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How to Write a Paper for Rapid Communications in Mass

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Protocol Received: 6 June 2012 Accepted: 6 June 2012 Published online in Wiley Online Library Rapid Commun. Mass Spectrom. 2012, 26, 1725–1734 (wileyonlinelibrary.com) DOI: 10.1002/rcm.6314 How to write a paper for Rapid Communications in Mass Spectrometry Robert K. Boyd* Unit 40, 1425 Lamey’s Mill Road, Vancouver, BC V6H3W2, Canada This is a non-scientific article about how to write a research paper for Rapid Communications in Mass Spectrometry (RCMS). It can be viewed as an elaboration of
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  How to write a paper for  Rapid Communications in MassSpectrometry Robert K. Boyd * Unit 40, 1425 Lamey ’ s Mill Road, Vancouver, BC V6H3W2, Canada This is a non-scienti 󿬁 c article about how to write a researchpaper for  Rapid Communications in Mass Spectrometry (RCMS) .It can be viewed as an elaboration of a recent Editorial [1] describing the adoption of a structured format for Abstracts,now incorporated in the journal ’ s  Instructions for Authors .However, the present paper is intended more as a guide tohelp authors present their work in the best possible light, ina fashion consistent with scienti 󿬁 c traditions. Many booksand articles have been published with this same objective.A particularly helpful series of articles written by T. M.Annesley has appeared in the journal  Clinical Chemistry . These14 articles have generously been made freely availableon-line, [2] and are strongly recommended as a more detaileddiscussion of many of the points raised here. (Many of thesearticles are also available as Chinese and Spanish translations).A similar series of articles by M. A. Foote [3 – 8] was writtenspeci 󿬁 cally for authors working in medical research andprovides advice very similar to that of Annesley, but require apersonalorinstitutionalsubscriptiontothejournal.Thepresentarticle emphasizes the requirements for a research journaldedicated to mass spectrometry rather than clinical chemistryor mainstream medicine.Mass spectrometry is a scienti 󿬁 c discipline. This meansthat a paper dealing with this discipline should followcertain broad conventions that characterize scienti 󿬁 c publi-cations. Scienti 󿬁 c research is a collegial activity, bothcommunal and cumulative. The  󿬁 rst of these propertiesimplies that, when we prepare our work for publication,we owe it to our peer group to provide as much informa-tion as possible. This point is discussed later in moredetail, but the general principle is based on the require-ment for suf  󿬁 cient information to permit an in-depthreassessment (including peer review) of the reportedobservations, plus possible replication of the research byan independent laboratory. Such replication is the secondstep of the quality control procedure in science (peerreview is the  󿬁 rst). Of course not every paper is replicatedin order to con 󿬁 rm its conclusions, but we should alwayswrite our papers as if we expect someone to attempt it.The second general property that characterizes scienti 󿬁 cresearch, its cumulative nature, simply re 󿬂 ects the obviousin that any research project undertaken today rests on theprevious accomplishments of others. This is true even if our paper raises questions about the validity of all or partof some earlier work. Accordingly, we should write ourpaper so as to set our new research in the context of relevant work reported previously, giving full credit whereit is due, and exercising proper scienti 󿬁 c caution whenexpressing concerns about some aspects of earlier publica-tions. A good scienti 󿬁 c paper does not claim to be thede 󿬁 nitive last word, but rather the best understandingpossible at present of the phenomena under investigation.How do we achieve these very general objectives in prac-tice? It does not seem possible to provide a one-size- 󿬁 ts-allprescription, particularly for a journal like  RCMS  thatpublishes papers covering a wide range of subject matter ina variety of formats, discussed later. However, before startingto write up the new work it is a good idea to  󿬁 rst decide onthe target audience. For example, a paper written for a morespecialized readership, such as those involved in analysis of pollutants in drinking water, will likely adopt a different tonefrom one written for a general mass spectrometry audience.An example of the latter might be a description of a new massspectrometer or