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Molecular and Cellular Proteomics Instructions for Authors
Table of Contents
Organization of the Manuscript
Text
References
Tables and Figures
RGB Workflow
Videos and Supplemental Data
Page Charges
Color Figures
Halftones
Reprints
NIH Funded Aritcles
Author Choice Option
Publication Guidlines for the Analysis and Documentation of Peptide and Protein Identifications
Check list for publication of Peptide & Protein Identification data in MCP
Publication Guidelines for Preparing Manuscripts Describing Research in Clinical Proteomics
Chemical and Mathematical Usage
Protein and Nucleic Acid Sequences
Crystallographic Studies
Database Accession Hyperlinks For MCP Online
All submitted research manuscripts should contain original information not previously published and not under consideration for publication elsewhere. Papers must be written in English. Authors must identify other manuscripts on related subjects from the authors’ laboratory in any journal and provide copies for the reviewers upon request.
Authors are required to submit manuscripts electronically using the Online Submission and Review System (OSRS) available at http://www.mcponline.org/submit.
Only PDF format may be submitted online to MCP.
All color art must be in RGB format (click here for further information).
WEB SUBMISSION
Initial Submission as a PDF — 5 Easy Steps
Step 1. Prepare the text in Microsoft Word 6.0 (Word 2001 for MAC) or a later version.
Step 2. Prepare graphics at publication quality resolution, using applications capable of generating high resolution TIFF or EPS files. It will be necessary to submit your graphics in one of these formats if it is accepted. For important information on the preparation of graphics in TIFF or EPS formats, go to http://art.cadmus.com/da/mcp/guidelines.jsp. Number each figure. All color art must be in RGB format. Rapid Inspector is now available for use by authors. The Rapid Inspector software allows authors to check their figure files against JBC standards for format, resolution, color space and other figure requirements. Click here to download Rapid Inspector to your computer.
Step 3. Using Adobe Acrobat (see http://adobe.com/products/main.html for information), save your manuscript text and graphics in a single file in PDF format with the figures at the end. The file name should be one word with no spaces and a .pdf extension at the end (e.g., manuscript.pdf ). Authors are responsible for assuring the accuracy and quality of the PDF. Please consult your Adobe Acrobat manual for instructions regarding PDF file creation.
Step 4. Print the PDF file and carefully review text and figures. It is the author’s responsibility to assure that the manuscript is suitable for review, particularly figures. Manuscripts that do not have figures of sufficient quality for scientific review will be returned to authors. Check the PDF file size. Most files should be around 1 MB, but not larger than 5 MB. If the file is larger than 5 MB, you may adjust the default settings of Adobe Acrobat to create a smaller size file. If you need help, please contact the MCP office at mcp{at}asbmb.org.
Step 5. Submit the necessary information using the submission template at the website http://www.mcponline.org/submit. You will need:
If your manuscript is accepted for publication, we will accept only graphics saved as TIFF or EPS files for the redactory process. The list of acceptable Mac OS and Microsoft Windows graphics applications may be found at http://art.cadmus.com/da/mcp/applications.jsp. These applications can be used to successfully create high quality TIFF and EPS files, and you will find instructions on how to properly save the files at this URL. Because more applications are added as testing continues, please review this list periodically. For graphics, we cannot accept certain application programs such as Microsoft Office (PowerPoint, Word, Excel, Access), Corel Perfect Office (WordPerfect, Quattro Pro, Presentation), Lotus SmartSuite (Freelance Graphics, 1-2-3, Approach, WordPro), and SigmaPlot.
Revisions – Easy Instructions:
Go to http://www.mcponline.org/submit and begin the submission of your revised manuscript. You will need.
In the event the revised manuscript is accepted, the PDF file version will be published as a Paper in Press. Therefore it is essential that the final revised version of your manuscript is of publication quality and free of errors. Please do not underline or highlight revisions.
ORGANIZATION OF THE MANUSCRIPT
Title:
Title Page:
Running Title:
Abbreviations:
Summary:
Introduction:
Experimental Procedures:
Results:
Discussion:
References for journals and books should be in the following styles:
1. MacDonald, G. M., Steenhuis, J. J., and Barry, B. A. (1995) A difference fourier transform infrared spectroscopic study of chlorophyll oxidation in hydroxylamine-treated photosystem II. J. Biol.Chem. 270, 8420-8428
2. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., pp. 1-50, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Journal names are abbreviated according to Chemical Abstracts. Authors are fully responsible for the accuracy of the references.
