, retrieval, and protein analysis as well as application-specific bioinformatic tools that can be used in disease detection, diagnosis, and treatment.
Informatics in Proteomics captures the current state-of-the-art and provides a valuable foundation for future directions. Table of Contents The Promise of Proteomics: As genetic differences among individuals are found, researchers expect to use these techniques to develop personalized drugs that are more effective for the individual. Proteomics is also used to reveal complex plant-insect interactions that help identify candidate genes involved in the defensive response of plants to herbivory. Interaction proteomics is the analysis of protein interactions from scales of binary interactions to proteome- or network-wide.
Most proteins function via protein—protein interactions , and one goal of interaction proteomics is to identify binary protein interactions , protein complexes , and interactomes. Several methods are available to probe protein—protein interactions. While the most traditional method is yeast two-hybrid analysis , a powerful emerging method is affinity purification followed by protein mass spectrometry using tagged protein baits.
Other methods include surface plasmon resonance SPR ,   protein microarrays , dual polarisation interferometry , microscale thermophoresis and experimental methods such as phage display and in silico computational methods. Knowledge of protein-protein interactions is especially useful in regard to biological networks and systems biology , for example in cell signaling cascades and gene regulatory networks GRNs, where knowledge of protein-DNA interactions is also informative.
Proteome-wide analysis of protein interactions, and integration of these interaction patterns into larger biological networks , is crucial towards understanding systems-level biology. Expression proteomics includes the analysis of protein expression at larger scale. It helps identify main proteins in a particular sample, and those proteins differentially expressed in related samples—such as diseased vs.
If a protein is found only in a diseased sample then it can be a useful drug target or diagnostic marker. Proteins with same or similar expression profiles may also be functionally related. Understanding the proteome, the structure and function of each protein and the complexities of protein—protein interactions is critical for developing the most effective diagnostic techniques and disease treatments in the future.
For example, proteomics is highly useful in identification of candidate biomarkers proteins in body fluids that are of value for diagnosis , identification of the bacterial antigens that are targeted by the immune response, and identification of possible immunohistochemistry markers of infectious or neoplastic diseases.
An interesting use of proteomics is using specific protein biomarkers to diagnose disease. A number of techniques allow to test for proteins produced during a particular disease, which helps to diagnose the disease quickly. Techniques include western blot , immunohistochemical staining , enzyme linked immunosorbent assay ELISA or mass spectrometry. In proteogenomics , proteomic technologies such as mass spectrometry are used for improving gene annotations. Parallel analysis of the genome and the proteome facilitates discovery of post-translational modifications and proteolytic events,  especially when comparing multiple species comparative proteogenomics.
Structural proteomics includes the analysis of protein structures at large-scale. It compares protein structures and helps identify functions of newly discovered genes. The structural analysis also helps to understand that where drugs bind to proteins and also show where proteins interact with each other. This understanding is achieved using different technologies such as X-ray crystallography and NMR spectroscopy.
Much proteomics data is collected with the help of high throughput technologies such as mass spectrometry and microarray. It would often take weeks or months to analyze the data and perform comparisons by hand. For this reason, biologists and chemists are collaborating with computer scientists and mathematicians to create programs and pipeline to computationally analyze the protein data. Using bioinformatics techniques, researchers are capable of faster analysis and data storage.
A good place to find lists of current programs and databases is on the ExPASy bioinformatics resource portal. The applications of bioinformatics-based proteomics includes medicine, disease diagnosis, biomarker identification, and many more. Mass spectrometry and microarray produce peptide fragmentation information but do not give identification of specific proteins present in the original sample. Due to the lack of specific protein identification, past researchers were forced to decipher the peptide fragments themselves.
However, there are currently programs available for protein identification. These programs take the peptide sequences output from mass spectrometry and microarray and return information about matching or similar proteins. This is done through algorithms implemented by the program which perform alignments with proteins from known databases such as UniProt  and PROSITE  to predict what proteins are in the sample with a degree of certainty. The biomolecular structure forms the 3D configuration of the protein. Understanding the protein's structure aids in identification of the protein's interactions and function.
