Guide for Authors

  • All journal information and instructions compiled in one document (PDF) in just one mouse-click Author information pack

    • Types of paper
    BEFORE YOU BEGIN
    • Ethics in publishing
    • Human and animal rights
    • Conflict of interest
    • Submission declaration
    • Authorship
    • Changes to authorship
    • Copyright
    • Role of the funding source
    • Funding body agreements and policies
    • Open access
    • Language (usage and editing services)
    • Submission
    • Referees
    PREPARATION
    • Use of word processing software
    • Article Structure
    • Graphical abstract
    • Highlights
    • Database linking
    • Artwork
    • Electronic artwork
    • Tables
    • References
    • Citation in Text
    • Video data
    • AudioSlides
    • Supplementary data
    • Submission checklist
    AFTER ACCEPTANCE
    • Online proof correction
    • Offprints
    • Appendix
    AUTHOR INQUIRIES


    Journal of Proteomics is an official journal of the European Proteomics Association (EuPA) and is aimed at both European and international protein scientists and analytical chemists in the field of proteomics, biomarker discovery, protein analytics, plant proteomics, microbial and animal proteomics, human studies, tissue imaging by mass spectrometry, non-conventional and non-model organism proteomics, and protein bioinformatics. The journal welcomes papers in new and upcoming areas such as metabolomics, genomics, systems biology, toxicogenomics, pharmacoproteomics. Journal of Proteomics unifies both fundamental scientists and clinicians, and includes translational research. Suggestions for reviews, webinars and thematic issues are welcome. All manuscripts are strictly peer reviewed and conform the highest ethical standards. Journal of Proteomics also publishes official EuPA reports and participates in the International Proteomics Tutorial Programme with HUPO and other partners.

    Types of paper

    The following types of paper are published:

    Original Articles: Original articles are the normal medium of publication. Although there is no fixed length, articles should be as concise as possible, while providing sufficient information for the work to be repeated and for the claims of the authors to be judged by the readers. Authors are encouraged to use proteomics data in the context of interdisciplinary projects to elaborate appropriate biological hypotheses, and use these hypotheses to validate the proteomics data through hypothesis-driven experiments and/or elaborate on future research to check the proposed biological model/mechanism.

    Mandatory requirements for reporting of clinical biomarker studies:

    1) A clinical biomarker is only relevant in specific contexts of use per disease, it must have a potential to improve the current state of the art (either being of added value, or based on its sole performance), and its application must be linked to a clear change in patient management. As such, the specific proposed context of use of the presented biomarker must be clearly provided and the expected practical consequence of the biomarker application should be discussed.
    2) A biomarker can only be assessed in an independent (ideally blinded) test set, containing sufficient samples to demonstrate significant value and justify relevant claims regarding biomarker use. Assessment of performance in a discovery set is inappropriate.
    3) This initial independent validation and performance assessment has to be performed in samples that reflect the typical clinical situation depending on the targeted context of use.
    4) Authors submitting clinical biomarker studies should address the above points in the cover letter, so that the Editor can assess and evaluate if the submitted manuscript fulfils the requirements for publication in Journal of Proteomics.

    Reviews: These are contributed by scientists who are leading specialists in their field of expertise, normally at the invitation of the Editors. Authors wishing to contribute a review paper are advised first to contact one of the responsible Editors (listed in the issues of Journal of Proteomics to avoid overlap with Reviews already commissioned.)

    Technical reports: Technical reports should present brief descriptions of novel apparatus, a new experimental or computational method, test or procedure, or an improvement or noteworthy modification of an already existing technique or platform used in the proteomic workflow. Technical reports should show a realistic application of the methodology described. Theoretical papers dealing with mechanistic aspects of proteomic techniques will also be considered. A technical report should be a short (no more than two pages when published) description written in a continuous style with no more than two figures and one table.

    Tutorials: The International Proteomics Tutorial Programme, initiated by the education committees of the Human Proteome Organisation (HUPO) and the European Proteomics Association (EuPA) is aimed at Masters/PhD level students who are starting out their research and who would benefit from a solid grounding in the techniques used in modern protein-based research. The tutorial program will cover core techniques and basics as an introduction to scientists new to the field. Authors are generally invited to contribute a Tutorial. For suggestions, prospective authors of high standing may contact the Journal's Tutorial editor Peter James.