Footnotes are used to cite manuscripts in preparation, unpublished observations, and personal communications. Authors are responsible for obtaining written approval for all personal communications and sending a copy of the manuscript to those cited. The Editor may request proof of such approval.
All abbreviations used in the text and not found in the MCP Glossary or list of standard abbreviations (Table I) must be defined on page 3 of the manuscript. These will be added to the MCP Glossary at the time of acceptance. Abbreviations or acronyms that have already been used must be changed to a unique description. The abbreviations of some important biochemical compounds, e.g., ATP, NADH, DNA, and amino acids in proteins, need not be defined. Names of enzymes are usually not abbreviated except in terms of the substrates for which there are accepted abbreviations, e.g., ATPase and RNase.
The trivial and systematic names of enzymes should be those recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) in "Enzyme Nomenclature, Recommendations, 1992" (1992, Academic Press).
Notes added in proof to a manuscript only with the consent of the Editor.
Errors in a published paper will be corrected in the Journal in the "Additions and Corrections" section. Although these may also be the subject of letters to the Editor, such comments will be hyperlinked to the original article.
The number of tables and figures used to present data essential to illustrate or prove a point should be kept to a minimum. Very complex or large tables (for example, amino acid or nucleic acid sequences with alignments) should be submitted as a figure. It is also possible to submit complex data that are difficult to print as a supplement to MCP Online (see below).
Tables should have titles and sufficient experimental detail in a legend immediately following the title, to be understandable without reference to the text. Each column in a table must have a heading, and abbreviations, when necessary, should be defined in the legend. Please include your tables in the Word file you submit with the text to Cadmus.
Figures should have titles and explanatory legends containing sufficient detail to make the figure easily understood. All legends should be printed consecutively in a separate section of the manuscript. Appropriately sized numbers, letters, and symbols should be used, so they are no smaller than 2 mm in size after reduction to a single column width (87 mm), a 1.5-column width (120 mm), or a full 2-column width (178 mm). Superscript and subscript characters are not excluded from this rule. Numbers, letters, and symbols used in multipaneled figures must be consistent. The abscissa and ordinate should be clearly labeled with appropriately sized type, and units of measurement must be given. Failure to comply with these specifications will require new figures and delay publication. Scales for plotting the data should be marked by short index lines, but every index line need not be numbered. Use standard symbols found in MS Word, with symbols and curves identified in the legend and not on the figure. Indicate the figure number on each figure.
On the rare occasion an author cannot prepare a figure as an electronic file, the ASBMB editorial office should be contacted for assistance and instructions at mcp{at}asbmb.org.
There will be a charge of $25 per figure for publication of halftone figures. We encourage authors to use color graphics when they will enhance the presentation of the data. The cost is $300 for each illustration containing color.
Note: As of January 2006 figures will be published in color only if identified as color by your "color mode" selection. If you select black and white, files supplied in color will be converted to black and white for publication purposes. As of January 2006 color figures should be supplied in RGB color mode rather than CMYK to optimize the quality of color for online publications.
ELECTRONIC FIGURES
The original submission of both text and graphics should be as a single Adobe Acrobat PDF file, because you can review the electronic version of your manuscript for accuracy before online submission. Submitting your manuscript in PDF format will also expedite the review process, because it is this version that is circulated on the Web for review. For more information on the Adobe Acrobat application program go to http://www.adobe.com/products/acrobat/main.html.
Create your graphics using applications that are capable of preparing high resolution TIFF or EPS files acceptable for publication. Although you will initially submit graphics within the PDF file, if your paper is accepted we will require submission of graphics as separate TIFF or EPS files at publication quality resolution for print and online publication. For important information on the preparation of graphics in TIFF or EPS, go to http://art.cadmus.com/da/mcp/guidelines.jsp.
We will accept only graphics saved as TIFF or EPS files. The list of acceptable graphic Mac OS and Microsoft Windows applications may be found at http://art.cadmus.com/da/mcp/applications.jsp. These applications can be used to successfully create high quality TIFF and EPS files, and you will find instructions on how to save them properly at this URL. Because more applications are added as testing continues, please review this list periodically. For graphics, we cannot accept certain application programs such as Microsoft Office (PowerPoint, Word, Excel, Access), Corel Perfect Office (WordPerfect, Quattro Pro, Presentations), Lotus SmartSuite (Freelance Graphics, 1-2-3, Approach, and WordPro), and SigmaPlot, which were not intended for high resolution imaging necessary for publication.
MCP is now in an RGB (Red, Green, Blue) workflow for color figures. Prior to January 1, 2006, authors were required to submit figures in CMYK (Cyan, Magenta, Yellow, blacK) color mode, as this is the native color mode for the printing process and thus optimizes color for press. As of January 1, 2006, all color figures should be submitted in RGB format. Images supplied by authors in RGB color will retain the brilliant reds, greens, and blues for online publication, but may experience a color shift in printed form. To learn more, please see http://art.cadmus.com/da/mcp/index.jsp.
If you require further information, please send an E-mail query to mcp{at}asbmb.org.
The MCP On-line provides the opportunity for authors to include data impossible or impractical to include in the printed JOURNAL. We feel that the ability to include such data in MCP On-line will substantially enhance an author's ability to communicate important research information and will also greatly benefit readers.
We strongly encourage authors to include data such as videos, 3-D structures/images, sequence alignments, and data sets that are very large such as those obtained with microarray hybridization experiments. These data will be reviewed as a part of the normal manuscript review process and will be judged by the same criteria. Only data that are uniquely suited to the On-line journal and which substantially contribute to the manuscript will be accepted. Data files can be prepared in Plain Text, MS Word, HTML Page, MS Excel, TIFF, JPEG or GIF. When practical supplemental data files should be converted and submitted as PDF files. Movies and large excel files should be submitted in their native formats.
VIDEOS
Videos should be submitted in QuickTime 3.0 or higher format and may be prepared on either a PC or Mac computer. All videos should be submitted at the desired reproduction size and length. To avoid excessive delays in downloading the files, videos should be no more than 5 MB in size and 30 to 60 seconds in length. Authors are encouraged to use QuickTime's "compress" option when preparing files, to help control file size. Additionally, cropping frames and image sizes can significantly reduce file sizes. Files submitted can be looped to play more than once, provided file size does not become excessive. Authors will be notified if problems exist with videos as submitted and will be asked to modify them. No editing will be done to the videos at the editorial office. All changes are the responsibility of the author.
IMPORTANT: One traditional still image of the author's choosing must be submitted per video. This image will be published to act as a link from the text to the full video file. It will also appear in the text of the printed journal in place of the video. Please indicate clearly in your text whether a figure has a video associated with it, and be sure to indicate the name of the corresponding video file. A brief figure legend should also be provided. The figures should be prepared using the guidelines for figures indicated earlier in these instructions. For more information regarding the submission of videos, please contact the MCP editorial office.
Chemical and Mathematical Usage
Table II lists the abbreviations for units of measurement and certain physical and chemical quantities used by MCP without definition. Also listed are the prefixes that can be added to names of units and the multipliers indicated by each prefix.
Chemical equations, structural formulas, and mathematical equations should be placed between successive lines of text. They should also be prepared the same way as figures for direct photographic reproduction and should be included at the end of the manuscript. In general, the rules and recommendations of the IUBMB and the International Union of Pure and Applied Chemistry (IUPAC) will be used for abbreviation of chemical names, nomenclature of chemical compounds, enzyme nomenclature, isotopic compounds, optically active isomers, and spectroscopic data. Table III lists references to publications of the rules and recommendations of the International Scientific Unions that may be consulted for detailed information.
Protein and Nucleic Acid Sequence
Newly reported nucleotide or protein sequences must be deposited in GenBank or EMBL databases, and an accession number must be obtained BEFORE the paper is accepted in the Associate Editor's office. Access to the information in the database must be available at the time of publication. Authors are responsible for arranging release of data at the time of publication. The authors must also provide a statement in the manuscript that this sequence has been scanned against the database, all sequences with significant relatedness to the new sequence must be identified, and their accession numbers must be included.