peripheral device.The present paper does not deal with conventions of style such as acronyms for instrument types, nor withrequired criteria for reported data such as for proteinidenti 󿬁 cation by mass spectrometry. Nor is this paperconcerned with appropriate use of the English language,other than to emphasize that papers for  RCMS  need not(and probably should not) be written in luminous evoca-tive prose. Rather the intended meaning of the authorsmust be clearly understandable (not obscured by languageproblems) by referees who have agreed to review the paper.All of these requirements are covered in the  Instructions for Authors availableonthe RCMS homepage.Theobjectiveofthispaperistoprovidesomehintsandsuggestionsforhowtowriteup new research so as to  󿬁 rst attract the attention of its targetaudience, then to provide suf  󿬁 cient detail about methodologyand the raw data thus acquired, then set the work in contextand provide a reasoned explanation for the conclusions, and 󿬁 nally leave a take-home message that will stick in the mindof the reader. TITLE AND ABSTRACT It is worthwhile to devote some time and care to writing aTitle and Abstract. Bear in mind that nowadays there is somuch published material available that a busy scientist*  Correspondence to:  R. K. Boyd, Unit 40, 1425 Lamey ’ s MillRoad, Vancouver, BC V6H3W2, Canada.E-mail: Robert.Boyd@nrc-cnrc.gc.ca Copyright © 2012 John Wiley & Sons, Ltd. Rapid Commun. Mass Spectrom.  2012 ,  26 , 1725 – 1734 Protocol Received: 6 June 2012 Accepted: 6 June 2012 Published online in Wiley Online Library Rapid Commun. Mass Spectrom.  2012 ,  26 , 1725 – 1734(wileyonlinelibrary.com) DOI: 10.1002/rcm.6314  1   7   2   5    simply does not have the time to read all papers from beginning to end. The Title is the  󿬁 rst thing that a busycolleague will notice while scanning the literature, so it isimportant to attract his or her attention and encouragefurther examination of your paper. The next thing a poten-tial reader will look at is the Abstract, so in order to attractthe reader ’ s interest this should also be written with careas described (with examples) in the cited Editorial. [1] It is agood idea to leave writing the Title and the Abstract untilthe main body of the paper is complete, since by then youwill have a much better idea of how your new work willimpact your  󿬁 eld of study.The keys [2] to writing a Title that will be successful incatching the eye of a potential reader are to be clear,concise and informative, and to carefully choose for inclu-sion some key words and terms. The latter should corre-spond to the  ’ key words ’  that many journals request andare used in indexing services and by search engines suchas Google Scholar. In the interests of being concise weshould avoid  ’ 󿬁 ller ’  phrases such as  ’ a study of  ’ ,  ’ investi-gation of  ’ ,  ’ development of  ’ , etc. These add nothing tothe information content of a Title. Similarly, for a journaldedicated to  srcinal  research, descriptors such as  ’ new ’ , ’ improved ’ ,  ’ more sensitive ’ , etc., are super 󿬂 uous. If theEditor and reviewers of such a journal do their jobs, apaper that does not satisfy at least one of these descriptorswould not be published in that journal anyway. It is pre-ferable that the Title of a paper should  not  use acronymsor other abbreviations.Clarity is a desired property of all scienti 󿬁 c writing, includ-ing paper Titles. The main problems in this regard usuallyarise from inattention to ambiguities arising from a poorchoice of word order. Here are a few  󿬁 ctitious examples tomake the point: “ Species identi  󿬁 cation for bacteria using MALDI mass spectrometry ”“ Limits to determination of molecular formulae from accurate mass data for molecules with poor precision ”“ Enzymes for site-speci  󿬁 c proteolysis of proteins derived from the clam Abra cadabra ” All of these invented titles are ambiguous because of poor choice of word order. The  󿬁 rst example appears tosuggest that bacteria routinely use MALDI mass spectro-metry, a trick that not even extensive horizontal genetransfer seems likely to accomplish. The second exampleis unclear as to whether the data or the molecules areimprecise, while the third example is entirely ambiguousas to whether it was the proteolytic enzymes or the testproteins that were derived from the clam. Clearer versionsof these titles might read as follows: “ Bacterial species identi  󿬁 cation using matrix-assisted laser desorption/ ionization mass spectrometry ”“ Limits to determination