    News & Views: News & Views point out the author(s) vision of the character and importance of a new direction in proteome research. They are not intended to be accounts or analyses of an individual's personal research. Although News & Views will usually be invited, they can be submitted without invitation. Author(s) are encouraged to suggest experts in the field who can act as reviewers.

    Letters to the Editor: Letters to the Editor are intended to stimulate discussion and debate in areas of general concern and controversy in proteomics, and generally reflect the personal opinions of the author(s). They should be written in a continuous style and should normally not exceed two printed pages and contain no more than one figure or table.

    Data in Brief: Authors have the option of converting any or all parts of their supplementary data into one or multiple Data in Brief articles, a new kind of article that houses and describes their data. Data in Brief articles ensure that your data, which is normally buried in supplementary material, is actively reviewed, curated, formatted, indexed, given a DOI and publicly available to all upon publication. Data in Brief may be submitted directly to the Journal of Proteomics alongside a research article. Authors are encouraged to convert their supplementary data into a Data in Brief article when they submit a revised version of their manuscript to the Journal of Proteomics. If your research article is accepted, your Data in Brief article will also be published in the new, Open Access journal, Data in Brief. As a preliminary offer, your Data in Brief article will be published free of charge. Please use the following template to write your Data in Brief.

    Ethics in publishing

    For information on Ethics in publishing and Ethical guidelines for journal publication see http://www.elsevier.com/publishingethics and http://www.elsevier.com/journal-authors/ethics.

    Human and animal rights

    If the work involves the use of animal or human subjects, the author should ensure that the work described has been carried out in accordance with The Code of Ethics of the World Medical Association (Declaration of Helsinki) for experiments involving humans http://www.wma.net/en/30publications/10policies/b3/index.html; EU Directive 2010/63/EU for animal experiments http://ec.europa.eu/environment/chemicals/lab_animals/legislation_en.htm; Uniform Requirements for manuscripts submitted to Biomedical journals http://www.icmje.org. Authors should include a statement in the manuscript that informed consent was obtained for experimentation with human subjects. The privacy rights of human subjects must always be observed.

    Animal experiments
    Where animals have been used in a study, the institutional ethical or animal welfare authority under which the work was conducted must be stated, along with the specific authorisation reference number. Circumstances relating to animal experimentation must meet the International Guiding Principles for Biomedical Research Involving Animals, as issued by the Council for the International Organizations of Medical Sciences. These guidelines are obtainable from: Executive Secretary C.I.O.M.S., c/o WHO, Appia, CH-1211 Geneva 27, Switzerland, or at the following URL: http://www.cioms.ch/frame_1985_texts_of_guidelines.htm.

    The Journal of Proteomics will reject any paper where there is reason to believe that animals have been subjected to unnecessary or avoidable pain or distress.

    Conflict of interest

    Journal of Proteomics follows the ICMJE recommendations regarding conflict of interest disclosures. All authors are required to report the following information with each submission: (1) All third-party financial support for the work in the submitted manuscript. (2) All financial relationships with any entities that could be viewed as relevant to the general area of the submitted manuscript. (3) All sources of revenue with relevance to the submitted work who made payments to you, or to your institution on your behalf, in the 36 months prior to submission. (4) Any other interactions with the sponsor of outside of the submitted work should also be reported. (5) Any relevant patents or copyrights (planned, pending, or issued). (6) Any other relationships or affiliations that may be perceived by readers to have influenced, or give the appearance of potentially influencing, what you wrote in the submitted work. As a general guideline, it is usually better to disclose a relationship than not. This information will be acknowledged at publication in a Transparency Document link directly in the article. Additional information on the ICMJE recommendations can be found at: http://www.icmje.org/. The form for conflict of interest disclosure can be downloaded here: http://www.icmje.org/coi_disclosure.pdf (if this link does not display properly in your browser, please right-click the link and select "Save Target As..." or "Save Link as..." from the pop-up menu).

    Submission declaration

    Submission of an article implies that the work described has not been published previously (except in the form of an abstract or as part of a published lecture or academic thesis or as an electronic preprint, see http://www.elsevier.com/postingpolicy), that it is not under consideration for publication elsewhere, that its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere including electronically in the same form, in English or in any other language, without the written consent of the copyright-holder.

    Authorship

    All authors should have made substantial contributions to all of the following: (1) the conception and design of the study, or acquisition of data, or analysis and interpretation of data, (2) drafting the article or revising it critically for important intellectual content, (3) final approval of the version to be submitted.

