High Performance Algorithms For Mass Spectrometry Based Omics
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High-Performance Algorithms for Mass Spectrometry-Based Omics
To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods. Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation must be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of multicore, manycore, CPU-GPU, CPU-FPGA, and IntelPhi architectures. The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.
Protein Bioinformatics
Author: Frédérique Lisacek
language: en
Publisher: Springer Nature
Release Date: 2024-07-12
This detailed volume explores techniques for protein bioinformatics research, including databases, software tools, and computational methods, in the context of protein science or proteomics and opening to other omics areas. Beginning with a section on proteogenomics, the book continues by covering posttranslational modifications, processing large-scale mass spectrometry data, protein structure and interactions, as well as protein feature inference. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice to ensure efficacious results. Authoritative and practical, Protein Bioinformatics serves as an ideal guide for researchers in disciplines encompassing the biotechnological, pharmaceutical, biological, and medical sciences, as well as the computational and engineering sciences.
Mass Spectrometry
"Mass Spectrometry: Techniques and Applications" is a comprehensive guide to understanding and mastering the principles, techniques, and applications of this powerful analytical method. We cover a wide range of topics, delving into the intricacies of ionization methods, mass analyzers, ion detection, and data analysis strategies crucial for accurate and reliable mass spectrometry results. We explore the fundamentals of mass spectrometry, including ionization and fragmentation principles, isotopic patterns, and mass-to-charge ratio calculations. Various ionization techniques such as electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI), and electron ionization (EI) are elucidated, providing insights into their mechanisms and applications. Advanced topics like tandem mass spectrometry (MS/MS), high-resolution mass spectrometry (HRMS), and ion mobility spectrometry (IMS) are also covered, offering a comprehensive understanding of cutting-edge techniques and instrumentation. Practical aspects of mass spectrometry, including method development, calibration strategies, data interpretation, and troubleshooting, are detailed to help researchers, students, and professionals navigate experiments effectively. Additionally, we showcase the diverse applications of mass spectrometry across fields such as pharmaceuticals, environmental analysis, metabolomics, proteomics, forensics, and materials science. Case studies, real-world examples, and emerging trends provide valuable insights into the role of mass spectrometry in advancing scientific discovery and addressing societal challenges. With clear explanations, illustrative diagrams, and practical tips, "Mass Spectrometry: Techniques and Applications" serves as an indispensable resource for anyone seeking a comprehensive and up-to-date reference on this essential analytical technique.