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Manuscript Requirements and Style Guide

  1. General Standards
    1. Article Types

      It is helpful to familiarise yourself with the different types of articles published by journals. Although it may appear there are a large number of types of articles published due to the wide variety of names they are published under, most articles published are one of the following types: Original Research, Review Articles, Short reports or Letters, Case Studies, Methodologies.

      Original Research

      This is the most common type of journal manuscript used to publish full reports of data from research. It may be called an Original Article, Research Article, Research, or just Article, depending on the journal. The Original Research format is suitable for many different fields and different types of studies. It includes full Introduction, Methods, Results, and Discussion sections.

      Short reports or Letters

      These papers communicate brief reports of data from original research that editors believe will be interesting to many researchers, and that will likely stimulate further research in the field. As they are relatively short the format is useful for scientists with results that are time sensitive (for example, those in highly competitive or quickly-changing disciplines). This format often has strict length limits, so some experimental details may not be published until the authors write a full Original Research manuscript. These papers are also sometimes called Brief communications.

      Review Articles

      Review Articles provide a comprehensive summary of research on a certain topic, and a perspective on the state of the field and where it is heading. They are often written by leaders in a particular discipline after invitation from the editors of a journal. Reviews are often widely read (for example, by researchers looking for a full introduction to a field) and highly cited. Reviews commonly cite approximately 100 primary research articles.

      TIP: If you would like to write a Review but have not been invited by a journal, be sure to check the journal website as some journals to not consider unsolicited Reviews. If the website does not mention whether Reviews are commissioned it is wise to send a pre-submission enquiry letter to the journal editor to propose your Review manuscript before you spend time writing it.

      Case Studies

      These articles report specific instances of interesting phenomena. A goal of Case Studies is to make other researchers aware of the possibility that a specific phenomenon might occur. This type of study is often used in medicine to report the occurrence of previously unknown or emerging pathologies.

      Methodologies or Methods

      These articles present a new experimental method, test or procedure. The method described may either be completely new, or may offer a better version of an existing method. The article should describe a demonstrable advance on what is currently available.

    2. Manuscript Length

      AEE encourages its authors to closely follow the article word count lengths. The abstract and manuscript should be a maximum of 350 and 12,000 words in length. The manuscript length includes only the main body of the text, footnotes and all citations within it, and excludes abstract, section titles, figure and table captions, funding statements, acknowledgments and references in the bibliography.

    3. Language Editing

      AEE requires manuscripts submitted to meet international standards for English language to be considered for publication.

      For authors who would like their manuscript to receive language editing or proofing to improve the clarity of the manuscript and help highlight their research, AEE recommends the language-editing services provided by the following external organizations:


      AEE is pleased to recommend language-editing service provided by Editage to authors who believe their manuscripts would benefit from professional editing. These services may be particularly useful for researchers for whom English is not the primary language. They can help to improve the grammar, syntax and flow of your manuscripts prior to submission. AEE authors can find it by visiting the following link:

      The Charlesworth Group

      AEE recommends the Charlesworth Group Author Services, who has a long standing track record in language editing and proofing. AEE authors can find it by visiting the following link:

      Note that sending your manuscript for language editing does not imply or guarantee that it will be accepted for publication by an AEE journal. Editorial decisions on the scientific content of a manuscript are independent of whether it has received language editing or proofing by the partner services, or other services.

    4. Search Engine Optimization (SEO)

      There are a few simple ways to maximize your article’s discoverability. Follow the steps below to improve search results of your article:

      • Include a few of your article's keywords in the title of the article;
      • Do not use long article titles;
      • Pick 5 to 8 keywords using a mix of generic and more specific terms on the article subject(s);
      • Use the maximum amount of keywords in the first 2 sentences of the abstract;
      • Use some of the keywords in level 1 headings.
    5. Title

      The title is written in title case, centred, and in 20 point bold Times New Roman font at the top of page.

      The title should be concise, omitting terms that are implicit and, where possible, be a statement of the main result or conclusion presented in the manuscript. Abbreviations should be avoided within the title.

