Preparing your Submission
This section will help you when preparing your manuscript for initial submission and resubmission to Nature Protocols. For information on our aims & scope, as well as our content types, please refer to the About the journal section. Once you have prepared your manuscript, the How to submit section will provide you with information on the submission system, while our editorial criteria and processes are described in the Peer review and publication section.
Editorial and publishing policies
Nature Protocols is a forum for the publication of proven Protocols. Thus, we do not publish novel primary research and Protocol authors must have used their method to generate results published in a peer-reviewed primary research journal. Nevertheless, we appreciate that Protocols are constantly evolving, so if the methodology has improved since the original publication, authors should notify us of the modifications and provide us with the latest version of the protocol. The procedure may deviate slightly from the version used in the supporting paper, but any major improvements, adaptations, or extensions of a Protocol should be supported by the publication of an additional supporting primary research paper.
As part of Nature Research, Nature Protocols follows a number of common policies (as detailed on our editorial policies page) and we request that authors abide by them. In particular, when you submit a manuscript to Nature Protocols, its content must not significantly overlap with any other papers from you or your co-authors’ groups that are under consideration or in press at other journals. If you submit a related manuscript to any other journal while the submission to Nature Protocols is under consideration, you must send us a copy of the related manuscript and details of its progress towards publication. We reserve the right to decline publication of a protocol even after it has been accepted if it becomes apparent that there are serious problems with the scientific content or violations of our publishing policies.
In addition to the general Nature Research policies, we provide additional Nature Protocols-specific guidance on avoiding potential duplicate publication and self-plagiarism. We require that all Nature Protocols articles are based on methods used in at least one published primary research paper. However, they should always expand upon the information available in the supporting paper(s), enabling users to more easily implement the approach in their own lab. Further, Nature Protocols articles must contain information not already available elsewhere in the scientific literature. To meet this requirement, a Nature Protocols article generally needs to be focused on a method for which the authors have not recently published a detailed protocol. If a method has previously been published in a protocol format, it is generally only appropriate to publish a Nature Protocols article after the publication of at least one additional primary research paper that demonstrates further development of the technique (e.g. refinement, optimization or extended applications). We therefore ask that potential authors upload, along with their Nature Protocols manuscript, a copy of:
- At least one supporting primary paper from the author’s lab where the method has been used.
- Any other publication(s) focused on the method with one or more authors in common with the proposed Nature Protocols article.
Providing comprehensive information about previous publications early in the editorial process helps to ensure the Nature Protocols article augments the published literature and avoids potential problems with self-plagiarism and duplicate publication. Submission is taken to imply that all co-authors have approved the contents of the protocol and its submission by the corresponding author, and that the corresponding author is authorized to represent all co-authors in pre-publication discussions with the journal. The corresponding author for editorial purposes does not need to be the senior author or the person to whom correspondence is addressed after publication. The primary affiliation for each author should be the institution where the majority of their work was done. If an author has subsequently moved, the current address may also be stated.
We recommend that all protocol authors follow these guidelines wherever possible to facilitate the refereeing and editorial process. Microsoft Word is our preferred format for text; however, we can also accept plain ASCII text (.txt) and RTF format (.rtf). When you are ready to submit, please check your manuscript using our author checklist.
Title: The title should succinctly describe the method and, if appropriate, its application. It should be no longer than 30 words.
Authors: Please include those who have contributed intellectually and practically to the development of the technique. For all authors, please include first name, middle initial (if appropriate), last names, postal address (Department, Institution, City and Country) and email address. Also include the telephone number and fax number for the corresponding author. A link to a lab home page or staff information page may also be included for appropriate authors.
Abstract: Please include a summary of the protocol (maximum 250 words), briefly describing the protocol and its applications. The suggested format is to include one or two sentences summarizing the protocol, then explain the stages of the protocol and how these compare with other protocols, and then include one or two sentences describing the results that can be expected. If possible, include a final sentence indicating how long the whole protocol takes and whether a specific level of expertise is required. The abstract should contain information about the procedure itself rather than a summary of the results that have been obtained previously using the method.
Introduction: The purpose of the introduction is to enable readers to make a decision as to the suitability of the protocol to their experimental problem. Initially you should introduce the technique under discussion. Include references to key papers where the protocol has been used previously, including those published by your own group, and any reviews that discuss applications of the protocol. You are actively encouraged, where appropriate, to reference other protocols in Nature Protocols. Use subheadings where appropriate; these could include:
- Development of the protocol: Include references to your own peer-reviewed primary research publications.
- Applications of the method: If you think the protocol could be adapted for use in a wider range of applications than presented, you should discuss the full diversity of the applications of the method.
