Author information pack

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.

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.

Page charges

This journal has no page charges.

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/ethicalguidelines.

Policy and ethics

The work described in your article must have 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. This must be stated at an appropriate point in the article.

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

All authors are requested to disclose any actual or potential conflict of interest including any financial, personal or other relationships with other people or organizations within three years of beginning the submitted work that could inappropriately influence, or be perceived to influence, their work. See also http://www.elsevier.com/conflictsofinterest. Further information and an example of a Conflict of Interest form can be found at: http://elsevier6.custhelp.com/app/answers/detail/a_id/286/p/7923/.

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

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). Acceptance of the agreement will ensure the widest possible dissemination of information. 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.

Retained author rights

As an author you (or your employer or institution) retain certain rights; for details you are referred to: http://www.elsevier.com/authorsrights.

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. Please see http://www.elsevier.com/funding.

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 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 wordprocessing software

It is important that the file be saved in the native format of the wordprocessor 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 wordprocessor'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 wordprocessor.

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.

Color artwork
Please make sure that artwork files are in an acceptable format (TIFF, EPS 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) regardless of whether or not these illustrations are reproduced in color in the printed version. For color reproduction in print, you will receive information regarding the costs from Elsevier after receipt of your accepted article. Please indicate your preference for color in print or on the Web only. For further information on the preparation of electronic artwork, please see Please note: Because of technical complications which can arise by converting color figures to "gray scale" (for the printed version should you not opt for color in print) please submit in addition usable black and white versions of all the color illustrations.

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.

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:
One author has been designated as the corresponding author with contact details:

• E-mail address
• Full postal address
• Phone numbers

All necessary files have been uploaded, and contain:

• Keywords
• Graphical Abstract
• Highlights bullets
• "Significance" paragraph after the Abstract
• All figure captions
• All tables (including title, description, footnotes)

• Manuscript has been 'spell-checked' and 'grammar-checked'
• References are in the correct format for this journal
• All references mentioned in the Reference list are cited in the text, and vice versa
• Permission has been obtained for use of copyrighted material from other sources (including the Web)
• Color figures are clearly marked as being intended for color reproduction on the Web (free of charge) and in print, or to be reproduced in color on the Web (free of charge) and in black-and-white in print
• If only color on the Web is required, black-and-white versions of the figures are also supplied for printing purposes.

For any further information please visit our customer support site at http://support.elsevier.com.

• Line numbers have been added to your manuscript file
• Does the information on mass spectrometry data meet the Guidelines of the journal? (JPROT encourages authors to read the MIAPE-MS document available addressing http://www.psidev.info/sites/default/files/MIAPE_MS_2.98.pdf).
• Does your paper cite databank accession codes? (J. Proteomics encourages authors to adopt the linking scheme to link out from ScienceDirect to CRAN, the Comprehensive R Archive Network (http://cran.r-project.org/). More info about this kind of linking is available at http://www.elsevier.com/databaselinking).

Offprints

The corresponding author, at no cost, will be provided with a PDF file of the article via e-mail. The PDF file is a watermarked version of the published article and includes a cover sheet with the journal cover image and a disclaimer outlining the terms and conditions of use.

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
CAN 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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