      Witty or creative titles are welcome, but only if relevant and within measure. Consider if a title meant to be thought-provoking might be misinterpreted as offensive or alarming. In extreme cases, the editorial office may veto a title and propose an alternative.

      Authors should try to avoid, if possible:

      • Titles that are a mere question without giving the answer.
      • Unambitious titles, for example starting with "Towards", "A description of", "A characterization of", "Preliminary study on".
      • Vague titles, for example starting with "Role of...", "Link between...", "Effect of..." that do not specify the role, link, or effect.
      • Include terms that are out of place, for example the taxonomic affiliation apart from species name.
    6. Authors and Affiliations

      All names are listed together and separated by commas. Provide exact and correct author names as these will be indexed in official archives. Affiliations should be keyed to the author's name with superscript numbers and be listed as follows: Laboratory, Institute, Department, Organization, City, State abbreviation (USA, Canada, Australia), and Country (without detailed address information such as city zip codes or street names).

      Example: Elezabeth Mathew, Faculty of Computer Science, Brawijaya University, Malang, East Java, Indonesia

      The Corresponding Author(s) should be marked with an asterisk. Provide the exact contact email address of the corresponding author(s) in a separate section.

      Corresponding Author: Prof. Elezabeth Mathew, [email protected]

    7. Consortium/Group and Collaborative Authors

      Consortium/group authorship should be listed in the manuscript with the other author(s). In cases where authorship is retained by the consortium/group, the consortium/group should be listed as an author separated by “,” or “and”. Consortium/group members can be listed in a separate section at the end of the manuscript.

      Example: D. Pitica, Barbara Smith and the Collaborative Working Group.

      In cases where work is presented by the author(s) on behalf of a consortium/group, it should be included in the manuscript author list separated with the wording “for” or “on behalf of”. The consortium/group will not retain authorship.

      Example: D. Pitica and Al Marin on behalf of The Collaborative Working Group.

    8. Headings and Sub-headings

      Except for special names (e.g. GABAergic), capitalize only the first letter of headings and subheadings. Headings and subheadings need to be defined in Times New Roman, 12, bold. You may insert up to 5 heading levels into your manuscript (not more than for example: Heading title).

    9. Abstract

      As a primary goal, the abstract should render the general significance and conceptual advance of the work clearly accessible to a broad readership. In the abstract, minimize the use of abbreviations and do not cite references. The text of the abstract section should be in 10 point normal Times New Roman.

    10. Keywords

      All article types: you may provide up to 8 keywords; at least 5 are mandatory.

    11. Text

      The body text is in 10 point normal Times New Roman. The entire document should be single-spaced. Your manuscript should be written using either LaTeX or MS-Word.

    12. Nomenclature
      • The use of abbreviations should be kept to a minimum. Non-standard abbreviations should be avoided unless they appear at least four times, and defined upon first use in the main text. Consider also giving a list of non-standard abbreviations at the end, immediately before the Acknowledgments.
      • Equations should be inserted in editable format from the equation editor.
      • Italicize Gene symbols and use the approved gene nomenclature where it is available. For human genes, please refer to the HUGO Gene Nomenclature Committee (HGNC). New gene symbols should be submitted here. Common Alternative gene aliases may also be reported, but should not be used alone in place of the HGNC symbol. Nomenclature committees for other species are listed here. Protein products are not italicized.
      • We encourage the use of Standard International Units in all manuscripts.
      • Chemical compounds and biomolecules should be referred to using systematic nomenclature, preferably using the recommendations by IUPAC.
      • Astronomical objects should be referred to using the nomenclature given by the International Astronomical Union provided here.
      • Life Science Identifiers (LSIDs) for ZOOBANK registered names or nomenclatural acts should be listed in the manuscript before the keywords. An LSID is represented as a uniform resource name (URN) with the following format:
        For more information on LSIDs please see Inclusion of Zoological Nomenclature section.
    13. Sections