of molecular formulae from accurate massdata of poor precision ”  (In this case the phrase  “  for molecules ”  issuper  󿬂 uous in view of the reference to  “ molecular formulae ” , so theclearer version is also more concise.) “ Enzymes derived from the clam Abra cadabra for site-speci  󿬁 c proteolysis of proteins ”  (This brilliant species name has now sadlybeen changed [9] to the more correct but much more dull Theoracadabra .) The required structure of Abstracts for  RCMS  papers [1] corresponds closely to the IMRAD format (Introduction,Methods, Results, and Discussion) frequently used for thestructure of the paper as a whole. This is discussed in a latersection of the present article. Here it is emphasized that thesame recommendations for conciseness without detractingfrom clarity, as well as good information content, apply alsoto a successful Abstract that can stand on its own. Many journals provide free access to Abstracts even though asubscription (personal or institutional) may be requiredto access the complete paper. Remember that Title andAbstract should attract attention to an extent that manycolleagues will be persuaded to read the entire paper. Itis easier to write several pages describing the experimentalmethod, for example, than a few sentences that summarizethe entire paper. This is an example of the well-known taleof an overworked scientist who sent a report to a supervi-sor with the message:  “ I am sorry I did not have time towrite a one-page report, so I wrote you ten ” . The extratime and effort devoted to devising a good Abstract arecertainly worthwhile. THE STRUCTURE OF THE PAPER Most science journals publish peer-reviewed research writtenin a variety of formats. In the case of   RCMS  most publishedpapers are  Research Articles  that describe major pieces of workwith no restrictions on length, although in the case of verylong manuscripts an Editor may suggest splitting the paperinto two more manageable parts. A  Letter to the Editor  pro-vides a point of view, a critique, or a re-analysis of an articlepreviously published in  RCMS  that highlights novel aspectsof this earlier research. A  Letter  contains no more than about2000 words, sometimes accompanied by 1 – 2 Figures or Tablesin support of the discussion. If the content of a  Letter  is con-tentious, the Editor may invite the authors of the critiquedpaper to respond. Most of the present article is intended tohelp with writing papers of these two types.However,  RCMS  does occasionally publish articles that donot 󿬁 t either of these categories. A  Perspective  is a lightly refer-enced (generally less than 50 references) scholarly opinionpiece about current or future directions in a 󿬁 eld, or an assess-ment of the science directly concerned with a particular topic,or a report on relevant issues that may arise from the disci-pline that are of interest to a broader audience (for examplegovernment policy, effects on society, regulatory issues, andother controversies). The Abstract for a  Perspective  articleobviously will not follow the prescription [1] for new researchpapers. The same is true for  Protocol  articles that describe indetail innovative experimental procedures for mass spectro-metry. Examples might comprise novel sample preparationmethods, chemical labeling techniques, clever or more ef  󿬁 -cient data acquisition routines, intelligent software toolsfor data extraction or mining, etc. Apart from the Abstract, Protocol  articles follow the full  Research  Article format withno restrictions on page length. Review  articles covering a  󿬁 eld of study in depthrequire a very different approach. Although such articlesare generally very highly cited,  RCMS  does not publishreview articles so the present paper can only referreaders to the  Instructions for Authors  of the journal  MassSpectrometry Reviews . [10] R. K. Boydwileyonlinelibrary.com/journal/rcm  Copyright © 2012 John Wiley & Sons, Ltd.  Rapid Commun. Mass Spectrom.  