- Comparison with other methods: Where applicable, reference should be made to alternative methods that are commonly used to achieve the same/similar results as the protocol. The advantages and disadvantages of your protocol compared to other alternatives should be discussed.
- Experimental design: In this section, please provide all information about the design of the experiments that readers would need to be able to adapt the protocol to their own experimental situation. This section should also include a discussion of the controls necessary for the protocol. For protocols describing the preparation of organic molecules, a scheme showing the sequence of reactions should be included (all schemes should be labeled as figures).
- Expertise needed to implement the protocol: If any part of the protocol cannot be implemented by a competent graduate student or postdoc, or if implementation requires the involvement of a specialised core facility (e.g. animal husbandry, deep sequencing), please advise who would be most qualified to perform it. This also applies where any part of the protocol should be performed by more than one person simultaneously.
- Limitations: The possible limitations of the protocol (including any situations where the protocol is likely to be unreliable or unsuccessful) should be discussed.
Materials: Please include a list of the essential materials, under headings REAGENTS and EQUIPMENT. This should include information about the suppliers used for reagents (e.g., Company, web address and catalog number). If you have found that deviations from a particular reagent, or its source, have adverse effects on the outcome of the protocol this should be made clear by the word CRITICAL followed by a brief explanation. Toxic or harmful agents should be made clear by the word CAUTION followed by a brief explanation of the hazard and the precautions that should be taken when handling the agent. Please also highlight any specialist equipment required. Please provide as much information as you can to help users successfully identify the product, e.g. company name, company website, product code. If you need to include detailed information about specific reagents or equipment, please list in additional optional sections, called REAGENT SETUP and EQUIPMENT SETUP. These sections are suitable for details of composition of buffers or the setup of equipment. Within these sections, the title of the reagent or equipment forms a second level of subheading.
REAGENT SETUP is the appropriate section to include details regarding, for example: the required sample specification (in terms of minimum protein quantity and allowed buffer components) for a mass spectrometry experiment; details for preparing a complicated buffer; and the pre-treatment of solvents or reagents to make sure they are moisture-free or air-free. For each item, please indicate whether it should be made up fresh or can be stored (if so, under which conditions and for how long). In addition, please state whether % solutions are wt/vol or vol/vol. EQUIPMENT SETUP is the appropriate section to include details regarding, for example, the setup of HPLC separation methods. Include diagrams or photographs of equipment set-up, where appropriate.
For protocols that use live vertebrates or higher invertebrates, authors must state that all experiments should be performed in accordance with relevant guidelines and regulations. For manuscripts reporting experiments on human subjects, authors must also include a statement confirming that informed consent must be obtained from all subjects. These statements should appear as CAUTIONS. These must be placed in the reagents section, procedure and in the legend of any tables and figures that show data collected using human or animal subjects.
Procedure: This must be provided as a numbered list of direct experimental instructions. Please use the active tense rather than the passive tense. If the protocol naturally breaks into separate stages, then include subheadings and resume the numbered list. Include a TIMING callout with each subheading and state how long the section will take to complete. Subheadings are particularly appropriate after steps where the procedure can be stopped and resumed at a later date, which should be indicated with a PAUSE POINT flag followed by a brief description of the options available (e.g. "Can be left overnight at 4°C or frozen for up to a month at -20°C").
Highlight critical steps in the protocol that must be performed in a very precise manner to maximize the likelihood of success (e.g. where the time and temperature of a step is crucial or the use of RNase free solutions is required). Make these clear with a CRITICAL STEP flag followed by a brief explanation. Highlight any toxic or harmful chemicals with a CAUTION flag upon their first mention and include brief details of the hazard and the appropriate handling information. Please state all centrifugation speeds in g and include the length of time and temperature of the centrifugation (e.g. centrifuge at 14,000 g for 5 mins, 4°C). Please include TROUBLESHOOTING flags after steps where problems are encountered. Include full details of the problem and solutions in the Troubleshooting section.
Where there are alternative routes to reach the next stage of the protocol, please provide enough information for readers to make an informed decision on the route to choose. Letters of the Latin alphabet (A), B), C)...) should be used to identify the different options, and Roman numerals (i), ii), iii)...) should be used to break down the appropriate steps. If you wish to include subheadings, add the subheading at the start of the first step within that section and make the text italic. This formatting can also be used to include second-level subheadings within the main procedure. If the protocol is complicated, consider including a flow diagram to demonstrate how the stages fit together. We encourage authors to submit videos for particularly complicated steps or stages.