      Your manuscript is organized by headings and subheadings. For Original Research Articles, it is recommended to organize your manuscript in the following sections or their equivalents for your field:

      • Introduction
        Succinct, with no subheadings.
      • Materials and Methods
        This section may be divided by subheadings. This section should contain sufficient detail so that when read in conjunction with cited references, all procedures can be repeated. For experiments reporting results on animal or human subject research, an ethics approval statement should be included in this section (for further information, see section Materials and Data Policies)
      • Results
        This section may be divided by subheadings. Footnotes should not be used and have to be transferred into the main text.
      • Discussion
        This section may be divided by subheadings. Discussions should cover the key findings of the study: discuss any prior art related to the subject so to place the novelty of the discovery in the appropriate context; discuss the potential short-comings and limitations on their interpretations; discuss their integration into the current understanding of the problem and how this advances the current views; speculate on the future direction of the research and freely postulate theories that could be tested in the future.
    14. Acknowledgments

      This is a short text to acknowledge the contributions of specific colleagues, institutions, or agencies that aided the efforts of the authors.

    15. Author Contributions Statement

      The Author Contributions Statement can be up to several sentences long and should briefly describe the tasks of individual authors. Please list only 2 initials for each author, without full stops, but separated by commas (e.g. JC, JS). In the case of two authors with the same initials, please use their middle initial to differentiate between them (e.g. REW, RSW). The Author Contributions Statement should be included at the end of the manuscript before the References.

    16. Conflict of Interest Statement

      A Conflict of Interest Statement needs to be included at the end of the manuscript before the references. Here, the authors need to declare whether or not the submitted work was carried out in the presence of any personal, professional or financial relationships that could potentially be construed as a conflict of interest.

    17. References

      All citations in the text, figures or tables must be in the reference list and vice-versa. The references should only include articles that are published or accepted. Data sets that have been deposited to an online repository should be included in the reference list, include the version and unique identifier when available. For accepted but unpublished works use "in press" instead of page numbers. Unpublished data, submitted manuscripts, or personal communications should be cited within the text only, for the article types that allow such inclusions. Personal communications should be documented by a letter of permission. Website urls should be included as footnotes. Any inclusion of verbatim text must be contained in quotation marks and clearly reference the original source. Preprints can be cited as long as a DOI or archive URL is available, and the citation clearly mentions that the contribution is a preprint. If a peer-reviewed journal publication for the same preprint exists, the official journal publication is the preferred source.

      The following formatting styles are meant as a guide, as long as the full citation is complete and clear, AEE referencing style will be applied during typesetting.

      SCIENCE, ENGINEERING, and HUMANITIES: For articles submitted in the domains of SCIENCE, ENGINEERING and HUMANITIES please apply Author-Year system for in-text citations.

      Reference list: provide the names of the first six authors followed by et al. and doi when available.

      In-text citations should be called according to the surname of the first author, followed by the year. For works by 2 authors include both surnames, followed by the year. For works by more than 2 authors include only the surname of the first author, followed by et al., followed by the year. For Humanities and Social Sciences articles please include page numbers in the in-text citations.


      Sondheimer, N., and Lindquist, S. (2000). Rnq1: an epigenetic modifier of protein function in yeast. Mol. Cell. 5, 163-172.


      Tahimic, C.G.T., Wang, Y., Bikle, D.D. (2013). Anabolic effects of IGF-1 signaling on the skeleton. Front. Endocrinol. 4:6. doi: 10.3389/fendo.2013.00006


      Sorenson, P. W., and Caprio, J. C. (1998). "Chemoreception," in The Physiology of Fishes, ed. D. H. Evans (Boca Raton, FL: CRC Press), 375-405.


      Cowan, W. M., Jessell, T. M., and Zipursky, S. L. (1997). Molecular and Cellular Approaches to Neural Development. New York: Oxford University Press.