    Changes to authorship

    This policy concerns the addition, deletion, or rearrangement of author names in the authorship of accepted manuscripts:
    Before the accepted manuscript is published in an online issue: Requests to add or remove an author, or to rearrange the author names, must be sent to the Journal Manager from the corresponding author of the accepted manuscript and must include: (a) the reason the name should be added or removed, or the author names rearranged and (b) written confirmation (e-mail, fax, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed. Requests that are not sent by the corresponding author will be forwarded by the Journal Manager to the corresponding author, who must follow the procedure as described above. Note that: (1) Journal Managers will inform the Journal Editors of any such requests and (2) publication of the accepted manuscript in an online issue is suspended until authorship has been agreed.
    After the accepted manuscript is published in an online issue: Any requests to add, delete, or rearrange author names in an article published in an online issue will follow the same policies as noted above and result in a corrigendum.

    Copyright

    This journal offers authors a choice in publishing their research: Open access and Subscription.

    For subscription articles
    Upon acceptance of an article, authors will be asked to complete a 'Journal Publishing Agreement' (for more information on this and copyright, see http://www.elsevier.com/copyright). An e-mail will be sent to the corresponding author confirming receipt of the manuscript together with a 'Journal Publishing Agreement' form or a link to the online version of this agreement.
    Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institutions. Permission of the Publisher is required for resale or distribution outside the institution and for all other derivative works, including compilations and translations (please consult http://www.elsevier.com/permissions). If excerpts from other copyrighted works are included, the author(s) must obtain written permission from the copyright owners and credit the source(s) in the article. Elsevier has preprinted forms for use by authors in these cases: please consult http://www.elsevier.com/permissions.

    For open access articles
    Upon acceptance of an article, authors will be asked to complete an 'Exclusive License Agreement' (for more information see http://www.elsevier.com/OAauthoragreement). Permitted reuse of open access articles is determined by the author's choice of user license (see http://www.elsevier.com/openaccesslicenses).

    Retained author rights
    As an author you (or your employer or institution) retain certain rights. For more information on author rights for:
    Subscription articles please see http://www.elsevier.com/journal-authors/author-rights-and-responsibilities.
    Open access articles please see http://www.elsevier.com/OAauthoragreement.

    Role of the funding source

    You are requested to identify who provided financial support for the conduct of the research and/or preparation of the article and to briefly describe the role of the sponsor(s), if any, in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication. If the funding source(s) had no such involvement then this should be stated.

    Funding body agreements and policies

    Elsevier has established agreements and developed policies to allow authors whose articles appear in journals published by Elsevier, to comply with potential manuscript archiving requirements as specified as conditions of their grant awards. To learn more about existing agreements and policies please visit http://www.elsevier.com/fundingbodies.

    Open access

    This journal offers authors a choice in publishing their research:

    Open access
    • Articles are freely available to both subscribers and the wider public with permitted reuse
    • An open access publication fee is payable by authors or their research funder
    Subscription
    • Articles are made available to subscribers as well as developing countries and patient groups through our access programs (http://www.elsevier.com/access)
    • No open access publication fee

    All articles published open access will be immediately and permanently free for everyone to read and download. Permitted reuse is defined by your choice of one of the following Creative Commons user licenses:
    Creative Commons Attribution (CC BY): lets others distribute and copy the article, to create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text or data mine the article, even for commercial purposes, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, and do not modify the article in such a way as to damage the author's honor or reputation.
    Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA): for non-commercial purposes, lets others distribute and copy the article, to create extracts, abstracts and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text and data mine the article, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, do not modify the article in such a way as to damage the author's honor or reputation, and license their new adaptations or creations under identical terms (CC BY-NC-SA).
    Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND): for non-commercial purposes, lets others distribute and copy the article, and to include in a collective work (such as an anthology), as long as they credit the author(s) and provided they do not alter or modify the article.

    To provide open access, this journal has a publication fee which needs to be met by the authors or their research funders for each article published open access.
    Your publication choice will have no effect on the peer review process or acceptance of submitted articles.

    The publication fee for Open Access in this journal is $3000, excluding taxes. Learn more about Elsevier's pricing policy: http://www.elsevier.com/openaccesspricing.

    Language (usage and editing services)

    Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who feel their English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English may wish to use the English Language Editing service available from Elsevier's WebShop (http://webshop.elsevier.com/languageediting/) or visit our customer support site (http://support.elsevier.com) for more information.