Timing: If possible, please include a timeline indicating the approximate time each step or stage will take (e.g. Steps 1–3, 30 min; Steps 4+5, 2 h). Please also provide this information as a list at the end of the procedure. If you think it would be more user friendly, you can show timing for each section or day of the protocol instead.
Troubleshooting: Please include information on how to troubleshoot the most likely problems users will encounter with the protocol. Please provide this information in the form of a table with the column headings ‘step’, ‘problem’, ‘possible reason’, and ‘solution’. The step number should be given for where the problem is first observed. The appropriate steps should also be highlighted in the procedure with TROUBLESHOOTING flags. If troubleshooting text refers to only one or two steps, it can also be formatted as normal text with subheadings referring to the relevant steps or sections.
Anticipated results: Please include information about the likely outcome of protocol (for example, likely yield of protein, typical microscopy images, etc.). If possible, please include one set of data from an experiment that worked very well and a second for an experiment that required troubleshooting to obtain meaningful results. Please also include advice on how to interpret and analyze raw data, including equations if necessary. Analytical data for chemical compounds synthesized as part of the procedure should be provided in following format:
Fmoc-L-Serine-OAll (1). White solid, mp 82.5-84.0 °C
[α]D = + 0.3 (c 7.5 in EtOAc at 20 °C)
TLC (CH2Cl2:CH3OH 15:1 v/v) Rf = 0.14
1H NMR (500 MHz, CDCl) δ 2.33 (br s, 1H), 3.94 (br d, J = 10.3 Hz, 1H), 4.03 (br d, J = 10.1 Hz, 1H), 4.23 (t, J = 6.9 Hz, 1H), 4.43 (m, 2H), 4.48 (m, 1H), 4.69 (d, J = 5.3 Hz, 2H), 5.26 (dd, J = 0.8 Hz, J = 10.5 Hz, 1H), 5.35 (dd, J = 0.8 Hz, J = 17.2 Hz, 1H), 5.79 (d, J = 7.4 Hz, 1H), 5.91 (ddt, J = 16.6 Hz, J = 11.0 Hz, J = 5.5 Hz, 1H), 7.32 (br t, J = 7.4 Hz, 2H), 7.41 (br t, J = 7.4 Hz, 2H), 7.61 (m, 2H), 7.77 (d, J = 7.6 Hz, 2H)
13C NMR (125 MHz, CDCl3) δ 47.30 (CH), 56.28 (CH), 63.48 (CH2), 66.59 (CH2), 67.42 (CH2), 119.25 (CH2), 120.21 (CH), 120.23 (CH), 125.30 (CH), 127.29 (CH), 127.32 (CH), 127.97 (CH), 131.51 (CH), 141.51 (C), 141.55 (C), 143.87 (C), 144.02 (C), 156.46 (C), 170.45 (C)
IR (CH2Cl2, cm-1) 3425, 3064, 2952, 2892, 1725, 1513, 1198
FAB-LRMS (m/z)(relative intensity) 368 ([M+1]+, 28 %)
Analysis (calculated, found for C21H21O5N) C (68.65, 68.38) H (5.76, 5.59) N (3.81, 3.90)
(Taken from: 10.1038/nprot.2006.470)
Figures: Please read the digital images integrity and standards policy before preparing your figures. When possible, we prefer to use original digital figures to ensure the highest quality reproduction in the journal. All figures should be uploaded separately via our online submission system, in one of our preferred formats (see section on Figure Format below). On initial submission, all panels of a figure or table should be combined into one file; please do not send as separate files. Please include a brief title and legend for every electronic figure submitted, and a title for every table. Please ensure that both axes of all graphs are labeled appropriately. Whilst Nature Protocols is an online product, many users will print your protocol prior to use. Thus figures should be sized to be legible to users and to facilitate printing. Figures should not contain more than one panel unless the parts are logically connected; each panel of a multipart figure should be sized so that the whole figure can be reduced by the same amount and reproduced on the printed page at the smallest size at which essential details are visible. When a protocol is accepted for publication, we might ask for high-resolution figure files, possibly in a different electronic format. This information will be included in the acceptance letter.
Lettering on figures should be in a clear, sans-serif typeface (for example, Helvetica); if possible, the same typeface and approximate font size (no smaller than 7 point) should be used for all figures in a paper. Use symbol font for Greek letters. Figures should be on a white background, and should avoid excessive boxing, unnecessary color, spurious decorative effects (such as 3D histograms) and highly pixelated computer drawings. The vertical axis of histograms should not be truncated to exaggerate small differences. Labeling must be of sufficient size and contrast to be readable after appropriate size reduction. The thinnest lines in the final figure should be no smaller than 0.5 point wide. Authors will see a proof of figures. Reasonable requests to enlarge figures will be considered, but editors will make the final decision on figure size.