      Hendricks, J., Applebaum, R., and Kunkel, S. (2010). A world apart? Bridging the gap between theory and applied social gerontology. Gerontologist 50, 284-293. Abstract retrieved from Abstracts in Social Gerontology database. (Accession No. 50360869)


      Marshall, S. P. (2000). Method and apparatus for eye tracking and monitoring pupil dilation to evaluate cognitive activity. U.S. Patent No 6,090,051. Washington, DC: U.S. Patent and Trademark Office.


      Perdiguero P, Venturas M, Cervera MT, Gil L, Collada C. Data from: Massive sequencing of Ulms minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease. Dryad Digital Repository. (2015)


      Smith, J. (2008) Post-structuralist discourse relative to phenomological pursuits in the deconstructivist arena. [dissertation/master’s thesis]. [Chicago (IL)]: University of Chicago


      Smith, J. (2008). Title of the document. Preprint repository name [Preprint]. Available at: https://persistent-url (Accessed March 15, 2018).

    18. Disclaimer

      Any necessary disclaimers which must be included in the published article should be clearly indicated in the manuscript.

    19. Supplementary Material

      AEE journals do not support pushing important results and information into supplementary sections. However, data that are not of primary importance to the text, or which cannot be included in the article because it is too large or the current format does not permit it (such as movies, raw data traces, power point presentations, etc.) can be uploaded during the submission procedure and will be displayed along with the published article.

      The Supplementary Material can be uploaded as Data Sheet (word, excel, csv, cdx, fasta, pdf or zip files), Presentation (power point, pdf or zip files), Supplementary Image (cdx, eps, jpeg, pdf, png or tif), Supplementary Table (word, excel, csv or pdf), Audio (mp3, wav or wma) or Video (avi, divx, flv, mov, mp4, mpeg, mpg or wmv).

      Supplementary material is not typeset so please ensure that all information is clearly presented, the appropriate caption is included in the file and not in the manuscript, and that the style conforms to the rest of the article. To avoid discrepancies between the published article and the supplementary material, please do not add the title, author list, affiliations or correspondence in the supplementary files.

  2. File Requirements
    1. Word Files

      If working with Word please use AEE Word templates.

    2. LaTeX Files

      If you wish to submit your article as LaTeX, we recommend our AEE LaTeX templates. These templates are meant as a guide, you are of course welcome to use any style or formatting and AEE journal style will be applied during typesetting.

      When submitting your article please ensure to upload all relevant manuscript files including:

      • tex file
      • PDF
      • .bib file (if the bibliography is not already included in the .tex file)

      Figures should be included in the provided pdf. In case of acceptance, our Production Office might require high resolution files of the figures included in the manuscript in eps, jpg or tif format. In order to be able to upload more than one figure at a time, save the figures (labeled in order of appearance in the manuscript) in a zip file, and upload them as ‘Supplementary Material Presentation’.

  3. Figure and Table Guidelines
    1. CC-BY Licence

      All figures, tables, and images will be published under a Creative Commons CC-BY licence and permission must be obtained for use of copyrighted material from other sources (including re-published/adapted/modified/partial figures and images from the internet). It is the responsibility of the authors to acquire the licenses, to follow any citation instructions requested by third-party rights holders, and cover any supplementary charges.

    2. General Style Guidelines for Figures

      The maximum number of figures and tables for all article types are 15. AEE requires figures to be submitted individually, in the same order as they are referred to in the manuscript, the figures will then be automatically embedded at the end of the submitted manuscript. Kindly ensure that each table and figure is mentioned in the text and in numerical order.

      For graphs, there must be a self-explanatory label (including units) along each axis. For figures with more than one panel, panels should be clearly indicated using labels (A), (B), (C), (D), etc. However, do not embed the part labels over any part of the image, these labels will be added during typesetting according to AEE journal style. Please note that figures which are not according to the guidelines will cause substantial delay during the production process.

      Permission must be obtained for use of copyrighted material from other sources (including re-published/adapted/modified/partial figures and images from the internet). It is the responsibility of the authors to acquire the licenses, to follow any citation instructions requested by third-party rights holders, and cover any supplementary charges.

