Guide to referees

Guideline of reviewing manuscript

Upon reviewing, the reviewer (or called “referee”) shall send the suggestion for decision as well as comments to the handling editor in two weeks.

The reviewer is requested to offer decision comments preceded by a summary stating suggestion: “accept as is”, “acceptable after minor revision”, “reconsideration for publication after major revision” or “rejection”.

The suggestion for decision shall be made based on the following evaluation points:

  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 language acceptable?

Additionally, the reviewer is requested to offer a view regarding the manuscript structure such as paper size, the number of figures and tables.

The decision comments shall be typically comprised of the following sections.

  1. Brief overview of the study in a few sentences.
  2. Reviewer’s remarks regarding the evaluation points 1-6 described above.
  3. Suggestion for decision.
  4. Other minor notes such as typographic errors

For Review of Revised Paper, the reviewer shall read the authors’ reply to the reviewer’s comments to the last version well, and offer the remark regarding the replies or rebuttal as well as suggestion for decision to the handling editor.

Editorial philosophy and guidelines of Mass Spectrometry

(1) General duties and responsibilities

  • actively seek the views of authors, readers, reviewers and editorial board members about ways of improving the journal processes
  • encourage and be aware of research into peer review and ‘journalology’ and reassess journal processes in the light of new findings
  • work to persuade the publisher to provide them with appropriate resources, guidance from experts (e.g. designers, lawyers) and adequate training to perform their role in a professional manner and raise the quality of the journal
  • support initiatives designed to reduce academic misconduct
  • support initiatives to educate researchers about publication ethics
  • assess the effects of their journal policies on author and reviewer behavior and revise policies, as required, to encourage responsible behavior and discourage misconduct
  • ensure that any press releases issued by the journal reflect the message of the reported article and put it into context

(2) Relations with readers

  • ensure that all published reports of research have been reviewed by suitably qualified reviewers (e.g. including statistical review where appropriate)
  • ensure that non-peer-reviewed sections of the journal are clearly identified
  • adopt processes that encourage accuracy, completeness and clarity of research reporting
  • consider developing a transparency policy to encourage maximum disclosure about the provenance of nonresearch articles
  • adopt authorship or contributorship systems that promote good practice (i.e. so that listings accurately reflect who did the work) and discourage misconduct (e.g. ghost and guest authors)
  • inform readers about steps taken to ensure that submissions from members of the journal’s staff or editorial board receive an objective and unbiased evaluation

(3) Relations with authors

  • publish clear instructions in the journal about submission and what they expect from authors
  • provide guidance about criteria for authorship and/or who should be listed as a contributor
  • review author instructions regularly and provide links to relevant guidelines
  • require all contributors to disclose relevant competing interests and publish corrections if competing interests are revealed after publication
  • ensure that appropriate reviewers are selected for submissions (i.e. individuals who are able to judge the work and are free from disqualifying competing interests)
  • respect requests from authors that an individual should not review their submission, if these are well-reasoned.
  • be guided by the COPE flowcharts* in cases of suspected misconduct or disputed authorship
  • publish details of how they handle cases of suspected misconduct

(4) Relations with reviewers

  • provide clear advice to reviewers (which should be straightforward and regularly updated)
  • require reviewers to disclose any potential competing interests before agreeing to review a submission
  • encourage reviewers to comment on ethical questions and possible research misconduct raised by submissions, (e.g. unethical research design, insufficient detail on patient consent or protection of research subjects, including animals)
  • encourage reviewers to ensure the originality of submissions and be alert to redundant publication and plagiarism
  • consider providing reviewers with tools to detect related publications (e.g. links to cited references and bibliographic searches)
  • seek to acknowledge the contribution of reviewers to the journal
  • encourage academic institutions to recognize peer-review activities as part of the scholarly process
  • monitor the performance of peer reviewers and take steps to ensure this is of high quality
  • develop and maintain a database of suitable reviewers, and update this on the basis of reviewer performance
  • remove from the journal’s database any reviewers who consistently produce discourteous, poor quality or late reviews
  • seek to add new reviewers to the database to replace those who have been removed (because of poor performance or other reasons)
  • ensure that the reviewer database reflects the academic community for the journal (e.g. by auditing the database in terms of reviewer age, gender, location, etc.)
  • use a wide range of sources (not just personal contacts) to identify potential new reviewers (e.g. author suggestions, bibliographic databases)
  • follow the COPE flowchart* in cases of suspected reviewer misconduct

