Peptidomics

ISSN: 2084-7203

First published: October 3, 2014

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Peptidomics is the very first journal devoted to the peptidome, i.e., the low molecular mass window of the proteome, which is still largely missed in proteomics studies. This subset of the proteome, representing essential gene products in all organisms from the most primitive to the most evolved, carries important biological information and deserves much more attention than it has received before. Peptidomics technologies involve state-of-the-art mass spectrometry systems, as well as continuously evolving dedicated bioinformatics and molecular biology approaches. Together with optimized analytical or synthetic methods, including (multidimensional) chromatography and orthogonal separations, or combinatorial synthesis, the modern-day ‘life scientist’ disposes of an ever expanding peptide chemical toolbox to study virtually every biological process using an innovative large-scale or systems approach

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Volume 3 Issue 1

February 2017

Review

Bioinformatic resources for the investigation of proteins and proteomes

Angelo Facchiano February 10, 2017 Page range: 1-10

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Abstract

Experimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.

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Manuscripts should be submitted to the journal via online submission system Editorial Manager available for this journal at http://www.editorialmanager.com/ped/. In case of problems, please contact the Editorial Office of this journal at Peptidomics.Editorial@degruyter.com.

Manuscript submitted to this journal should:

contain original work - not published elsewhere in any medium (in the whole or in part) by the authors or anyone else and not under consideration for publication in any other medium,
focus on the aims and scope of the journal,
be clearly and correctly written - should contain all essential features of a scientific publication that is easy to understand for the target audience,
written in English - attention to detail of the language will avoid severe misunderstandings which might lead to rejection of the paper,
be delivered in electronic format.

SUBMISSION OF MANUSCRIPTS
Manuscripts should be submitted in MS Word - standard DOCUMENT (.DOC) format, or in LATEX. We do not accept papers in Plain TEX format. For detailed information, please see Instruction for Authors.

EDITORIAL POLICY
Unpublished material: Submission of a manuscript implies that the work described is not copyrighted, published or submitted elsewhere, except in abstract form. The corresponding author should ensure that all authors approve the manuscript before its submission.

Ethical conduct of research: The authors must describe and confirm safeguards to meet ethical standards when applicable. See Editorial Policy for details.

Conflict of interest: When authors submit a manuscript, they are responsible for recognizing and disclosing financial and/or other conflicts of interest that might bias their work and/or could inappropriately influence his/her judgment. If no specified acknowledgement is given, the Editors assume that no conflict of interest exists. Authors are encouraged to fill in the ICMJE Conflicts of Interest Form (available here) and send it in the electronic format to the Managing Editor.

Copyright: All authors retain copyright, unless – due to their local circumstances – their work is not copyrighted. The copyrights are governed by the Creative-Commons Attribution Only license (CC-BY) which is compliant with Plan-S. We may also publish a paper under CC-BY-NC-ND license on author's request. The corresponding author grants the journal the license to use of the article, by signing the License To Publish. Scanned copy of license should be sent to the journal, as soon as possible.

Authorship: Authorship should be limited to those who have made a significant contribution to the conception, design, execution, or interpretation of the reported study. All those who have made significant contributions should be listed as co-authors. Where there are others who have participated in certain substantive aspects of the research project, they should be named in an Acknowledgement section. The corresponding author should ensure that all appropriate co-authors (according to the above definition) and no inappropriate co-authors are included in the author list of the manuscript, and that all co-authors have seen and approved the final version of the paper and have agreed to its submission for publication.

Peer Review process: Our standard policy requires each paper to be reviewed by at least two Referees and the peer-review process is single-blind. The Editors reserve the right to decline the submitted manuscript without review, if the studies reported are not sufficiently novel or important to merit publication in the journal. Manuscripts deemed unsuitable (insufficient originality or of limited interest to the target audience) are returned to the author(s) without review. The Editor seeks advice from experts in the appropriate field. Research articles and communications are refereed by a minimum of two reviewers, review papers by at least three. Authors are requested to suggest persons competent to review their manuscript. However, please note that this will be treated only as a suggestion, and the final selection of reviewers is exclusively the Editor's decision. The final decision of acceptance in made by Managing Editor or, in case of conflict, by the Editor-in-Chief.

Scientific Misconduct: This journal publishes only original manuscripts that are not also published or going to be published elsewhere. Multiple submissions/publications, or redundant publications (re-packaging in different words of data already published by the same authors) will be rejected. If they are detected only after publication, the journal reserves the right to publish a Retraction Note. In each particular case Editors will follow COPE’s Core Practices and implement the advices.

Editorial

Journal Editor
Pasquale Ferranti, University of Naples “Federico II”, Italy

Associate Editors
Christian W. Gruber, Medical University of Vienna, Austria
Andrea Urbani, University of Rome “Tor Vergata”, Italy

Editorial Advisory Board
Günter Allmaier, Technical University of Vienna, Austria
Per Andrén, Uppsala Universitet, Sweden
Mimoun Ayoub, Peptisyntha, Switzerland
Massimo Castagnola, Facoltà di Medicina – Università Cattolica, Italy
Michelle Colgrave, CSIRO Livestock Industries, Australia
Lieve Dillen, Johnson&Johnson, Belgium
Maria Dolores del Castillo, Institute of Food Science Research (CIAL) (CSIC/UAM), Spain
Georges Gaudriault, MedinCell, France
Ulf Göransson, Uppsala University, Sweden
Elvira Maria Hebert, Centro de Referencia para Lactobacilos (CERELA) - CONICET, Argentina
Djuro Josic, Brown University, USA
Oleg Krokhin, University of Manitoba, Canada
Sylvain Lehmann,CHU de Montpellier, Institut de Recherches en Biothérapie (IRB) Biochimie - Protéomique Clinique, France
Gianfranco Mamone, Istituto di Scienze dell' Alimentazione - CNR, Italy
Jason Mulvenna, Queensland Institute of Medical Research, Australia
Gianluca Picariello, Istituto di Scienze dell'Alimentazione – CNR, Italy
Paola Roncada, Istituto Sperimentale “Lazzaro Spallanzani”, Italy
Peter Schulz-Knappe, Protagen AG, Germany
Martina Schnölzer, German Cancer Research Center, Germany
Christopher Shaw, Queen's University Belfast, Ireland
Hans-Dieter Zucht, Proteome Sciences R&D GmbH & Co KG, Germany

Assistant Editors
Johannes Koehbach, Medical University of Vienna, Austria
Chiara Nitride, University of Naples “Federico II”, Italia

Language Editors
Garret Rochford, Dublin Institute of Technology, Ireland
Julia Richards, University of Pennsylvania, USA

Publisher
DE GRUYTER Poland
Bogumiła Zuga 32A Str.
01-811 Warsaw, Poland
T: +48 22 701 50 15

Editorial Contact
Peptidomics.Editorial@degruyter.com

Peptidomics

Bioinformatic resources for the investigation of proteins and proteomes

Abstract

Details