    Submission

    Submission to this journal proceeds totally online and you will be guided stepwise through the creation and uploading of your files. The system automatically converts source files to a single PDF file of the article, which is used in the peer-review process. Please note that even though manuscript source files are converted to PDF files at submission for the review process, these source files are needed for further processing after acceptance. All correspondence, including notification of the Editor's decision and requests for revision, takes place by e-mail removing the need for a paper trail.

    Referees

    Please provide the names and addresses of 4 - 5 suitable potential reviewers. If there are compelling reasons for excluding some individuals as potential reviewers, these can be mentioned. However, choice of reviewers is at the Editors' discretion.

    Use of word processing software

    It is important that the file be saved in the native format of the word processor used. The text should be in single-column format. Keep the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. In particular, do not use the word processor's options to justify text or to hyphenate words. However, do use bold face, italics, subscripts, superscripts etc. When preparing tables, if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs, not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also the Guide to Publishing with Elsevier: http://www.elsevier.com/guidepublication). Note that source files of figures, tables and text graphics will be required whether or not you embed your figures in the text. See also the section on Electronic artwork.
    To avoid unnecessary errors you are strongly advised to use the 'spell-check' and 'grammar-check' functions of your word processor.

    To assist in the reviewing of your paper, please add line numbering to your manuscript file

    Article Structure

    Original articles are usually divided into the sections Introduction, Materials and methods, Results, Discussion and Conclusions:

    Abstract

    The Abstract should describe in a single paragraph the findings of the study, and should be comprehensible to readers before they have read the paper. Non-standard abbreviations and reference citations should be avoided.

    Significance

    Starting January 2013, manuscripts submitted to Journal of Proteomics must include a paragraph entitled "Significance" detailing the biological relevance of the reported research or technological innovation. Authors shortly but realistically state how the paper impacts its field of research (please consult Calvete JJ (2012) Updating JPROT's publication standards for large-scale proteomic studies: towards hypothesis-driven interpretation of predictive biological models. J Proteomics 76, 1-2).

    Introduction
    This is a short section in which the authors should state the reasons for performing the work, with brief reference to relevant previous work.

    Material and methods
    Provide sufficient detail to allow the work to be reproduced. Methods already published should be indicated by a reference: only relevant modifications should be described.

    Results
    Results should be clear and concise.

    Discussions
    This should explore the significance of the results of the work, not repeat them. A combined Results and Discussion section is often appropriate. Avoid extensive citations and discussion of published literature.

    Conclusions
    The main conclusions of the study may be presented in a short Conclusions section, which may stand alone or form a subsection of a Discussion or Results and Discussion section.

    Technical reports, News & Views, Letters to the Editor: These types of papers are not divided into sections after the summary, except for the reference list. The first paragraph serves as an introduction; acknowledgments are added as a final paragraph before the reference list.

    Tutorials are a combination of article and slides. Specific instructions are provided upon invitation. Authors are encouraged to submit Author Vitae at first submission. Please include in the manuscript a short (maximum 100 words) biography of each author, along with a passport-type photograph accompanying the other figures.

    Experimental design data analysis for 2-D PAGE and MS-based experiments:
    The experimental design must be provided and must include details of the number of biological and analytical replicates. Only one biological/analytical replicate will not be acceptable. In clinical studies, it is highly desirable that a power analysis predicting the appropriate sample size for subsequent statistical analysis of the data is carried out.

    For expression analysis studies, summary statistics (mean, standard deviation) must be provided and results of statistical analysis must be shown. Reporting fold differences alone is not acceptable. For comparative proteomics multivariant analysis of the variance should be used (Please consult: Valledor, L., Jorrin, JV (2010). Back to the basics: Maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses. J. Proteomics 74, 1-18).



    Proper terminology should be used. "Protein species" or "Gene product" are preferred terms when referring to "isoforms" and "allelic variants", respectively, (please consult Jungblut et al. The speciation of the proteome. Chemistry Central Journal 2008; 2: 16, and Schlüter et al. Finding one's way in proteomics: a protein species nomenclature. Chemistry Central Journal 2009; 3: 11). Terms, such as "differences in protein expression" and "induction/repression" should be avoided, since this terminology relates to gene regulation, and quantitative proteomics deals with the measure of differential abundances of spots (2DE) or peptide ions (LC-MS/MS).