      AEE takes concerns regarding image manipulation seriously. We request that no individual features within an image are modified (e.g. enhanced, obscured, moved, recycled, removed or added). Image processing methods (e.g. changes to the brightness, contrast or colour balance) must be applied to every pixel in the image and the changes should not alter the information illustrated in the figure. Where cropped images of blots are shown in figures, a full scan of the entire original gel(s) must be submitted as part of the supplementary material. Where control images are re-used for illustrative purposes, this must be clearly declared in the figure legend. Image grouping and splicing must be clearly stated in the manuscript and the figure text.

    3. General Style Guidelines for Tables

      If you use a word processor, build your table in word. If you use a LaTeX processor, build your table in LaTeX.

      Please note that large tables covering several pages cannot be included in the final PDF for formatting reasons. These tables will be published as supplementary material on the online article abstract page at the time of acceptance. The author will notified during the typesetting of the final article if this is the case. A link in the final PDF will direct to the online material.

    4. Figure and Table Requirements


      Figure and table legends are required to have the same font as the main text (10 point normal Times New Roman, single spaced). Legends should be preceded by the appropriate label, for example "Figure 1" or "Table 4". Figure legends should be placed at the end of the manuscript (for supplementary images you must include the caption with the figure, uploaded as a separate file). Table legends must be placed immediately before the table. Please use only a single paragraph for the legend. Figure panels are referred to by bold capital letters in brackets: (A), (B), (C), (D), etc.

      Image Size

      Figure images should be prepared with the PDF layout in mind, individual figures should not be longer than one page and with a width that corresponds to 1 column or 2 columns.

    5. Format

      The following formats are accepted:

      EPS (.eps) EPS files can be uploaded upon acceptance

      Colour Image Mode

      Images must be submitted in the colour mode RGB.

      Resolution Requirements

      All images must be uploaded separately in the submission procedure and have a resolution of 300 dpi at final size. Check the resolution of your figure by enlarging it to 150%. If the resolution is too low, the image will appear blurry, jagged or have a stair-stepped effect.

      Please note saving a figure directly as an image file (JPEG, TIF) can greatly affect the resolution of your image. To avoid this, one option is to export the file as PDF, then convert into TIFF or EPS using a graphics software. EPS files can be uploaded upon acceptance.

      Chemical Structures

      Chemical structures should be prepared using ChemDraw or a similar program. If working with another program please follow the guidelines given below:

      Drawing settings: chain angle, 120° bond spacing, 18% of width; fixed length, 14.4 pt; bold width, 2.0 pt; line width, 0.6 pt; margin width 1.6 pt; hash spacing 2.5 pt. Scale 100% Atom Label settings: font, Arial; size, 8 pt.

      Assign all chemical compounds a bold, Arabic numeral in the order in which the compounds are presented in the manuscript text. Figures containing chemical structures should be submitted in a size appropriate for incorporation into the manuscript.


      Figures must be legible. Check the following:

      • The smallest visible text is no less than 8 points in height, when viewed at actual size.
      • Solid lines are not broken up.
      • Image areas are not pixilated or stair stepped.
      • Text is legible and of high quality.
      • Any lines in the graphic are no smaller than 2 points width.
  4. Funding Disclosure

    Details of all funding sources must be provided in the funding section of the manuscript including grant numbers, if applicable. All AEE articles are published with open access under the CC-BY Creative Commons attribution license. Articles published with AEE automatically fulfil or exceed the requirements for open access mandated by many institutions and funding bodies, including the National Institutes of Health, the Medical Research Council, Research Councils UK, and the Wellcome Trust. AEE submits funding data to the Open Funder Registry which is a funder identification service from CrossRef resulting from collaboration between scholarly publishers and funding agencies.

  5. Materials and Data Policies

    AEE is committed to open science and open data, and we strongly encourage authors to maximize the availability of data included in their articles by making generated data publicly available where possible, and ensuring that published data sets are cited in accordance with our data citation guidelines. We aim to achieve the best community standards regarding data availability, ensuring increased levels of transparency and reproducibility in our published articles.

