Instructions to authors

Manuscript Types

Mass Spectrometry publishes original research articles, reviews, and technical reports. All manuscript types are subject to peer review.

Research articles should follow the format described below and not exceed 16 typeset pages (approximately 500 words per page). A maximum of 8 figures and/or tables are allowed.

Reviews do not have a fixed style but should focus on recent developments with minimal historical documentation. They should not exceed 30 typeset pages.

Technical reports are typically short articles (within 8 typeset pages) describing novel or improved approaches or protocols for performing a particular aspect of analyses or experiments.

Journal & Ethics Policies

Mass Spectrometry upholds the highest standards in scholarly publishing.

Before submitting a manuscript to the journal, authors must ensure that they have read and complied with the journal’s policies. The journal reserves the right to reject without review, or retract, any manuscript that the Editor believes may not comply with these policies.

The responsibilities of the journal’s authors, editors, reviewers and publisher regarding research and publication ethics are described in full below.

Submission to the journal implies that the manuscript has not been previously published (in part or in whole, in any language), is not in press, and is not under consideration for publication elsewhere.

Authors must inform the editors if any related manuscripts are under consideration, in press or published elsewhere. The availability of a manuscript on a publicly accessible preprint server does not constitute prior publication (see ‘Preprints’).

If authors choose to submit their manuscript elsewhere before a final decision has been made on its suitability for publication in Mass Spectrometry, they should first withdraw it from the journal.


Mass Spectrometry welcomes manuscript submissions from authors based anywhere in the world.

Submission of a manuscript to the journal implies that all authors: have approved it, warrant it is factual, have agreed to its submission, and have the right to publish it.


Submission to the journal implies that the manuscript is original work. The journal may use iThenticate plagiarism software to screen manuscripts for unoriginal content. By submitting a manuscript to the journal, authors agree to this screening. Any manuscript with an unacceptable level of unoriginal material may be rejected or retracted at the Editors’ discretion.


To support the wide dissemination of research, the journal encourages authors to post their research manuscripts on community-recognized preprint servers, either before or alongside submission to the journal. This policy applies only to the original version of a manuscript that describes primary research. Any version of a manuscript that has been revised in response to reviewers’ comments, accepted for publication or published in the journal should not be posted on a preprint server. Instead, forward links to the published manuscript may be posted on the preprint server.

Authors should retain copyright in their work when posting to a preprint server.


When assessing the novelty of a manuscript submitted to the journal, the editors will not be influenced by other manuscripts that are posted on community-recognized preprint servers after the date of submission to Mass Spectrometry (or after the date of posting on a preprint server, if the manuscript is submitted to the journal within 2 months).


Authors are required to obtain the consent of all co-authors prior to submitting a manuscript. The submitting author accepts the responsibility of notifying all co-authors that the manuscript is being submitted. Changes to the author list after manuscript submission – such as the insertion or removal of author names, or a rearrangement of author order – must be approved by all authors and the editor.

No changes in the author list will be permitted after a manuscript has been accepted.

During manuscript submission, the submitting author must provide contact information (full name, email address, institutional affiliation, and mailing address) for all of the co-authors.

Image integrity

Authors may digitally manipulate or process images, but only if the adjustments are kept to a minimum, are applied to the entire image, meet community standards, and are clearly described in the manuscript. All images in a manuscript must accurately reflect the original data on which they are based. Authors must not move, remove, add or enhance individual parts of an image. The editors reserve the right to request original, unprocessed images from the authors. Failure to provide requested images may result in a manuscript being rejected or retracted.

Reproducing copyrighted material

If a manuscript includes material that is not under the authors’ own copyright, the authors must obtain permission from the copyright holder(s) to reproduce it.

If a manuscript includes previously published material, the authors must obtain permission from the copyright owners and the publisher of the original work to reproduce it. The authors must cite the original work in their manuscript.

Copies of all reproduction permissions must be included with the manuscript when it is first submitted.

Animal/human experimentation

Authors of manuscripts describing experiments involving humans or materials derived from humans must demonstrate that the work was carried out in accordance with the principles embodied in the Declaration of Helsinki, its revisions, and any guidelines approved by the authors’ institutions. Where relevant, the authors must include a statement in their manuscript that describes the procedures for obtaining informed consent from participants regarding participation in the research and publication of the research.

Authors of manuscripts describing experiments involving animals or materials derived from animals must demonstrate that the work was carried out in accordance with the guidelines approved by the authors’ institution(s).

Specimen collection

Manuscripts describing the collection of archaeological, geological, paleontological or wildlife specimens or samples should include detailed information on their provenance and collection methods. Authors must include a statement in their manuscript describing the relevant ethics guidelines, local laws and collection permits under which the research was conducted.

Author competing interests and conflicts of interest

In the interests of transparency, the journal requires all authors to declare any competing or conflicts of interest in relation to their submitted manuscript. A conflict of interest exists when there are actual, perceived or potential circumstances that could influence an author’s ability to conduct or report research impartially. Potential conflicts include (but are not limited to) competing commercial or financial interests, commercial affiliations, consulting roles, or ownership of stock or equity.

Authors should list all funding sources for their work in the Acknowledgements section of their manuscript.


The journal maintains the confidentiality of all unpublished manuscripts. By submitting their manuscript to the journal, the authors warrant that they will keep all correspondence about their manuscript (from the Editorial Office, editors and reviewers) strictly confidential.

Self-archiving (Green Open Access) policy

Self-archiving, also known as Green Open Access, enables authors to deposit a copy of their manuscript in an online repository. Mass Spectrometry encourages authors of original research manuscripts to upload their article to an institutional or public repository immediately after publication in the journal.

Long-term digital archiving

J-STAGE preserves its full digital library, including Mass Spectrometry, with Portico in a dark archive (see In the event that the material becomes unavailable at J-STAGE, it will be released and made available by Portico.

Peer Review Process

Editorial and peer review process

The journal uses single-blind peer review. When a manuscript is submitted to the journal, it is assigned to the Editor-in-Chief, who performs initial screening. Manuscripts that do not fit the journal’s scope or are not deemed suitable for publication are rejected without review. The remaining manuscripts are assigned to a handling Editor who assigns at least two reviewers to assess each manuscript. Reviewers are selected based on their expertise, reputation and previous experience as peer reviewers. The deadline for submission of the reviewers’ reports varies by article type.

Reviewers are requested to provide a recommendation on each manuscript’s suitability for publication in the journal. In addition, reviewers are requested to comment on aspects of a manuscript’s structure, such as its length, number of figures and tables, and so forth. Reviewer’s comments typically comprise the following sections:

  1. Brief overview of the study, outlined in a few sentences.
  2. Adherence or otherwise of the manuscript to the journal’s acceptance criteria (as detailed in the ‘Acceptance criteria’ section, below)
  3. Decision recommendation.
  4. Comments on other minor aspects of the manuscript requiring improvement, such as typographical errors.

Upon receipt of the two reviewers’ reports, the Editor makes the first decision on the manuscript. This can be: “accept as is”, “acceptable after minor revisions”, “reconsider for publication after major revisions”, or “reject”. If the decision is to request revision of the manuscript, authors have 3 months to resubmit their revised manuscript. Revised manuscripts submitted after this deadline may be treated as new submissions. If additional time is needed to complete experiments for a revised manuscript, authors may request an extension from the Editor handling their manuscript. The Editor may send revised manuscripts to peer reviewers for their feedback or may use his or her own judgment to assess how closely the authors have followed the Editor’s and the reviewers’ comments on the original manuscript. When reviewing revised manuscripts, reviewers are requested to comment on the authors’ reply to the reviewers’ comments and to make a new recommendation to the Editor.

The Editor is responsible for making the final decision on the handled manuscripts and the Editor-in-Chief acts as an arbitrator when necessary.

The members of the Editorial Committee act in advisory roles, providing feedback as reviewers and making suggestions to improve the journal. In cases where the Editor-in-Chief is an author on a manuscript submitted to the journal, a member of the Editorial Committee is responsible for making the final decision on the manuscript’s suitability for publication in the journal.

Prearranged Editor review

As a commitment to innovation in peer review, Mass Spectrometry has introduced a new peer review process called “Prearranged Editor” (PE) peer review. This process aims to ensure rapid turnaround while maintaining a robust review process. PE’s must be members of the Mass Spectrometry Editorial Board or otherwise qualified to act in the role. When submitting a manuscript via the journal’s online submission system at, authors will be asked if they plan to use the PE process. If they do, they are then able to select an appropriate PE from the provided list. If the PE agrees to proceed, they critically assess the manuscript against the journal’s acceptance criteria and obtain external advice from qualified reviewers as necessary.

When the PE has sufficient information, they make a decision on the manuscript; where relevant they invite the authors to prepare a revised version by taking into account the supplied comments. After completion of any revisions that are requested from the PE, the author(s) upload the revised version of the paper via the submission system. The Editor-in-Chief or Associate Editors of Mass Spectrometry will then make a final decision on the paper, taking into account the recommendation from the PE.

The PE’s name shall appear in the top page of the article as the editor-in-charge of the paper. PE’s must not be co-authors on the manuscript under review, and none of the authors listed on the paper can be in the same laboratory as the PE. The Editor-in-Chief will assess any conflicts-of-interest between the authors and the PE. In cases where the PE is not available, the author will be requested to submit the paper by the regular submission process.

Reviewer selection, timing and suggestions

Reviewers are selected based on their expertise in the field, reputation, recommendation by others, and/or previous experience as peer reviewers for the journal. Reviewers are asked to submit their first review within 10 days of accepting the invitation to review. Reviewers who anticipate any delays should inform the Editorial Office as soon as possible.

When submitting a manuscript to the journal, authors may suggest reviewers that they would like included in or excluded from the peer review process. The Editor may consider these suggestions but is under no obligation to follow them. The selection, invitation and assignment of peer reviewers is at the Editor’s sole discretion.

Reviewer reports

It is the journal’s policy to transmit reviewers’ comments to the authors in their original form. However, the journal reserves the right to edit reviewers’ comments, without consulting the reviewers, if they contain offensive language, confidential information or recommendations for publication.

Acceptance criteria

If a manuscript satisfies the journal’s requirements and represents a significant contribution to the published literature, the Editor may recommend acceptance for publication in the journal.

The questions guiding the acceptance of articles in the journal are:

  1. Does the manuscript contain new and significant information to justify publication?
  2. Is the purpose of the study significant? Is the problem clearly stated in the manuscript?  
  3. Are the experimental and/or theoretical methods described comprehensively?
  4. Are the interpretations and conclusion justified by the results?
  5. Is the abstract concise?
  6. Is the manuscript written in clear and correct English?

If a manuscript does not meet the journal’s requirements for acceptance or revision, the Editor may recommend rejection.

Editorial independence

As the journal owner, the MSSJ has granted the journal’s Editorial Board complete and sole responsibility for all editorial decisions. The MSSJ will not become involved in editorial decisions, except in cases of a fundamental breakdown of process.

Editorial decisions are based only on a manuscript’s scientific merit and are kept completely separate from the journal’s other interests.


Authors who believe that an editorial decision has been made in error may lodge an appeal with the Editorial Office. Appeals are only considered if the authors provide detailed evidence of a misunderstanding or mistake by a reviewer or editor. Appeals are considered carefully by the Editor-in-Chief, whose decision is final. The guidelines of the Committee on Publication Ethics (COPE) are followed where and when relevant.

Confidentiality in peer review

The journal maintains the confidentiality of all unpublished manuscripts. Editors will not:

  • disclose a reviewer’s identity unless the reviewer makes a reasonable request for such disclosure
  • discuss the manuscript or its contents with anyone not directly involved with the manuscript or its peer review
  • use any data or information from the manuscript in their own work or publications
  • use information obtained from the peer review process to provide an advantage to themselves or anyone else, or to disadvantage any individual or organization.

Conflicts of interest in peer review

A conflict of interest exists when there are actual, perceived or potential circumstances that could influence an editor’s ability to act impartially when assessing a manuscript. Such circumstances might include having a personal or professional relationship with an author, working on the same topic or in direct competition with an author, or having a financial stake in the work or its publication.

Members of the journal’s Editorial Board undertake to declare any conflicts of interest when handling manuscripts. An editor who declares a conflict of interest is unassigned from the manuscript in question and is replaced by a new editor.

Errata and retractions

The journal recognizes the importance of maintaining the integrity of published literature.

A published article that contains an error may be corrected through the publication of an Erratum. Errata describe errors that significantly affect the scientific integrity of a publication, the reputation of the authors, or the journal itself. Authors who wish to correct a published article should contact the editor who handled their manuscript or the Editorial Office with full details of the error(s) and their requested changes. In cases where co-authors disagree over a correction, the Editor-in-Chief may consult the Editorial Board or external peer reviewers for advice. If a Correction is published, any dissenting authors will be noted in the text.

A published article that contains invalid or unreliable results or conclusions, has been published elsewhere, or has infringed codes of conduct (covering research or publication ethics) may be retracted. Individuals who believe that a published article should be retracted are encouraged to contact the journal’s Editorial Office with full details of their concerns. The Editor-in-Chief will investigate further and contact the authors of the published article for their response. In cases where co-authors disagree over a retraction, the Editor-in-Chief may consult the Editorial Board or external peer reviewers for advice. If a Retraction is published, any dissenting authors will be noted in the text.

The decision to publish Errata or Retractions is made at the sole discretion of the Editor-in-Chief.