    Authors must report the following: methods of data normalization, transformation, missing value handling, the statistical tests used, the degrees of freedom and the statistical package or program used. Where biologically important differences in protein (gene) expression are reported, confirmatory data (e.g. from Western blot, RT-PCR analysis, etc.) are desirable. For biomarker discovery/validation studies, the sensitivity and specificity of the biomarker(s) should be provided wherever possible. It is desirable that receiver operator characteristic (ROC) curves and areas under the curves are given. The method(s) used to generate the mass spectrometry data must be described. The name and version of the program used for database searching, the values of critical search parameters (e.g. the mass over charge (m/z) and the charge (z) of the precursor ion, fragment mass tolerance, cleavage rules used, allowance for number of missed cleavages and modifications) and the name and version of the database(s) searched must be provided. For each protein identified, measures of certainty (e.g. pvalues) must be provided. For MS/MS, the number of peptides used to identify a protein must be given as well as the sequence and charge state of each peptide. If new software or bioinformatic tool are employed or described, these should be made available (free or shareware) at least for reviewing purposes.



    Identification of proteins based solely on mass fingerprinting will be considered only if the sequence of the genome of the organism under study is known. For peptide mass fingerprinting, the number of peptides that match the sequence, the number of unmatched peaks, and the total percent of sequence coverage must be stated.

    Identification of proteins from organisms with unknown genome sequence will be accepted only if MS/MS-derived peptide sequence data have been used for database searching or BLAST analysis. The score for the highest ranked hit to an homologous, orthologous, or paralogous protein should be indicated.

    For experiments with large MS/MS data sets, estimates of the false positive rates are required (e.g. through searching randomized or reversed sequence databases). This information should be provided as supporting information. Where post-translational modifications are reported, the methods used to discover the modification must be described. The modification should be mapped to amino acid(s) by fragmentation analysis, but reported as ambiguous if mapping to a single amino acid is not possible. For isobaric modifications, evidence for assigning a specific modification must be provided and the spectra included as supporting information. Where protein sequence isoforms are reported, the peptide sequence that matches the unique amino acid sequence of a particular isoform must be provided. Fragmentation analysis of the appropriate peptides should be described.

    Graphical abstract

    A Graphical abstract is mandatory for this journal. It should summarize the contents of the article in a concise, pictorial form designed to capture the attention of a wide readership online. Authors must provide images that clearly represent the work described in the article. Graphical abstracts should be submitted as a separate file in the online submission system. Image size: please provide an image with a minimum of 531 × 1328 pixels (h × w) or proportionally more. The image should be readable at a size of 5 × 13 cm using a regular screen resolution of 96 dpi. Preferred file types: TIFF, EPS, PDF or MS Office files. See http://www.elsevier.com/graphicalabstracts for examples.
    Authors can make use of Elsevier's Illustration and Enhancement service to ensure the best presentation of their images also in accordance with all technical requirements: Illustration Service.

    Highlights

    Highlights are mandatory for this journal. They consist of a short collection of bullet points that convey the core findings of the article and should be submitted in a separate file in the online submission system. Please use 'Highlights' in the file name and include 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point). See http://www.elsevier.com/highlights for examples.

    Database linking

    Elsevier encourages authors to connect articles with external databases, giving their readers one-click access to relevant databases that help to build a better understanding of the described research. Please refer to relevant database identifiers using the following format in your article: Database: xxxx (e.g., TAIR: AT1G01020; CCDC: 734053; PDB: 1XFN). See http://www.elsevier.com/databaselinking for more information and a full list of supported databases.

    Artwork

    Electronic artwork

    General points
    • Make sure you use uniform lettering and sizing of your original artwork.
    • Save text in illustrations as "graphics" or enclose the font.
    • Only use the following fonts in your illustrations: Arial, Courier, Times, Symbol.
    • Number the illustrations according to their sequence in the text.
    • Use a logical naming convention for your artwork files.
    • Provide captions to illustrations separately.
    • Produce images near to the desired size of the printed version.
    • Submit each figure as a separate file.

    A detailed guide on electronic artwork is available on our website:
    http://www.elsevier.com/artworkinstructions
    You are urged to visit this site; some excerpts from the detailed information are given here.
    Formats
    Regardless of the application used, when your electronic artwork is finalised, please "save as" or convert the images to one of the following formats (note the resolution requirements for line drawings, halftones, and line/halftone combinations given below):
    EPS: Vector drawings. Embed the font or save the text as "graphics".
    TIFF: color or grayscale photographs (halftones): always use a minimum of 300 dpi.
    TIFF: Bitmapped line drawings: use a minimum of 1000 dpi.
    TIFF: Combinations bitmapped line/half-tone (color or grayscale): a minimum of 500 dpi is required.
    DOC, XLS or PPT: If your electronic artwork is created in any of these Microsoft Office applications please supply "as is".
    Please do not:
    • Supply embedded graphics in your wordprocessor (spreadsheet, presentation) document;
    • Supply files that are optimised for screen use (like GIF, BMP, PICT, WPG); the resolution is too low;
    • Supply files that are too low in resolution;
    • Submit graphics that are disproportionately large for the content.

    Figure captions
    Ensure that each illustration has a caption. Supply captions separately, not attached to the figure. A caption should comprise a brief title (not on the figure itself) and a description of the illustration. Keep text in the illustrations themselves to a minimum but explain all symbols and abbreviations used.

    Color artwork
    Please make sure that artwork files are in an acceptable format (TIFF (or JPEG), EPS (or PDF) or MS Office files) and with the correct resolution. If, together with your accepted article, you submit usable color figures then Elsevier will ensure, at no additional charge, that these figures will appear in color on the Web (e.g., ScienceDirect and other sites) in addition to color reproduction in print. For further information on the preparation of electronic artwork, please see http://www.elsevier.com/artworkinstructions.

    Tables

    Number tables consecutively in accordance with their appearance in the text. Place footnotes to tables below the table body and indicate them with superscript lowercase letters. Avoid vertical rules. Be sparing in the use of tables and ensure that the data presented in tables do not duplicate results described elsewhere in the article.

    References

    Citation in Text

    The numerical system of references should be used. References in the text should be cited by numbers in square brackets in the order of their citation.

    References are listed together in their order of appearance in a separate section at the end of the text under the heading References. All references should be numbered consecutively. References to journals should contain initials and names of all authors, article title, abbreviation of the name of the journal according to the List of Serial Title World Abbreviations (International Series Data System, 20, rue Bachaumont, 75002 Paris, France. ISBN 2-904938-02-8), year of publication, volume number, and page numbers. References to books should also include the title (of series and volumes), initials and names of the editor(s), the publisher and place of publication.

    Examples:

    Reference to a journal publication:
    [1] Resing KA, Ahn NG. Proteomics strategies for protein identification. FEBS Letters 2005;579:885-9.

    Reference to a book:
    [2] Rehm H. Protein Biochemistry and Proteomics. San Diego: Academic Press/Elsevier Inc; 2006.

    Reference to a chapter in an edited book or book series:
    [3] Morgan JW, Hettick JM, Russell DH. Peptide sequencing by MALDI 193-nm photodissociation TOF MS. In: Burlingame AL, editor. Methods in Enzymology, vol 402: Biological Mass Spectrometry. San Diego: Academic Press/Elsevier Inc; 2005, p.186-209.

    Reference to a paper as "in press" implies that it has been accepted for publication. Evidence (e.g., a photocopy of the note of acceptance from the journal concerned) should accompany the submitted typescript. Papers that are "in press" should be included as a number in the text. Other papers submitted before or simultaneously with the paper in question should be included as a number in the text and in the References section, stating the name of the journal. Copies of papers that are submitted elsewhere should be provided for inspection by the Editors. Omission of this information will delay publication and may lead to redating of a submitted manuscript. Papers presented at scientific meetings that are not available in published form should not be cited as references in the References section.

    Unpublished results should not be listed in the References section. In the text they are mentioned as follows: "(Tervoort MV and Glimcher J, unpublished data)". When unpublished results are cited, the data should be provided for the Editors' information when essential for proper evaluation, or if requested.

    A personal communication should be mentioned in the text as follows: "(Tervoort MV, personal communication)". Authors should not make unauthorized use of personal communications. Personal communications are not to be included in the Reference section.

    Reference management software
    This journal has standard templates available in key reference management packages EndNote (http://www.endnote.com/support/enstyles.asp) and Reference Manager (http://refman.com/support/rmstyles.asp). Using plug-ins to wordprocessing packages, authors only need to select the appropriate journal template when preparing their article and the list of references and citations to these will be formatted according to the journal style which is described below.