    Our policies on data availability are informed by community-driven standards, which AEE endorses, such as the Transparency and Openness (TOP) guidelines, and the joint declaration of data citation principles produced by FORCE 11.

    1. Availability of Materials

      Authors are strongly encouraged to make all materials used to conduct their research available to other researchers. Research materials necessary to enable the reproduction of an experiment should be clearly indicated in the Materials and Methods section. Relevant materials such as protocols, analytic methods, and study material should preferably be uploaded to an online repository providing a global persistent link/identifier. If this is not possible, authors are strongly encouraged to make this material available upon request to interested researchers, and this should be stated in the manuscript.

    2. Availability of Data

      AEE requires that authors make all data relevant to the conclusions of the manuscript available to editors and reviewers during peer-review to enable complete and objective evaluation of the work described.

      We strongly encourage authors to make the raw data supporting the conclusions of the manuscript available in publicly accessible repositories. To comply with best practice in their field of research, authors are required to make certain types of data available to readers at time of publication in specific stable, community-supported repositories.

    3. Data Citation Guidelines

      Authors are encouraged to cite all datasets generated or analyzed in the study. Where datasets are cited, they should be included in the references list to maximize future usability. The following format should be used:

      [Dataset] Author names. (year) Data Title. Repository name. Version. Persistant identifier

    4. Data Availability Statements

      Data availability statements are required for all manuscripts published with AEE. During the submission process, authors will be asked to detail the location of the raw data underlying the conclusions made in the manuscript, and whether it will be made available to other researchers following publication. Authors will also be asked for the details of any existing datasets that have been analysed in the manuscript. These datasets should be cited in accordance with our data citation guidelines.

      A statement will be automatically generated using the information provided in the submission form; however, manuscripts containing incomplete or incorrect statements will be prevented from entering the review process.

      Examples of acceptable statements

      • Datasets are in a publicly accessible repository:

        The datasets [GENERATED/ANALYZED] for this study can be found in the [NAME OF REPOSITORY] [LINK]

      • Datasets are available on request:

        The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher.

      • All relevant data is contained within the manuscript:

        All datasets [GENERATED/ANALYZED] for this study are included in the manuscript and the supplementary files.

      • Restrictions apply to the datasets:

        The datasets for this manuscript are not publicly available because: [VALID REASON]. Requests to access the datasets should be directed to [NAME, EMAIL].

      • Data has been obtained from a third party:

        The data analyzed in this study was obtained from [SOURCE], the following licenses/restrictions apply [RESTRICTIONS]. Requests to access these datasets should be directed to [NAME, EMAIL].

      • No datasets were generated for this study
    5. Recommended and Required Repositories

      Authors are required to deposit the following data-types in public, community-supported repositories, such as those listed below, prior to publication of an associated AEE manuscript:

      Data-type Recommended Repositories Metadata Standard
      Genetic and genomic sequence (DNA/ RNA)^ GenBank
      DNA Data Bank of Japan (DDBJ)
      European Nucleotide Archive (ENA)
      Metagenomic sequence EBI Metagenomics MiXS
      DNA and RNA trace or short-read sequencing data NCBI Trace Archive NCBI Sequence Read Archive MiXS
      Genetic polymorphism data, including SNP and CNV data dbSNP
      European Variation Archive
      Gene expression data; chromatin immunoprecipitation data (deep-sequencing or microarray) ArrayExpress
      Gene Expression Omnibus (GEO)
      Data linking genotype to phenotype dbGaP
      Protein sequence data UniProt
      Proteome profiling data PRIDE
      Small molecule, protein, protein complex data structural data Crystallography Open Database
      Cambridge Structural Database
      wwPDB (Protein DataBank)
      Electron Microscopy Databank
      Taxonomy data Zoobank

      ^ Genetic sequence variants should be annotated according to the guidelines established by the Human Variome Project.