Authors of accepted papers containing nucleotide sequences must submit the sequence data, preferably in computer-readable form or by electronic mail, and a copy of the paper to any of the following:
GenBank: GenBank Submissions, National Center for Biotechnology Information, 8600 Rockville Pike, Building 38A, Room 8N-805, Bethesda, MD 20894. Tel.: 301-496-2475; World Wide Web: http://www.ncbi.nih.gov/Genbank/
EMBL Nucleotide Sequence Submissions: European Bioinformatics Institute, Hinxton Hall, Hinxton, Cambridge CB10 1SD,
DNA Data Bank of Japan, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411, Japan; Tel.: 81-559-81-6853; Fax: 81-559-81-6849; World Wide Web: http://www.ddbj.nig.ac.jp/.
An accession number must be obtained before the manuscript is sent to the printer. A footnote will be included in the paper, indicating that such a deposit has been made. Submission to any data bank is sufficient to ensure entry in all. When nucleotide probes are used, the ends of the probes should be explicitly identified by reference to published nucleotide number or restriction maps, or, if unpublished, the information should be included in the Experimental Procedures section.
Authors of papers describing new structure determinations must submit to the Protein Data Bank at Research Collaboratory for Structural Bioinformatics http://www.rcsb.org/pdb all structural data required to validate the conclusions, including both x-ray amplitudes and phases and the derived atomic coordinates. MCP policy requires that such data be available upon request immediately after publication. For NMR structures, data deposited should include resonance assignments and all restraints used in structure determination (NOEs, spin-spin coupling constants, amide exchange rates, etc.) and the derived atomic coordinates for both an individual structure and for a family of acceptable structures. A footnote will be inserted in the manuscript saying that the necessary data have been deposited. If the paper discusses a protein structure only at the level of the main chain -carbon atoms, only -carbon coordinates need be deposited.
If the discussion involves higher resolution data (for example, all atoms in the active site of an enzyme), the full set of x-ray data and the coordinate list must be deposited. After completion of the editorial process, the manuscript will not be accepted until confirmation has been received from the author, if not initially supplied, that the required information has been sent to the Protein Data Bank and will be available at the time of publication.
Database Accession Hyperlinks for MCP Online
The electronic version of MCP employs direct hyperlink access to entries in databases such as GenBank. Authors are required to provide accession numbers to databases for all newly described molecular structures reported in their manuscripts.
In addition, authors are strongly encouraged to include accession numbers for any database information that would aid a reader in understanding the authors' paper, regardless of who had deposited the database information.
For the database hyperlinks to be generated, the citation must appear as a footnote and be written exactly as follows:
1. GenBank = GenBank Accession Number XYYYYY
2. Molecular Modeling Database = MMDB Number XYYY
3. NCBI Protein Database = NCB Accession Number XXXXX
4. Swiss Protein Database = Swiss-Prot Number XXXX
5. Enzyme Collection Number = xx.yy.zz.bb
6. Research Collaboratory for Structural Bioinformatics Protein Databank = PDB Number XXXX
The molecule or structure that an accession number refers to can be identified through the NCBI Entrez utility at http://www.ncbi.nlm.nih.gov/Entrez/.
The following shows how references to databases should be written in a footnote:
"The nucleotide sequence for the artificial sperm whale myoglobin gene has been deposited in the GenBank database under GenBank Accession Number (Reference). The amino acid sequence of this protein can be accessed through the NCBI Protein Database under NCBI Accession Number (Reference). The atomic coordinates for the crystal structure of this protein are available in the Molecular Modeling Database http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.dtl under MMDB Number (Reference)."
Authors may include their E-mail address and home page URL. However, authors cannot cite in the manuscript that additional data not presented in the manuscript are available at the home page. Home page URLs will not be hyperlinked.
There is a per-page charge for all published manuscripts, currently $65 per page for the first 10 pages and, starting with page 11, a charge of $130 per-page. All page and color fees must be paid by the authors. It is ASBMB Journal policy not to accept requests for page or color waivers. In extreme situations for developing economies, an exemption may be considered for only page charges if requested at the time of submission.
Page Charges -- $65 per journal page for the first 10 pages; $130 for each additional page
Color Figures -- We encourage authors to use color figures when they will enhance the presentation of the data. The cost is $300 for each illustration containing color. (Note: When using the electronic submission system, any figure submitted in color will be reviewed and processed with the understanding that the figure will be published in color.)
Halftones -- $25 per figure
Reprints – Pricing is based on quantity ordered.
NIH Funded Articles automatically deposited in PubMed Central.
Author Choice Option - $1500 for ASBMB Members. $2000 for Non-ASBMB Members. Join ASBMB NOW!
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