Editors as authors in the journal

Any member of the journal’s Editorial Board, including the Editor-in-Chief who is an author on a submitted manuscript is excluded from the peer review process. Within the journal’s online manuscript submission and tracking system, they will be able to see their manuscript as an author but not as an editor, thereby maintaining the confidentiality of peer review.

A manuscript authored by an editor of Mass Spectrometry is subject to the same high standards of peer review and editorial decision making as any manuscript considered by the journal.

Responding to potential ethical breaches

The journal will respond to allegations of ethical breaches by following its own policies and, where possible, the guidelines of COPE.

Reviewer confidentiality

As part of their responsibilities, reviewers agree to maintain the confidentiality of unpublished manuscripts at all times. By accepting the invitation to review a manuscript, reviewers agree not to:

  • disclose their role in reviewing the manuscript
  • reveal their identity to any of the authors of the manuscript
  • discuss the manuscript or its contents with anyone not directly involved in the review process
  • involve anyone else in the review (for example, a post-doc or PhD student) without first requesting permission from the Editor
  • use any data or information from the manuscript in their own work or publications
  • use information obtained from the peer review process to provide an advantage to themselves or anyone else, or to disadvantage any individual or organization.

Reviewer conflicts of interest

A conflict of interest exists when there are actual, perceived or potential circumstances that could influence a reviewer’s ability to assess a manuscript impartially. Such circumstances might include having a personal or professional relationship with an author, working on the same topic or in direct competition with an author, having a financial stake in the work or its publication, or having seen previous versions of the manuscript.

Editors try to avoid conflicts of interest when inviting reviewers, but it is not always possible to identify potential bias. Reviewers are asked to declare any conflicts of interest to the Editor, who will determine the best course of action.

Copyright, Open Access and Fees

Mass Spectrometry is fully Open Access and uses Creative Commons (CC) licenses, which allow users to use, reuse and build upon the material published in the journal without charge or the need to ask prior permission from the publisher or author. More details on the CC licenses are below.

Copyright and licensing

Copyright in articles published in the journal is retained by the author(s). Authors grant the MSSJ a license to publish the article and identify itself as the original publisher.

All articles in the journal are Open Access. Creative Commons license: CC BY-NC 4.0 (Attribution-NonCommercial 4.0 International). This License permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Some funding bodies require articles funded by them to be published under a specific Creative Commons license. Before submitting your work to the journal, check with the relevant funding bodies to ensure that you comply with any mandates.

Article Processing Charge

Mass Spectrometry does not levy Article Processing Charges, page charges or submission fees. The journal is free to publish in and free to access.

If authors require reprints, costs are charged for this service. Prices are available from the journal (see Contact section) or at the time of the acceptance of your article.

Manuscript Submission

All manuscripts must be submitted via the journal’s online submission system: The original or revised manuscript text may be uploaded as a PDF or Microsoft Word file, but a Word file is required for the final manuscript text. Figures may be submitted separately in several other formats.

If you encounter any problems with online submission, please contact the Editorial Office per the Contact section.

Manuscript Preparation

English standard

Manuscripts should be written in clear, grammatically correct English. Authors whose native language is not English are strongly encouraged to have their manuscript checked by a native English speaker or by an editing service prior to submission. If a manuscript is not clear due to poor English, it may be rejected without undergoing peer review.

Title page

The title page must have the following information:

  • Title. Be concise and informative (no more than 150 characters including spaces). Avoid abbreviations and formulae where possible.
  • Author names and affiliations. Provide the full postal address of each author’s affiliation, including the relevant country.
  • Corresponding author. Clearly indicate who will handle correspondence at all stages of refereeing and publication and post-acceptance. Ensure that telephone and fax numbers (with country and area code) are provided in addition to an e-mail address.
  • Present address. If an author has moved since the work described in the article was done, or was visiting at the time, a ‘Present address’ may be indicated as a footnote to that author’s name. The address at which the author actually did the work must be retained as the main affiliation address.

Running title

The running title should not exceed 50 characters, including spaces.


Each abbreviation should be defined in footnotes together with its non-abbreviated term when it first appears in the text (except in the Title and Abstract). Common abbreviations can be used without definition. Ensure consistency of abbreviations throughout the article.


SI or SI-derived units should be used. More information on SI units is available at the Bureau International des Poids et Mesures (BIPM) website.


The Abstract is a concise summary of the manuscript and should be no more than 250 words. The Abstract should state: (1) the purpose of the research based on the background to the problem; (2) the principal results; and (3) major conclusions. The Abstract is often presented separately from the article, so non-standard or uncommon abbreviations should be avoided. Also, references, if necessary, should be indicated by the DOI (Digital Object Identifier), but not by the reference number.