    Video data

    Elsevier accepts video material and animation sequences to support and enhance your scientific research. Authors who have video or animation files that they wish to submit with their article are strongly encouraged to include links to these within the body of the article. This can be done in the same way as a figure or table by referring to the video or animation content and noting in the body text where it should be placed. All submitted files should be properly labeled so that they directly relate to the video file's content. In order to ensure that your video or animation material is directly usable, please provide the files in one of our recommended file formats with a preferred maximum size of 50 MB. Video and animation files supplied will be published online in the electronic version of your article in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com. Please supply 'stills' with your files: you can choose any frame from the video or animation or make a separate image. These will be used instead of standard icons and will personalize the link to your video data. For more detailed instructions please visit our video instruction pages at http://www.elsevier.com/artworkinstructions. Note: since video and animation cannot be embedded in the print version of the journal, please provide text for both the electronic and the print version for the portions of the article that refer to this content.

    AudioSlides

    The journal encourages authors to create an AudioSlides presentation with their published article. AudioSlides are brief, webinar-style presentations that are shown next to the online article on ScienceDirect. This gives authors the opportunity to summarize their research in their own words and to help readers understand what the paper is about. More information and examples are available at http://www.elsevier.com/audioslides. Authors of this journal will automatically receive an invitation e-mail to create an AudioSlides presentation after acceptance of their paper.

    Supplementary data

    Elsevier accepts electronic supplementary material to support and enhance your scientific research. Supplementary files offer the author additional possibilities to publish supporting applications, high-resolution images, background datasets, sound clips and more. Supplementary files supplied will be published online alongside the electronic version of your article in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com. In order to ensure that your submitted material is directly usable, please provide the data in one of our recommended file formats. Authors should submit the material in electronic format together with the article and supply a concise and descriptive caption for each file. For more detailed instructions please visit our artwork instruction pages at http://www.elsevier.com/artworkinstructions.

    Submission checklist

    The following list will be useful during the final checking of an article prior to sending it to the journal for review. Please consult this Guide for Authors for further details of any item.
    Ensure that the following items are present:
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    Appendix

    Standard abbreviations allowed to be used without explanation or definition in all articles published in the Journal of Proteomics.

    A absorbance
    ACES 2-[(2-amino-2-oxoethyl)amino] ethanesulphonic acid
    ACN acetonitrile
    A/D analog to digital converter
    AEBSF 4-(2-aminoethyl)benzenesulphonyl fluoride
    amu atomic mass unit
    ANOVA analysis of variance
    API atmospheric pressure ionization
    AUC area under curve
    Bis N,N'-methylenebisacrylamide
    bp base pairs
    BSA bovine serum albumin
    %C cross-linking agent (g/100 mL)/%T
    CAPS 3-(cyclohexylamino)-1-propanesulphonic acid
    CBB Coomassie Brilliant Blue
    CCD charge-coupled device
    CD circular dicroism
    CE capillary electrophoresis
    CEC capillary electrochromatography
    CFE continuous flow electrophoresis
    CHAPS 3-[(3-cholamidopropyl)dimethylamonio]-1-propanesulphonate
    CHCA &agr;-cyano-4-hydroxycinnamic acid
    CHES 2-(N-cyclohexylamino)ethanesulphonic acid
    CID collision-induced dissociation
    CIEF capillary isoelectric focusing
    CMC critical micelle concentration
    Con A Concanavalin A
    CNS central nervous system
    cpm counts per minute
    CTAB etyltrimethylammonium bromide
    CV coefficient of variation
    CZE capillary zone electrophoresis
    1-D one-dimensional
    2-D two-dimensional
    Da dalton (molecular mass)
    2-DE two-dimensional electrophoresis
    DIGE fluorescence difference gel electrophoresis
    DGGE denaturing gradient gel electrophoresis
    DMEM Dulbecco's modified Eagle medium
    DMF N,N-dimethylformamide
    DMSO dimethyl sulphoxide
    DOC sodium deoxycholate
    dsDNA double-stranded DNA
    DTE dithioerithriol
    DTT dithiothreitol
    ECL enhanced chemiluminescence
    EDTA ethylenediaminetetraacetic acid
    EEO electroendosmosis
    EGTA ethylene glycol-bis(&bgr;-aminoethylether)-N,N,N',N'-tetraacetic acid
    EKC electrokinetic chromatography
    ELISA enzyme-linked immunosorbent assay
    EMSA electrophoretic mobility shift assay
    EOF electroosmotic flow
    ER endoplasmic reticulum
    ESI electrospray ionization
    EST expressed sequence tag
    EUPA European Proteome Association
    FAB fast atom bombardment
    FACS fluorescence activated cell sorting
    FBS fetal bovine serum
    FCS fetal calf serum
    FIGE field inversion gel electrophoresis
    FITC fluorescein isothiocyanate
    FT Fourier transform
    FT-ICR Fourier transform-ion cyclotron resonance
    GC gas chromatography
    GIF graphic interchange format
    GRAVY grand average hydrophobicity
    GSH glutathione
    GST glutathione-S-transferase
    HE hematoxylin and eosin
    HEPES N-(2-hydroxyethyl)piperazine-2'-(2-ethanesulphonic acid)
    HPCE high-performance capillary electrophoresis
    HPLC high-performance liquid chromatography
    HRP horseradish peroxidase
    HSA human serum albumin
    HSP heat shock protein
    HTML hypertext mark-up language
    HUPO Human Proteome Organisation
    HVR hypervariable region
    ICAT isotop-coded affinity tag
    ICR ion cyclotron resonance
    id inside diameter
    IEF isoelectric focusing
    Ig immunoglobulin
    IMAC immobilized metal affinity capture
    IPG immobilized pH gradient
    IT ion trap
    iTRAQ isobaric tag for relative and absolute quantitation
    kbp kilobase pairs
    kDa kilodalton (molecular mass)
    LC liquid chromatography
    LED light-emitting diode
    LOD limit of detection
    LOQ limit of quantitation
    mAb monoclonal antibody
    MALDI-MS matrix-assisted laser-desorption ionization-mass spectrometry
    Mbp megabase

