The book is illustrated by a number of figures and examples, and contains exercises for the reader. Written in an accessible yet rigorous style, it is a valuable reference for both informaticians and biologists.
Author: Ingvar Eidhammer
Publisher: John Wiley & Sons
Proteomics is the study of the subsets of proteins present in different parts of an organism and how they change with time and varying conditions. Mass spectrometry is the leading technology used in proteomics, and the field relies heavily on bioinformatics to process and analyze the acquired data. Since recent years have seen tremendous developments in instrumentation and proteomics-related bioinformatics, there is clearly a need for a solid introduction to the crossroads where proteomics and bioinformatics meet. Computational Methods for Mass Spectrometry Proteomics describes the different instruments and methodologies used in proteomics in a unified manner. The authors put an emphasis on the computational methods for the different phases of a proteomics analysis, but the underlying principles in protein chemistry and instrument technology are also described. The book is illustrated by a number of figures and examples, and contains exercises for the reader. Written in an accessible yet rigorous style, it is a valuable reference for both informaticians and biologists. Computational Methods for Mass Spectrometry Proteomics is suited for advanced undergraduate and graduate students of bioinformatics and molecular biology with an interest in proteomics. It also provides a good introduction and reference source for researchers new to proteomics, and for people who come into more peripheral contact with the field.
The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, ...
Author: Ingvar Eidhammer
Publisher: John Wiley & Sons
The definitive introduction to data analysis in quantitativeproteomics This book provides all the necessary knowledge about massspectrometry based proteomics methods and computational andstatistical approaches to pursue the planning, design and analysisof quantitative proteomics experiments. The author’scarefully constructed approach allows readers to easily make thetransition into the field of quantitative proteomics. Throughdetailed descriptions of wet-lab methods, computational approachesand statistical tools, this book covers the full scope of aquantitative experiment, allowing readers to acquire new knowledgeas well as acting as a useful reference work for more advancedreaders. Computational and Statistical Methods for ProteinQuantification by Mass Spectrometry: Introduces the use of mass spectrometry in proteinquantification and how the bioinformatics challenges in this fieldcan be solved using statistical methods and various softwareprograms. Is illustrated by a large number of figures and examples aswell as numerous exercises. Provides both clear and rigorous descriptions of methods andapproaches. Is thoroughly indexed and cross-referenced, combining thestrengths of a text book with the utility of a reference work. Features detailed discussions of both wet-lab approaches andstatistical and computational methods. With clear and thorough descriptions of the various methods andapproaches, this book is accessible to biologists, informaticians,and statisticians alike and is aimed at readers across the academicspectrum, from advanced undergraduate students to post doctoratesentering the field.
Hutchens, T. W. and Yip, T. T. (1993). Techniques for producing high throughput spectometry data. Rapid Communications in Mass Spectrometry, 7,576–580. Jeffries, N. (2005). Algorithms for alignment of mass spectrometry proteomic data.
Author: Ravindra Khattree
Publisher: CRC Press
Continuing advances in biomedical research and statistical methods call for a constant stream of updated, cohesive accounts of new developments so that the methodologies can be properly implemented in the biomedical field. Responding to this need, Computational Methods in Biomedical Research explores important current and emerging computational statistical methods that are used in biomedical research. Written by active researchers in the field, this authoritative collection covers a wide range of topics. It introduces each topic at a basic level, before moving on to more advanced discussions of applications. The book begins with microarray data analysis, machine learning techniques, and mass spectrometry-based protein profiling. It then uses state space models to predict US cancer mortality rates and provides an overview of the application of multistate models in analyzing multiple failure times. The book also describes various Bayesian techniques, the sequential monitoring of randomization tests, mixed-effects models, and the classification rules for repeated measures data. The volume concludes with estimation methods for analyzing longitudinal data. Supplying the knowledge necessary to perform sophisticated statistical analyses, this reference is a must-have for anyone involved in advanced biomedical and pharmaceutical research. It will help in the quest to identify potential new drugs for the treatment of a variety of diseases.
The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics.
Author: Rune Matthiesen
The aim of this new edition is to provide detailed information on each topic and present novel ideas and views that can influence future developments in mass spectrometry-based proteomics. In contrast to the previous editions, this third edition aims to provide the most relevant computational methods, focusing on computational concepts. 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, Mass Spectrometry Data Analysis in Proteomics, Third Edition to ensure successful results in the further study of this vital field.
A guided tour of the Trans-Proteomic Pipeline. Proteomics. 2010;10:1150–9. 35. Lam H, Aebersold R. Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics. Methods. 2011;54:424–31. 36.
Author: Alessandro Laganà
Publisher: Springer Nature
Precision medicine holds great promise for the treatment of cancer and represents a unique opportunity for accelerated development and application of novel and repurposed therapeutic approaches. Current studies and clinical trials demonstrate the benefits of genomic profiling for patients whose cancer is driven by specific, targetable alterations. However, precision oncologists continue to be challenged by the widespread heterogeneity of cancer genomes and drug responses in designing personalized treatments. Chapters provide a comprehensive overview of the computational approaches, methods, and tools that enable precision oncology, as well as related biological concepts. Covered topics include genome sequencing, the architecture of a precision oncology workflow, and introduces cutting-edge research topics in the field of precision oncology. This book is intended for computational biologists, bioinformaticians, biostatisticians and computational pathologists working in precision oncology and related fields, including cancer genomics, systems biology, and immuno-oncology.