Figures divided into parts should be labeled with lower-case, bold letters (a, b, c...) in the same typesize as used elsewhere in the figure. Lettering in figures should be in lower-case type, with only the first letter of each label capitalized. Units should have a single space between the number and the unit, and follow SI nomenclature (for example, ms rather than msec) or the nomenclature common to a particular field. Thousands should be separated by commas (1,000). Unusual units or abbreviations should be spelled out in full or defined in the legend. Scale bars should be used rather than magnification factors, with the length of the bar defined in the legend rather than on the bar itself. In general, please use visual cues rather than verbal explanations, such as "open red triangles", in the legend.
We aim to produce chemical structures in a consistent format throughout our articles. Please use the Nature Research Chemical Structures Guide and ChemDraw template to ensure that you prepare your figures in a format that will require minimal changes by our art and production teams. Submit final files at 100% as .cdx files.
Tables: Please submit tables in Word format at the end of your text document, or as a separate file. Tables should be created using the Microsoft Word table editor, where possible.
Supplementary information: Supplementary Information should fit into one of three categories:
1. EXTENDED DATA: Extended Data is an integral part of the paper and only data that directly contribute to the main message should be presented. These figures will be integrated into the full-text HTML version of your paper and will be appended to the online PDF. There is a limit of 10 Extended Data figures, and each must be referred to in the main text/online methods ( cited as ‘Extended Data Figure 1’, ‘Extended Data Figure 2,’ etc.). Each Extended Data figure should be of the same quality as the main figures, and should be supplied at a size that will allow both the figure and legend to be presented on a single A4 page. Each figure should be submitted as an individual .jpg, .tif or .eps file with a maximum size of 10 MB each, using the ‘Figure File’ article type in our Manuscript Tracking system.
2. SUPPLEMENTARY INFORMATION: Supplementary Information is material that is essential background to the study but which it is not practical to include in the PDF version of the paper (for example, video files, large data sets and calculations). Each item must be referred to in the main manuscript/online methods and detailed in the attached Inventory of Supplementary Information. Tables containing large data sets should be in Excel format, with the table number and title included within the body of the table. All textual information and any additional Supplementary Figures (which should be presented with the legends directly below each figure) should be provided as a single, combined PDF. Please note that Supplementary Information is not copyedited and we cannot replace any Supplementary Information after the paper has been formally accepted unless there has been a critical scientific error. Supplementary Figures and other items are not required to be called out in your manuscript text, but should be numerically numbered, starting at one, as ‘Supplementary Figure 1’, etc., not SI1.
3. SOURCE DATA: We encourage you to provide Source Data for your Figures whenever possible. Full-length, unprocessed blots and gels must be provided as Source Data for any relevant Figures, and should be provided as individual PDF files (one for each figure) containing all supporting blots and/or gels with the linked figure noted within the PDF file. Data underlying any relevant graphical Figures should be provided as individual Excel files (one for each figure) with the linked figure noted within the Excel file. We encourage deposition of all types of Source Data into a relevant repository, for example figshare (https://figshare.com/) or the Image Data Resource (https://idr.openmicroscopy.org). Please see more information about data availability: https://www.nature.com/nature-research/editorial-policies/reporting-standards#availability-of-data.
Each piece of SI should be cited in order in the text. Please list all pieces of Supplementary Information, including a title and legend for each, at the end of your Manuscript File. If any references are cited in SI that are not included in the main reference list, please include full citation details in the legend for the SI (for items with legends) or in a reference list within the individual SI item. If any references are cited in both the main text and the SI, they can be repeated in the SI reference list. Please use one of our approved titles for your SI:
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- Supplementary Equation(s) (one file; use plural "Equations" in title if more than one equation is included in file)
- Supplementary Figure(s) (always numbered)
- Supplementary Figure Legend(s) (required, as part of figure or accompanying figure)
- Supplementary Manual
- Supplementary Software
- Supplementary Methods
- Supplementary Note(s) (numbered if >1)
- Supplementary Results
- Supplementary Sequence Archive
- Supplementary Table(s) (always numbered)
- Supplementary Tutorial
- Supplementary Video(s) (always numbered)
- Supplementary Video Legend(s) (optional, to accompany videos; posted in online Supp. Info. title page rather than as separate file)
File sizes should be as small as possible (maximum size of 30 MB) so that they can be downloaded quickly. The combined total size of all files must not exceed 150 MB. Supplementary Figures must be provided in JPEG format in RGB colour mode, and at a resolution of between 150-300 dpi. Allowable formats for other types of SI include (but are not restricted to) the following: Adobe Acrobat file (.pdf), Audio Visual Interleave (.avi), Compressed Archive file (.zip), Flash movie (.swf), HTML doc (.html), MPEG animation (.mpg), MS Excel spreadsheet (.xls, .xlsx), plain ASCII text (.txt), QuickTime movie (.mov), Rich Text format (.rtf), Systems Biology Markup Language (.sbml, .xml, .owl), TAR archive file (.tar), and Waveform audio file (.wav). If a file format that you wish to include as Supplementary Information is not listed, please contact our editorial team, who will advise you as to whether its inclusion is possible.