2012 ,  26 , 1725 – 1734  1   7   2   6    Obviously it is important to decide which of these paperformats you are going to use before starting the write-up pro-cess. As part of this initial step it is important for the author todetermine that the quantity and quality of work are suf  󿬁 cientto justify submission as a paper in the chosen format. More-over, the author should ensure that he/she has satis 󿬁 ed thecriteria set out in the journal ’ s  “ Instructions for Authors ” concerning acceptable levels of due diligence in someapplications, such as hypothesized product ion structuresand fragmentation mechanisms, [11] deduction of molecularformulae from accurate mass measurements [12] identi 󿬁 cationof proteins based on peptide sequencing by massspectrometry, [13] etc.A  Research Article  is written in a structured fashion analo-gous to that prescribed [1] for Abstracts in  RCMS , most com-monly using the so-called IMRAD structure [2] (Introduction,Methods, Results and Discussion). In a  Research Article  thesefour sections are indicated by sub-headings usually in boldfont. The Discussion section typically ends with a summaryof the signi 󿬁 cant  󿬁 ndings and their signi 󿬁 cance (andlimitations!), and is typically an expanded version of theConclusions section of the structured Abstract. [1] Someauthors prefer to include this summary as a separateConclusions section with its own sub-heading. Many readerswho have been persuaded by the Title and Abstract to lookfurther at the paper will next turn to the Conclusions part,with or without a sub-heading. So once again it is worthwhilefor an author to expend particularcare in writing this portion.The IMRAD structure is ideal for many kinds of investiga-tion, particularly those for which the experiments can beplanned in advance with little probability that a signi 󿬁 cantchange of plan will be necessary. Typical examples involvingmass spectrometry include method development and valida-tion of a quantitative assay for a target analyte, comparisonof stable isotopic compositions for similar samples fromdifferent srcins, quantum theoretical calculations of poten-tial energy surfaces for gaseous ion reactions, identi 󿬁 cationof proteins from an organism with a well-characterizedgenome via sequencing of tryptic peptides, etc. In the IMRADstructure, [2] the Introduction should describe the problem orhypothesis that was studied, provide a mini-review of previous work on this and related topics, and explain whythe reader would be interested. The Methods section (in RCMS  called the Experimental section) must describe howthe study was conducted in suf  󿬁 cient detail that, in principle,a competent scientist could replicate the study. The Resultssection describes the  󿬁 ndings in the context of the problemor hypothesis described in the Introduction, using a mixtureof Tables and Figures with appropriate text. In cases wherethe raw datasets are very large, these can be made availableelectronically through the  “ Supporting Information ”  facilitiesprovided by many journals including  RCMS . The Discussion(possibly with a separate Conclusions section) should answerthe key question as to what the Results mean in the largercontext of potential value for the scienti 󿬁 c literature summar-ized in the Introduction. In the scienti 󿬁 c spirit this discussionshould also mention any limitations that the authors perceivein their work.Suggestions for how to approach writing each of these sec-tions within an IMRAD structure areincluded later.However,it is appropriate to describe brie 󿬂 y the alternative IRDAMstructure (Introduction, Results, Discussion, and Methods). [2] Some basic research studies begin with a hypothesis to betested, but the experiments are not all planned in advance.Instead the results of one experiment often suggest whichexperiments should be done next. Such experimental inves-tigations are typical of those published in some basic research journals such as  Nature ,  Science ,  Proceedings of the USANational Academy of Sciences , etc. Papers in these journals usea structure in which the Results section immediately followsthe Introduction and the Methods are described at the end.This IRDAM structure implies that the Results section must be organized very differently from that in papers followingthe IMRAD structure. Each experiment must be described ina separate sub-section that includes the reasons why thepreceding experiments required the present new one to beperformed, an overview of the new experimental procedure(details are given in the Methods section at the end of thepaper), a summary and analysis of the observations and adiscussion of their signi 󿬁 cance with respect to the rationaleprovided for this part of the overall study. Thus each of thesesub-sections within the Results section is in effect a sort of mini-paper on its own. The overall conclusions drawn fromthis intrinsically contingent experimental plan are describedin the Discussion section.Some papers that describe investigations whose experi-mental plans involve a signi 󿬁 cant contingent component,where