Proteomics

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General Information

Proteomics
The objective of this course is to instruct active proteomics researchers in the use of a suite of software tools designed for the analysis, validation, storage and interpretation of data obtained from large-scale quantitative proteomics experiments using the ICAT reagent labeling method, multi-dimensional chromatography and tandem mass spectrometry - [e]

Proteomics
A short introduction - [e]

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Data and Databases

Proteomics tools
ExPASy Proteomics tools - [e]

Swiss-Prot
Protein knowledgebase - [e]

World-2DPAGE List
This page contains references to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services - [e]

World-2DPAGE Portal
Portal for distributed two-dimensional polyacrylamide gel electrophoresis databases - [e]

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Journals

Current Proteomics
... publishes review articles in all aspects of the fast-expanding field of proteomics. All areas of proteomics are covered together with the methodology, softwares, databases, technological advances and applications of proteomics, including functional proteomics. Bentham - [e]

Journal of Proteome Research
... integrates the fields of chemistry, mathematics, applied physics, biology, and medicine in order to better understand the function of proteins in biological systems. ACS - [e]

Molecular & Cellular Proteomics
HUPO Official Journal - [e]

Proteome Science
... is ready to receive papers based on all aspects of functional and structural proteomics. BioMedCentral - [e]

Proteomics
... is the premier international source for information on all aspects of applications and technologies in proteomics. It provides the most comprehensive coverage in the field, spanning significant technical developments in all major gel and non-gel based proteomic platforms and their application in every area of life sciences. Wiley-Interscience - [e]

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Organisations

Australasian Proteomics Society
APS aims to promote and facilitate proteomics research in the Australasian region, by organising and managing conferences, instructional courses and workshops - [e]

Austrian Proteomics Association
The AuPA is also an official member of the European Proteomics Association (EuPA), which comprises the federation of the national European associations - [d, e]

British Society for Proteome Research
BSPR is a registered incorporated charity and aims to advance the science of proteomics, to further public education therein and to promote study and research work in proteomics and related subjects for the public benefit - [e]

Czech Proteomics Section
... of the Czech Society for Biochemistry and Molecular Biology - [cz, e]

European Proteomics Association
EuPA has been established to coordinate and integrate national initiatives within the proteomics field. The main objectives are to strengthen and promote fundamental research and applications, as well as education and training in all areas of proteomics throughout Europe - [e]

France
La Société Française d'Electrophorèse et d'Analyse Protéomique (SFEAP) - [f]

German Society for Proteome Research
The DGPF is a platform for bringing proteomics activities in Germany at different locations and within the frame of different programs below one roof and further for promoting proteome research by nationally and internationally harmonized initiatives - [d, e]

Hellenic Proteomics Society
... is a non-profit organization established with the goal to promote the proteomics science in Greek research institutions and to establish international collaborations in Proteomics and related fields - [e]

Human Proteome Organisation's
HUPO is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training - [e]

Italian Proteomic Association
ItPA - [e]

Netherlands Proteomics Platform
... aims to organize biannual meetings with a focus on exchange of information via workshops and posters - [e]

Norwegian Proteomics Society
... is established to promote proteomics-related research, activities and training in Norway, as well as facilitate collaboration with other national societies - [e]

Proteomics Standards Initiative
The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification - [e]

Spanish Society of Proteomics
The SEProt is born with the aim of stimulating the development of Proteomics in our country, gathering researchers in the field of the Proteomics, users of Proteomics Services, Companies of the sector, and students interested in the study of the proteomes - [e]

Swedish Proteomics Society
The SPS will actively take part in the LifeGene Project, one of the largest health projects. The responsibility will be to aid support for sample storage for future protein analysis. These activities will incorporate basic understanding of protein stability and standardisation procedure required to ensure high quality of human biofluid samples - [e]

Swiss Proteomics Society
The aim of the SPS is to stimulate and coordinate proteomic activities in Switzerland as well as in other countries - [e]

Other notes:

Related Books and Scientific Literature: Proteomics:

Katrin Marcus

Quantitative Methods in Proteomics
(Methods in Molecular Biology)

Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.

Humana Press; 2012

Ingvar Eidhammer, Kristian Flikka, Lennart Martens, Svein-Ole Mikalsen

Computational Methods for Mass Spectrometry Proteomics

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.

Wiley-Interscience; 2008