Author contributions statements: Authors are required to include a statement of responsibility in the manuscript that specifies the contribution of every author. Examples of published statements can be seen at this Nautilus post (http://blogs.nature.com/nautilus/2007/11/post_12.html). Nature journals also allow two coauthors to be specified as having contributed equally to the work being described (most often used for co-first authors), but prefer the use of detailed author contributions statements.
ORCID for corresponding authors: As part of our efforts to improve transparency in authorship, we request that all corresponding authors of published papers provide their Open Researcher and Contributor Identifier (ORCID) ID, before resubmitting the final version of the manuscript. ORCID helps the scientific community achieve unambiguous attribution of all scholarly contributions.
Corresponding authors should link their ORCID to their account in the manuscript tracking system (MTS). From the MTS homepage, click Modify my Springer Nature account and then ORCID Create/link an Open Researcher Contributor ID (ORCID) in the Personal Profile tab. This will re-direct you to the ORCID website. If you already have an ORCID account, enter your ORCID email and password and click on Authorize. If you don’t have one, you can create one at this stage. Linking ORCID and MTS accounts can be done at any time prior to acceptance. For more information please visit ORCID at Springer Nature. If you experience technical issues please contact the Platform Support Helpdesk.
Non-corresponding authors do not have to link their ORCID but are encouraged to do so. Please note that it is not possible to add/modify ORCID details at proof.
Acknowledgments: Please note an acknowledgments section can be included.
Competing interests: Submission of a signed Competing Interests Statement is required for all content of the journal. This statement will be published at the end of all papers, whether or not a competing interest is reported. In cases where the authors declare a competing interest, a short statement to that effect is published at the end of article, which is linked to a more detailed version available online.
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All authors should be included in reference lists unless there are more than five, in which case only the first author should be given, followed by 'et al.'. Authors should be listed last name first, followed by a comma and initials of given names. Titles of cited articles are required and should be in Roman text and titles of books in italics; the first word of the title is capitalized, the title written exactly as it appears in the work cited, ending with a full stop. Journal names are italicized and abbreviated (with full stops) according to common usage; refer to the National Library of Medicine for details. Volume numbers appear in bold. For book citations, the publisher and city of publication are required (e.g. John Wiley & Sons, Hoboken, New Jersey, USA, 2003). Please see examples below:
- Helms, C. et al. A putative RUNX1 binding site variant between SLC9A3R1 and RAT9 is associated with susceptibility to psoriasis. Nat. Genet. 35, 349-356 (2003).
- Lovett, M. Direct selection of cDNAs with large genomic DNA clones. In Molecular Cloning: A Laboratory Manual Edn. 3 Vol. 2 (eds. Sambrook., J. & Russell, D.W.) 11.98-11.133 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).
- Petroff, M.D. & Stapelbroek, M.G. Blocked impurity band detectors. US Patent 4,586,960 filed 23 Oct. 1980, and issued 4 Feb. 1986.
- Babichev, S. A., Ries, J. & Lvovsky, A. I. Quantum scissors: teleportation of single-mode optical states by means of a nonlocal single photon. Preprint at http://arXiv.org/quant-ph/0208066 (2002).
Preparing production quality figures: Please read the digital images integrity and standards policy. When possible, we prefer to use original digital figures to ensure the highest-quality reproduction in the journal. For optimal results, prepare figures at actual size for the journal. Figures that do not meet these standards will not reproduce well and publication may be delayed until we receive high-resolution images. We cannot offer to provide corrected reprints with higher image quality if only poor quality images were supplied at accept stage. Authors are responsible for informing the journal of any requirements to obtain permission to publish any figures or illustrations that are protected by copyright, including figures published elsewhere and pictures taken by professional photographers. The journal cannot publish images downloaded from the internet without appropriate permission.
When creating and submitting digital files, please follow the guidelines found here. See page 3 of the document for guidance specific to Nature Protocols.
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