Informatics In Proteomics - CRC Press Book
It used to be that the 3D structure of proteins could only be determined using X-ray crystallography and NMR spectroscopy. As of , Cryo-electron microscopy is a leading technique, solving difficulties with crystallization in X-ray crystallography and conformational ambiguity in NMR ; resolution was 2. Now, through bioinformatics, there are computer programs that can in some cases predict and model the structure of proteins.
These programs use the chemical properties of amino acids and structural properties of known proteins to predict the 3D model of sample proteins. This also allows scientists to model protein interactions on a larger scale. In addition, biomedical engineers are developing methods to factor in the flexibility of protein structures to make comparisons and predictions. Most programs available for protein analysis are not written for proteins that have undergone post-translational modifications. It is important to account for these modifications since they can affect the protein's structure. In turn, computational analysis of post-translational modifications has gained the attention of the scientific community.
The current post-translational modification programs are only predictive.
Proteome informatics I: bioinformatics tools for processing experimental data.
One example of the use of bioinformatics and the use of computational methods is the study of protein biomarkers. Computational predictive models  have shown that extensive and diverse feto-maternal protein trafficking occurs during pregnancy and can be readily detected non-invasively in maternal whole blood. This computational approach circumvented a major limitation, the abundance of maternal proteins interfering with the detection of fetal proteins , to fetal proteomic analysis of maternal blood. Computational models can use fetal gene transcripts previously identified in maternal whole blood to create a comprehensive proteomic network of the term neonate.
The proteomic networks contain many biomarkers that are proxies for development and illustrate the potential clinical application of this technology as a way to monitor normal and abnormal fetal development. An information theoretic framework has also been introduced for biomarker discovery, integrating biofluid and tissue information. By conceptualizing tissue-biofluid as information channels, significant biofluid proxies can be identified and then used for guided development of clinical diagnostics.
Candidate biomarkers are then predicted based on information transfer criteria across the tissue-biofluid channels. Significant biofluid-tissue relationships can be used to prioritize clinical validation of biomarkers. A number of emerging concepts have the potential to improve current features of proteomics. Obtaining absolute quantification of proteins and monitoring post-translational modifications are the two tasks that impact the understanding of protein function in healthy and diseased cells. For many cellular events, the protein concentrations do not change; rather, their function is modulated by post-translational modifications PTM.
Methods of monitoring PTM are an underdeveloped area in proteomics.
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Selecting a particular subset of protein for analysis substantially reduces protein complexity, making it advantageous for diagnostic purposes where blood is the starting material. Another important aspect of proteomics, yet not addressed, is that proteomics methods should focus on studying proteins in the context of the environment. The increasing use of chemical cross linkers, introduced into living cells to fix protein-protein, protein-DNA and other interactions, may ameliorate this problem partially.
The challenge is to identify suitable methods of preserving relevant interactions. Another goal for studying protein is to develop more sophisticated methods to image proteins and other molecules in living cells and real time. Advances in quantitative proteomics would clearly enable more in-depth analysis of cellular systems. Transcriptional and translational responses to these perturbations results in functional changes to the proteome implicated in response to the stimulus.
Therefore, describing and quantifying proteome-wide changes in protein abundance is crucial towards understanding biological phenomenon more holistically , on the level of the entire system. In this way, proteomics can be seen as complementary to genomics , transcriptomics , epigenomics , metabolomics , and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively. Characterizing the human plasma proteome has become a major goal in the proteomics arena, but it is also the most challenging proteomes of all human tissues.
It also contains tissue leakage proteins due to the blood circulation through different tissues in the body. The blood thus contains information on the physiological state of all tissues and, combined with its accessibility, makes the blood proteome invaluable for medical purposes.
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It is thought that characterizing the proteome of blood plasma is a daunting challenge. The depth of the plasma proteome encompassing a dynamic range of more than 10 10 between the highest abundant protein albumin and the lowest some cytokines and is thought to be one of the main challenges for proteomics. The turnover of some proteins is quite faster than others and the protein content of an artery may substantially vary from that of a vein. Generate a file for use with external citation management software.
Abstract Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination.
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