A maximum of 5 keywords should be provided. Do not include any words that are in the title.


State the objectives of the work and provide an adequate background, avoiding a detailed literature survey or a summary of the results of previous studies. When citing previous work, preference should be given to original research articles rather than review articles.

Experimental procedures

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

Data availability

Authors must disclose the source of publicly available data and materials, such as public repositories or commercial manufacturers, by including accession numbers or company details in their manuscript, as appropriate. The journal also encourages authors to grant reasonable requests from colleagues to share any materials and experimental protocols described in their manuscript.

Authors are encouraged to deposit the data described in the manuscript in submission, which will be linked to the article, if it is accepted for publication. The data are assessed and examined during the peer review process and may be made publicly available. The data can be seen from the journal site after being published, if the authors permit it. The mass spectral data (.txt or csv files) can be seen by the MSSJ’s viewing software, which is available at

Mass Spectrometry also encourages authors to submit mass spectral data to the MSSJ’s official data repository, MassBank (


Results should be clear and concise.


The Discussion should explore the significance of the results and provide context and perspective. Do not repeat information already stated in the Results section. Authors may combine the Results and Discussion sections if appropriate.


This section should be brief. Authors should list all funding sources for their work in the Acknowledgements section.


References should be cited in the text in numerical order by superscript numbers and listed at the end of the paper in the order in which they appear in the text. References should be listed in the following style:

Journal articles

1)J. Aoki, H. Hazama, M. Toyoda. Novel ion extraction method for imaging mass spectrometry. J. Mass Spectrom. Soc. Jpn. 59: 57–61, 2011.


2)Y. Wada. in The Protein Protocol Handbook, 3rd Ed. (Ed: J. M. Walker), Humana Press, New York, 2009, pp. 1081–1094.

For authors using EndNote, IAP provides an output style that supports the formatting of in-text citations and the reference list. See EndNote style (MassSpectrometry(IAP).ens) or Citation Style Language style (mass-spectrometry.csl).


Number tables consecutively using Arabic numerals (Table 1, Table 2, etc.). A title should be given to each table and it must use capital letters. Explanatory material and footnotes should be typed below the table and should be designated with superscript letters, such as a) or b). Units of measurement should be included with numerical values at the top of columns. Avoid detailed explanations of the experimental conditions used to obtain the data shown in tables (which should be included in other sections as relevant). Do not use vertical lines in Tables.


Figures should be of high enough resolution for direct reproduction for printing. The minimum acceptable resolution for all figures is 300 dpi. Figures will be placed in 1 (3.1 in/8.0 cm), 1.5 (4.7 in/12.0 cm) or 2 (6.7 in/17.0 cm) column widths. Note that ‘figures’ includes line drawings and photographs, as well as charts. Magnifications of photographs should be indicated in the legends and/or by scales included in the photographs. Illustrations must be self-explanatory and they should be numbered consecutively with Arabic numerals (i.e., Fig. 1, Fig. 2, etc.). Each figure should have a short title. Figure legends should be typed together in a separate sheet(s).

Figure captions should include sufficient experimental details to make the figures intelligible; however, duplicating the descriptions provided in other sections should be avoided.

Supporting information

Supporting information adds, but is not essential, to a reader’s understanding of a manuscript. Authors are encouraged to submit supporting information for online-only publication. Supporting information may comprise data, text, audio or movie files, and is published online alongside the accepted manuscript. It is not reproduced in the print version or reprints.

As supporting information is peer-reviewed, authors must submit it in its final form as part of their manuscript submission. After a manuscript has been accepted for publication, authors may not make any changes to the supporting information.

Accepted Manuscripts

Manuscripts that are accepted for publication are copyedited and typeset by the journal’s production team before publication. The journal is published continuously online. All communication regarding accepted manuscripts is with the corresponding author.

Advance Publication

Accepted manuscripts are first published online as it is, before copyediting and typesetting, at the journal’s J-STAGE site as an “Advance Publication”.


After average of approximately 20 days after acceptance, page proofs are sent to the corresponding author, who should check and return them within 48 hours. Only essential corrections to typesetting errors or omissions are accepted; excessive changes are not permitted at the proofing stage.


Order forms for reprints are sent with the proofs to the corresponding author and should be returned with the proofs.


To contact the Editorial Office or the Editor-in-Chief, please write to:

Publishing Center
332-6 Yamabuki-cho, Shinjuku-ku, Tokyo, 162-0801, Japan
Phone: +81-3-6824-9363 Fax: +81-3-5206-5332

Updated: August 29, 2022