      Authors are encouraged to consider deposition in public, community-supported repositories of the data-types listed below:

      Data-type Recommended Repositories Metadata Standard
      Protein-protein interaction data Database of Interacting Proteins (DIP) MIMIx
      Metabolite and metabolome profiling data MetaboLights
      Human Metabolome Database
      Small-molecule screening data, chemical compound data PubChem CIF
      Flow cytometry data Flow Repository
      Brain Imaging data / Neuroimaging data OpenNeuro
      NeuroVault [Statistical maps]
      Trait data TRY database
      Phenology data National Phenology Network
      Any data FigShare
      Dryad Digital Repository
    6. Inclusion of Zoological Nomenclature

      The International Code of Zoological Nomenclature, in a recent 2012 amendment to the 1999 Zoological Code, allows all electronic-only papers, such as those published by the AEE journals, to have valid new taxon names and nomenclatural acts. However, these new names or nomenclatural acts must be registered in ZOOBANK and have associated Life Science Identifiers (LSIDs). Registration must be done by the authors before publication. Should your manuscript include any zoological new taxon names and/or nomenclatural acts, please ensure that they are registered prior to final publication.

    7. Inclusion of RNAseq Data

      Studies employing RNASeq for comparative transcriptomic analyses must contain at least 3 biological replicates (unless otherwise justified). Each biological replicate should be represented in an independent library, each with a unique barcode if libraries are multiplexed for sequencing. Validation on a number of key transcripts highlighted in the study is also highly recommended.

      Full data accompanying these experiments must be made available to reviewers at the time of submission in a freely accessible resource e.g the sequence read archive (SRA) or European Nucleotide Archive (ENA). Depending on the question addressed in a manuscript, de novo assemblies of transcriptomes may also require multiple replicates and assembled sequences together with sequence annotation must be made freely available e.g figshare or dryad.

    8. Inclusion of Proteomics Data

      Authors should provide relevant information relating to how peptide/protein matches were undertaken, including methods used to process and analyse data, false discovery rates (FDR) for large-scale studies and threshold or cut-off rates for peptide and protein matches. Further information should include software used, mass spectrometer type, sequence database and version, number of sequences in database, processing methods, mass tolerances used for matching, variable/fixed modifications, allowable missed cleavages, etc.

      Authors should provide as supplementary material information used to identify proteins and/or peptides. This should include information such as accession numbers, observed mass (m/z), charge, delta mass, matched mass, peptide/protein scores, peptide modification, miscleavages, peptide sequence, match rank, matched species (for cross-species matching), number of peptide matches, etc. Ambiguous protein/peptide matches should be indicated.

      For quantitative proteomics analyses, authors should provide information to justify the statistical significance, including biological replicates, statistical methods, estimates of uncertainty, and the methods used for calculating error.

      For peptide matches with biologically relevant post-translational modifications (PTMs) and for any protein match that has occurred using a single mass spectrum, authors should include this information as raw data or annotated spectra, or submit data to an online repository (recommended option; see table below).

      Raw or matched data and 2-DE images should be submitted to public proteomics repositories such as those participating in ProteomeXchange. Submission codes and/or links to data should be provided within the manuscript.

  6. Statistics

    AEE requires that all statements concerning quantitative differences should be based on quantitative data and statistical testing. For example, if a quantitative statement is made regarding the abundance of a certain protein based on a western blot, we request that the blot be scanned and the abundance assessed quantitatively using the correct analytic software (e.g. ImageJ) and statistics in order to support that statement.

    Statistics should/must be applied for independent experiments. The number of independent samples and the deviation parameters (e.g. Standard Error of the Mean, Standard Deviation, Confidence Intervals) should be clearly stated in the Methods or the Figure legends. In general, technical replicates within a single experiment are not considered to be independent samples. Where multiple comparisons are employed (e.g. microarray data or Genome-wide association studies), any analysis should correct for false positive results. Descriptions of statistical procedures should include the software and analysis used, and must be sufficiently detailed to be reproduced.