the next experiment is de 󿬁 ned by the results of theprevious one, are indeed published in mass spectrometry journals including  RCMS . Examples include descriptions of development of conceptually new instruments. However, noexamples of papers published in mass spectrometry research journals and written using a formal IRDAM structure areknown to the present writer. Accordingly, unless otherwiseindicated, the following discussion refers to papers writtenusing the IMRAD structure. WHAT MAKES A GOOD INTRODUCTION? The purpose of an Introduction is to introduce the back-ground literature relevant to the new work, describe theknowledge gap or hypothesis to be tested that led to theinvestigation described in the paper, and provide a brief general overview of the experimental or theoretical approachthat was adopted. (Details of the approach belong in theMethods section.) The following suggestions apply to paperswritten using both the IMRAD and IRDAM structures.A common problem in writing an Introduction arises whendeciding whether the amount of information included is toomuch or too little. It can be helpful in this regard to adopt adegree of structure for the Introduction, [2] with a gradualtransition from a general overview to the particular questionor hypothesis investigated in this new work. The  󿬁 rst sub-section discusses the broad context underlying the investiga-tion. For example, suppose the objective was to investigatethe parameters that determine both whether co-eluting com-pounds suppress or enhance the ef  󿬁 ciency of electrosprayionization (ESI) of a target analyte, and the extent of thephenomenon. The  󿬁 rst paragraphs of the Introduction wouldthen outline the development of ESI as a practical techniqueand the progress in understanding the underlying mechan-isms. In view of the extensive literature on this subject,including in-depth reviews, this micro-review need not beextensive although it will be necessary to describe principlesHow to write a paper for RCMwileyonlinelibrary.com/journal/rcm Copyright © 2012 John Wiley & Sons, Ltd. Rapid Commun. Mass Spectrom.  2012 ,  26 , 1725 – 1734  1   7   2   7    that will be important in the subsequent description. Otherthan that, this  󿬁 rst sub-section is really there to set the scenefor what is to follow.The next sub-section begins the process of narrowingdown. In the case of our 󿬁 ctitious example this would involvemoving on to the application of ESI as an interface betweenhigh-performance liquid chromatography (HPLC) and massspectrometry. Again this is a well-established  󿬁 eld, so thissub-section need not be extensive. Only a few sentencesreferencing key papers and reviews will suf  󿬁 ce in thisexample. The last sentence of this sub-section would mentionthe widespread use of HPLC/ESI-MS in quantitative analysisof compounds present in complex matrices, as a transitioninto the third sub-section.In the next sub-section the Introduction really gets downto business and zeroes in on the speci 󿬁 c problem to beaddressed. In our example this will involve the problemsfaced in quantitative analyses as a result of inter-compoundinterferences in the ESI process itself. Here we should acceptthat a more detailed mini-review of the relevant literature, both experimental and theoretical, is required. How muchdetail is appropriate? This will always be a judgement call but some general guidelines can be helpful. It is importantto provide enough information that an interested readerwho is not an expert in the  󿬁 eld of study can  ’ tune-in ’  suf  󿬁 -ciently that he or she can understand the importance of theinvestigation. The author of this paper may have some dif  󿬁 -culty in evaluating this sub-section from the perspective of anon-expert, so it may be helpful to ask a colleague to read itover. At the other limit, that of too much detail, it is importantto avoid too much overlap of the Introduction and Discussionsections. Some overlap is unavoidable, but the author would be well advised to examine the  󿬁 rst complete draft of thepaper with a critical eye in order to avoid needless anddistracting repetition. The Discussion will typically be givenpreference here, since that is where the new observationsare compared with the existing literature.The  󿬁 nal sub-section of the Introduction starts with anexplicit statement by the author of the speci 󿬁 c problem orhypothesis that is addressed in the paper. This statementmust be consistent with the Abstract, in particular (for paperspublished in  RCMS ) with the  ’ Rationale ’  section of the struc-tured Abstract, [1] and can be regarded as a somewhatexpanded version of the latter. This statement is followed byan overview of the approach that was used to investigatethe problem or hypothesis. The technical details belong inthe Methods (Experimental) section. This part of the  󿬁 nalsub-section of the Introduction should be a description of the broad approach. In the case of our ESI example, thisgeneral description might involve use of the best theoreticalunderstanding of the ESI mechanisms as a guide to choiceof test compounds and mobile phase compositions. Amention of the mass spectrometric and HPLC parameters thatwere varied systematically would be appropriate also,though speci 󿬁 c details belong in the Methods section.Appendix1isanexampleofhowsuchanIntroductionmight be written. It is not suggested that the investigation introducedthere is particularly relevant for a mass spectrometry research journal in2012. Rather its purpose istoillustrate how adoptinga general-to-speci 󿬁 c structure, [2] summarized above, can helpproduce an informative Introduction that sets the stage for thedescription and discussion of the new research. WHAT, HOW AND WHY? THEMETHODS SECTION The “ Methods ” sectionisfrequentlylabelledthe “ Experimental ” section or, for some chemistry journals, the  “ Materials andMethods ”  section. For mass spectrometry journals the keyquestions to be answered in this section are  “ what was done ” , “ how was it done ” , and  “ why were these choices made ” . In thecase of clinical chemistry, [2] or indeed any discipline in whichresearch deals with human and/or animal subjects, additionalquestions of   “ who did what and when and where ”  must beaddressed for ethical and legal reasons. However, for mostpapers published in  RCMS  and similar journals, the morelimited set of questions is appropriate when describing themethod in our mass spectrometric madness.In the Methods section conciseness and writing style areless important than completeness. The information must besuf  󿬁 cient to permit a critical reader to judge whether thepaper ’ s conclusions can be legitimately reached from theexperimental or theoretical investigations, and/or to attemptto replicate the reported results if it is suspected that someundetected complication or error might have misled theauthors. Thus, in the Methods section errors of omissionare far more serious than errors of long-winded descriptionsof irrelevant detail. Once again there will always be judge-ment calls as to whether some particular detail is useful orirrelevant. For example, if one of the chemicals is hazardousit is essential that this be drawn to the reader ’ s attention (e.g.in bold type), together with recommendations. For example,it might be suggested that protective gloves should be wornand/or the chemical manipulated in a fume hood. However,a speci 󿬁 cation of the brand of gloves or the manufacturer of the fume hood used in the author ’ s laboratory wouldusually be considered to be an extraneous detail.It is helpful to the reader to organize the Methods sectionwith sub-headings. For example, in our  󿬁 ctitious example of a paper on interference effects in ESI-MS the sub-headingsmight be as follows: Chemicals All chemicals and solvents used should be listed, eachwith its manufacturer or source and its quality (e.g. reagent,analytical or HPLC grade). The latter is important becausethe high but compound-speci 󿬁 c sensitivity of mass spectro-metry implies that it could be susceptible to trace impuritiesthat could preclude reaching any valid conclusions. (A  󿬁 cti-tious account of such a problem, not involving mass spec-trometry, is described by Robert Louis Stevenson in hisnovel about Dr. Jekyll and Mr. Hyde. Dr. Jekyll becomesincreasingly desperate to acquire a sample of an earlier batchof one of the chemicals he used that apparently contained animpurity that was the active ingredient in transforming him between his benign and evil personae:  “ For God ’ s sake,  󿬁 ndme some of the old ” . [14] ) Preparation of compounds, buffer solutions, mobilephases, etc. The amount of detail providedhere should be suf  󿬁 cient that aprofessional chemist should reasonably be expected to repro-duce the same preparations with the same properties as thoseobtained by the author.R. K. Boydwileyonlinelibrary.com/journal/rcm  Copyright © 2012 John Wiley & Sons, Ltd.  Rapid Commun. Mass Spectrom.  2012 ,  26 , 1725 – 1734  1   7   2   8  

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