Fundamentals of Data Mining in Genomics and Proteomics. Kluwer, Boston (2007) 8. Eidhammer, I., Flikka, K., Martens, L., Mikalsen, S.: Computational Methods for Mass Spectrometry Proteomics. Jon Wiley & Sons, Ltd., England (2008) 9.
Author: Mohd Saberi Mohamad
Publisher: Springer Science & Business Media
Category: Technology & Engineering
The growth in the Bioinformatics and Computational Biology fields over the last few years has been remarkable and the trend is to increase its pace. In fact, the need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology is still increasing driven by new advances in Next Generation Sequencing, several types of the so called omics data and image acquisition, just to name a few. The analysis of the datasets that produces and its integration call for new algorithms and approaches from fields such as Databases, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Within this scenario of increasing data availability, Systems Biology has also been emerging as an alternative to the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information requiring tools from the computational sciences. In the last few years, we have seen the surge of a new generation of interdisciplinary scientists that have a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific fields is, more than ever, of foremost importance boosting the research efforts in the field and contributing to the education of a new generation of Bioinformatics scientists. PACBB‘13 hopes to contribute to this effort promoting this fruitful interaction. PACBB'13 technical program included 19 papers from a submission pool of 32 papers spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the conference will certainly have promoted the interaction of scientists from diverse research groups and with a distinct background (computer scientists, mathematicians, biologists). The scientific content will certainly be challenging and will promote the improvement of the work that is being developed by each of the participants.
Protein identification and characterization by MS. In: Computational Methods for Mass Spectrometry Proteomics. New York: Wiley, and reference therein. 15 Waridel, P., Frank, A., Thomas, H. et al. (2007).
Author: Marek Smoluch
Publisher: John Wiley & Sons
Provides a comprehensive description of mass spectrometry basics, applications, and perspectives Mass spectrometry is a modern analytical technique, allowing for fast and ultrasensitive detection and identification of chemical species. It can serve for analysis of narcotics, counterfeit medicines, components of explosives, but also in clinical chemistry, forensic research and anti-doping analysis, for identification of clinically relevant molecules as biomarkers of various diseases. This book describes everything readers need to know about mass spectrometry—from the instrumentation to the theory and applications. It looks at all aspects of mass spectrometry, including inorganic, organic, forensic, and biological MS (paying special attention to various methodologies and data interpretation). It also contains a list of key terms for easier and faster understanding of the material by newcomers to the subject and test questions to assist lecturers. Knowing how crucial it is for young researchers to fully understand both the power of mass spectrometry and the importance of other complementary methodologies, Mass Spectrometry: An Applied Approach teaches that it should be used in conjunction with other techniques such as NMR, pharmacological tests, structural identification, molecular biology, in order to reveal the true function(s) of the identified molecule. Provides a description of mass spectrometry basics, applications and perspectives of the technique Oriented to a broad audience with limited or basic knowledge in mass spectrometry instrumentation, theory, and its applications in order to enhance their competence in this field Covers all aspects of mass spectrometry, including inorganic, organic, forensic, and biological MS with special attention to application of various methodologies and data interpretation Includes a list of key terms, and test questions, for easier and faster understanding of the material Mass Spectrometry: An Applied Approach is highly recommended for advanced students, young scientists, and anyone involved in a field that utilizes the technique.
Sahar S, Zocchi L, Kinoshita C et al (2010) Regulation of BMAL1 protein stability and circadian function by GSK3β-mediated phosphorylation ... Choudhary C, Mann M (2010) Decoding signalling networks by mass spectrometrybased proteomics.
Author: Dukka B. KC
Publisher: Springer Nature
This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge, Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction.
Mass Spectrometry-based proteomics (Aebersold and Mann, 2003) requires computational methods for analyzing data in qualitative (e.g. peptide/protein identification in tandem mass spectrometry) and in quantitative proteomics (e.g. ...
Author: Cannataro, Mario
Publisher: IGI Global
"This book provides methodologies and developments of grid technologies applied in different fields of life sciences"--Provided by publisher.
Computational methods for mass spectrometry proteomics; John Wiley & Sons: New YorN, USA, 2008.  Colinge, J.; Bennett, K.L. Introduction to computational proteomics. PLOS Comput. Biol., 2007, 3(7): e114.
Publisher: Bentham Science Publishers
Applications of Modern Mass Spectrometry covers the latest advances in the use of mass spectrometry in scientific research. The series attempts to present readers information on the broad range of mass spectrometry techniques and configurations, data analysis and practical applications. Each volume contains contributions from eminent researchers who present their findings in an easy to read format. The multidisciplinary nature of the works presented in each volume of this book series make it a valuable reference on mass spectrometry to academic researchers and industrial R&D specialists in applied sciences, biochemistry, life sciences and allied fields. The first volume of the series presents 5 reviews: - Applications of mass spectrometry for the determination of the microbial crude protein synthesis in ruminants - Qualitative and quantitative LC-MS analysis in food proteins and peptides - Chemometrics as a powerful and complementary tool for mass spectrometry applications in life sciences - Recent developments of allied techniques of qualitative analysis of heavy metal ions in aqueous solutions with special reference to modern mass spectrometry - New techniques and methods in explosive analysis.