Proteoform Identification


Book Description

This volume discusses the latest mass spectrometry (MS)-based technologies for proteoform identification, characterization, and quantification. Some of the topics covered in this book include sample preparation, proteoform separation, proteoform gas-phase fragmentation, and bioinformatics tools for MS data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Proteoform Identification: Methods and Protocols is a valuable resource for researchers in both academia and the biopharmaceutical industry who are interested in proteoform analysis using MS.




Proteoforms


Book Description

A proteoform is the basic unit in a proteome, defined as its amino acid sequence + post-translational modifications + spatial conformation + localization + cofactors + binding partners + a function, which is the final functional performer of a gene. Studies on proteoforms offer in-depth insights and can lead to the discovery of reliable biomarkers and therapeutic targets for effective prediction, diagnosis, prognostic assessment, and therapy of disease. This book focuses on the concept, study, and applications of proteoforms. Chapters cover such topics as methodologies for identifying and preparing proteoforms, proteoform pattern alteration in pituitary adenomas, and proteoforms in leukemia.




Proteomic and Metabolomic Approaches to Biomarker Discovery


Book Description

Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution




Detection and Analysis of Microorganisms by Mass Spectrometry


Book Description

In the human body, there are millions of living microorganisms involved in protecting the body from invaders, helping digestion and regulating moods, but there are also harmful pathogens that cause infectious diseases. For instance, the coronavirus (COVID-19) has caused considerable loss of life since its outbreak. Comprehensive analysis and characterization of microbes is of significant importance to understand the function and role of microorganisms, and rapid detection and identification of unknown pathogens are essential in early diagnosis, treatment monitoring and personalized medicine. Mass spectrometry is a technique to ionize molecules and detect the mass-to-charge ratio of the generated ions. The technique is widely used in hospitals for pathogenic bacteria identification, as well as in environmental science and food science for biosafety control. This book summarizes the most recent development of mass spectrometry techniques in microbial analysis, including mass spectrometry-based microbial identification, bacterial antimicrobial resistance study, data mining algorithm development, omics for microbial research, applications in clinical diagnosis, environmental science and food science, and more. It will guide researchers in the field, and those who are about to enter the field, in the most appropriate methods to characterize microbes and enable their detection.




Proteomics Sample Preparation


Book Description

This long-awaited first guide to sample preparation for proteomics studies overcomes a major bottleneck in this fast growing technique within the molecular life sciences. By addressing the topic from three different angles -- sample, method and aim of the study -- this practical reference has something for every proteomics researcher. Following an introduction to the field, the book looks at sample preparation for specific techniques and applications and finishes with a section on the preparation of sample types. For each method described, a summary of the pros and cons is given, as well as step-by-step protocols adaptable to any specific proteome analysis task.




Algorithms in Bioinformatics


Book Description

This book constitutes the refereed proceedings of the 16th International Workshop on Algorithms in Bioinformatics, WABI 2016, held in Aarhus, Denmark. The 25 full papers together with 2 invited talks presented were carefully reviewed and selected from 54 submissions. The selected papers cover a wide range of topics from networks, tophylogenetic studies, sequence and genome analysis, comparative genomics, and mass spectrometry data analysis.




Proteomics for Biomarker Discovery


Book Description

This volume presents modern and enhanced methods that detail techniques to perform proteomics analyses dedicated to biomarker discovery for human health. Chapters guide readers through pre/post analytical factors, protocols for the preparation of extracellular vesicles and exosomes, and various analytical pipelines including Data Independent Acquisition (DIA), discovery, as well as targeted and top-down proteomics analysis workflows. Bioinformatics tools and workflows to select and evaluate candidate biomarkers or combinations of biomarkers are also presented. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Proteomics for Biomarker Discovery: Methods and Protocols aims to ensure successful results in the further study of this vital field.




Bioinformatics Research and Applications


Book Description

This book constitutes the proceedings of the 13th International Symposium on Bioinformatics Research and Applications, ISBRA 2017, held in Honolulu, HI, USA, in May/June 2017. The 27 full papers presented together with 18 short papers and 24 invited abstracts were carefully reviewed and selected from 131 submissions. They cover topics such as: biomarker discovery; biomedical databases and data integration; biomedical text mining and ortologies; biomolecular imaging; comparative genomics; computational genetic epidemiology; computational proteomics; data mining and visualization; gene expression analysis; genome analysis; high-performance bio-computing; metagenomics; molecular evolution; molecular modelling and simulation; next-generation sequencing data analysis; pattern discovery and classification; population genetics; software tools and applications; structural biology; and systems biology.




Encyclopedia of Bioinformatics and Computational Biology


Book Description

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases




Subcellular Proteomics


Book Description

This volume summarizes the new developments that made subcellular proteomics a rapidly expanding area. It examines the different levels of subcellular organization and their specific methodologies. In addition, the book includes coverage of systems biology that deals with the integration of the data derived from these different levels to produce a synthetic description of the cell as a system.