    MEKC micellar electrokinetic capillary chromatography
    MES 2-(N-morpholino)ethanesulphonic acid
    MHC major histocompatibility complex
    MOPS 3-(N-morpholino)propanesulphonic acid
    Mr relative molecular mass (dimensionless)
    MS mass spectrometry
    MS/MS tandem mass spectrometry
    MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
    m/z mass-to-charge ratio
    NC nitrocellulose NEPHGE nonequilibrium pH gradient electrophoresis
    NMR nuclear magnetic resonance
    NP-40 Nonidet P-40
    od outside diameter
    OD optical density
    OFAGE orthogonal field alternation gel electrophoresis
    ORF open reading frame
    PAGE polyacrylamide gel electrophoresis
    PBS phosphate-buffered saline
    PCR polymerase chain reaction
    PDMS polydimethylsiloxane
    PED pulsed electrochemical detection PEG polyethylene glycol
    PFGE pulsed-field gel electrophoresis
    PFU plaque-forming units
    pI isoelectric point
    PMF peptide mass fingerprinting
    PMS phenazine methosulphate
    PMSF phenylmethylsulphonyl fluoride
    PMT photomultiplier tube
    PSD post-source decay
    PTFE polytetrafluoroethylene
    PTH phenylthiohydantoin
    PTM post-translational modification
    PVA polyvinyl alcohol
    PVDF polyvinylidene difluoride
    PVP polyvinylpyrrolidone
    Q-TOF quadrupole time-of-flight
    RACE rapid amplification of cDNA ends
    RFLP restriction fragment length polymorphism
    RIA radioimmunoassay
    ROS reactive oxygen species
    RP reversed phase
    rpm revolutions per minute
    RSD relative standard deviation
    RT-PCR reverse transcriptase-PCR
    SAGE serial analysis of gene expression
    SD standard deviation
    SDS sodium dodecyl sulphate
    SEC size-exclusion chromatography
    SELDI surface-enhanced laser desorption/ionization
    SEM standard error of the mean
    SIM selected ion monitoring
    S/N signal-to-noise ratio
    SPE solid-phase extraction
    SPR surface plasmon resonants
    SSCP single-strand conformation polymorphism
    ssDNA single-stranded DNA
    SSP sample spot number
    STR short tandem repeat
    %T total gel concentration (acrylamide plus cross-linking agent; g/100 mL)
    TBS Tris-buffered saline
    TCA trichloroacetic acid
    TEMED N,N,N',N'-tetramethylethylenediamine
    TFA trifluoroacetic acid
    THF tetrahydrofuran
    TIC total ion current
    TLC thin-layer chromatography
    TNF tumour necrosis factor
    TOF time of flight
    Tris tris(hydroxymethyl)aminomethane
    TRITC tetramethylrhodamine isothiocyanate
    URL uniform resource locator
    UTR untranslated region
    UV ultraviolet
    Vh volt ×hours
    z ion charge



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