(5) Relations with editorial board members

  • identify suitably qualified editorial board members who can actively contribute to the development and good management of the journal
  • appoint editorial board members for a fixed term of office (e.g. three years)
  • provide clear guidance to editorial board members about their expected functions and duties, these might include:
    • acting as ambassadors for the journal
    • supporting and promoting the journal
    • seeking out the best authors and best work (e.g. from meeting abstracts) and actively encouraging submissions
    • reviewing submissions to the journal
    • accepting commissions to write editorials, reviews and commentaries on papers in their specialist area
    • attending and contributing to editorial board meetings
  • consult editorial board members regularly (at least once a year) to gauge their opinions about the running of the journal, inform them of any changes to journal policies, and identify future challenges

(6) Relations with journal owners and publishers

  • establish mechanisms to handle disagreements between themselves and the journal owner/publisher with due process
  • have a written contract(s) setting out their relationship with the journal’s owner and/or publisher (the terms of this contract should be in line with the COPE Code of Conduct**) • communicate regularly with their journal’s owners and publishers

(7) Editorial and peer-review processes

  • ensure that people involved with the editorial process (including themselves) receive adequate training and keep abreast of the latest guidelines, recommendations and evidence about peer review and journal management
  • keep informed about research into peer review and technological advances
  • adopt peer-review methods best suited for their journal and the research community it serves
  • review peer-review practices periodically to see if improvement is possible
  • refer troubling cases to COPE, especially when questions arise that are not addressed by the COPE flow charts*, or new types of publication misconduct are suspected
  • consider appointing an ombudsperson to adjudicate in complaints that cannot be resolved internally

(8) Quality assurance

  • have systems in place to detect falsified data, e.g. manipulated photographic images or plagiarized text (either for routine use or when suspicions are raised)
  • base decisions about journal house style on relevant evidence of factors that raise the quality of reporting rather than simply on aesthetic grounds or personal preference

(9) Protecting individual data

  • publish their policy on publishing individual data (e.g. identifiable patient details or images) and explain this clearly to authors

(10) Encouraging academic integrity

  • request evidence of ethical research approval for all relevant submissions and be prepared to question authors about aspects such as how patient consent was obtained or what methods were employed to minimize animal suffering
  • ensure that reports of clinical trials cite compliance with the Declaration of Helsinki, Good Clinical Practice and other relevant guidelines to safeguard participants
  • ensure that reports of experiments on, or studies of, animals cite compliance with the US Department of Health and Human Services Guide for the Care and Use of Laboratory Animals or other relevant guidelines (e.g. the guideline from MEXT, Japan***) • consider appointing a journal ethics panel to advise on specific cases and review journal policies periodically

(11) Ensuring the integrity of the academic record

  • take steps to reduce covert redundant publication, e.g. by requiring all clinical trials to be registered
  • ensure that published material is securely archived (e.g. via online permanent repositories, such as PubMed Central and J-STAGE) • have systems in place to give authors the opportunity to make original research articles freely available

(12) Intellectual property

  • adopt systems for detecting plagiarism (e.g. software, searching for similar titles) in submitted items (either routinely or when suspicions are raised)
  • support authors whose copyright has been breached or who have been the victims of plagiarism
  • be prepared to defend authors’ rights and pursue offenders (e.g. by requesting retractions or removal of material from websites) irrespective of whether their journal holds the copyright

(13) Commercial considerations

  • have policies and systems in place to ensure that commercial considerations do not affect editorial decisions (e.g. advertising departments should operate independently from editorial departments)
  • publish a description of their journal’s income sources (e.g. the proportions received from display advertising, reprint sales, special supplements, page charges, etc.)
  • ensure that the peer-review process for sponsored supplements is the same as that used for the main journal
  • ensure that items in sponsored supplements are accepted solely on the basis of academic merit and interest to readers and is not influenced by commercial considerations

(14) Conflicts of interest

  • publish lists of relevant interests (financial, academic and other kinds) of all editorial staff and members of editorial boards (which should be updated at least annually)
  • adopt suitable policies for handling submissions from themselves, employees or members of the editorial board to ensure unbiased review (and have these set out in writing)

This guideline was made after the COPE (Committee on Publication Ethics) Best Practice Guidelines for Journal Editors:


* COPE flowcharts:

** COPE Code of Conduct:

** Japan MEXT guideline for the use of laboratory animals: