Browse journals > International Journal for Parasitology: Drugs and Drug Resistance > Guide for authors
Guide for Authors
The International Journal for Parasitology: Drugs and Drug Resistance publishes the results of original research in the area of anti-parasite drug identification, development and evaluation, and parasite drug resistance. The journal also covers research into natural products as anti-parasitic agents, and bioactive parasite products. Studies can be aimed at unicellular or multicellular parasites of human or veterinary importance. Because of its breadth of organism coverage, all contributions should include relevant information about the parasite of interest in order to be comprehensible to non-experts in the particular subject of the articles.
Types of article
The principal form of publication is the full length article which contains substantial results from a major program of research. The journal also accepts brief reports that have similar subject scope as the full-length article, but do not merit a full-length publication.
In addition, the journal provides a medium for highlighting selected articles reporting highly significant original findings, as Editor's Choice Manuscripts. It also commissions articles with emphasis on shorter, focused Reviews of topical issues and strategically important subjects. The journal encourages critical comment and debate on matters of current controversy in the area of parasite drug resistance and anti-parasite drugs via "Current Opinions".Contact details for submission
General enquiries prior to submission should be directed to the Editorial Office: IJPDDR@elsevier.com
Author processing feePolicy and ethics
International Journal for Parasitology – Drugs and Drug Resistance follows an author-pays open access model. The charge for publication is $US1750. This charge is necessary to offset publishing costs - from managing article submission to typesetting, tagging and indexing of articles, hosting articles on dedicated servers, supporting sales and marketing costs to ensure global dissemination via ScienceDirect, and permanently preserving the journal article. The fee excludes taxes.
Care of experimental animals. It is the responsibility of authors to ensure that their practices conform with their national animal ethics guidelines. Submitted papers must contain precise details on the care and use of animals and of experimental procedures, especially interventions such as surgery and tissue sampling, and methods of euthanasia. Referees are asked to indicate whether there is any reason to consider that experimental animals were not well treated or care not taken to avoid distress, and papers may ultimately be rejected on such grounds.
Clinical studies. If the work involves the use of human subjects, the author should ensure that the manuscript contains a statement that all procedures were performed in compliance with relevant laws such as The Code of Ethics of the World Medical Association (Declaration of Helsinki) for experiments involving humans http://www.wma.net/en/30publications/10policies/b3/index.html and institutional guidelines and that the appropriate institutional committee(s) has approved them. Authors should include a statement in the manuscript that informed consent was obtained for experimentation with human subjects. The privacy rights of human subjects must always be observed.Conflict of interest
All authors are requested to disclose any actual or potential conflict of interest including any financial, personal or other relationships with other people or organizations within three years of beginning the submitted work that could inappropriately influence, or be perceived to influence, their work. See also http://www.elsevier.com/conflictsofinterest. Further information and an example of a Conflict of Interest form can be found at: http://elsevier6.custhelp.com/app/answers/detail/a_id/286/p/7923/.
Submission declaration and verificationChanges to authorship
Submission of an article implies that the work described has not been published previously (except in the form of an abstract or as part of a published lecture or academic thesis or as an electronic preprint, see http://www.elsevier.com/postingpolicy), that it is not under consideration for publication elsewhere, that its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere in the same form, in English or in any other language, including electronically without the written consent of the copyright-holder. To verify originality, your article may be checked by the originality detection service CrossCheck http://www.elsevier.com/editors/plagdetect.
This policy concerns the addition, deletion, or rearrangement of author names in the authorship of accepted manuscripts:
Before the accepted manuscript is published: Requests to add or remove an author, or to rearrange the author names, must be sent to the Journal Manager from the corresponding author of the accepted manuscript and must include: (a) the reason the name should be added or removed, or the author names rearranged and (b) written confirmation (e-mail, fax, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed. Requests that are not sent by the corresponding author will be forwarded by the Journal Manager to the corresponding author, who must follow the procedure as described above. Note that: (1) Journal Managers will inform the Journal Editors of any such requests and (2) publication of the accepted manuscript in an online issue is suspended until authorship has been agreed.
After the accepted manuscript is published : Any requests to add, delete, or rearrange author names in an article published in an online issue will follow the same policies as noted above and result in a corrigendum.
CopyrightFollowing signature of this form and payment of the Author Fee, articles will be made universally accessible through ScienceDirect. If excerpts from other copyrighted works are included, the author(s) must obtain written permission from the copyright owners and credit the source(s) in the article.
Upon acceptance of an article, authors will be asked to sign a 'Journal Publishing Agreement'. This includes details of the rights that you retain as author (for more information on this and copyright see http://www.elsevier.com/wps/find/authorsview.authors/authorsrights).
An e-mail will be sent to the corresponding author confirming receipt of the manuscript together with a 'Journal Publishing Agreement form'.
Requests may be completed online via the Elsevier homepage (http://www.elsevier.com/permissions).Retained author rights
As an author you (or your employer or institution) retain certain rights; for details you are referred to: http://www.elsevier.com/authorsrights.
Role of the funding sourceFunding body agreements and policies
You are requested to identify who provided financial support for the conduct of the research and/or preparation of the article and to briefly describe the role of the sponsor(s), if any, in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the article for publication. If the funding source(s) had no such involvement then this should be stated. Please see http://www.elsevier.com/funding.
Elsevier has established agreements and developed policies to allow authors whose articles appear in journals published by Elsevier, to comply with potential manuscript archiving requirements as specified as conditions of their grant awards. To learn more about existing agreements and policies please visit http://www.elsevier.com/fundingbodies.
Language (usage and editing services)Submission
Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who feel their English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English may wish to use the English Language Editing service available from Elsevier's WebShop http://webshop.elsevier.com/languageediting/ or visit our customer support site http://support.elsevier.com for more information.
Submission to this journal proceeds totally online at http://ees.elsevier.com/ijpddr and you will be guided stepwise through the creation and uploading of your files. The system automatically converts source files to a single PDF file of the article, which is used in the peer-review process. Please note that even though manuscript source files are converted to PDF files at submission for the review process, these source files are needed for further processing after acceptance. All correspondence, including notification of the Editor's decision and requests for revision, takes place by e-mail removing the need for a paper trail.
The final pdf should be no larger than 5 MB.Required Information:
If file size cannot be reduced to less than 10 MB, the author should contact the IJPDDR Editorial Office for instructions (IJPDDR@elsevier.com).
Name, affiliation, email, telephone and fax numbers and mail address information for one corresponding author.
This must be the same person nominated as corresponding author on the manuscript title page and this person must submit the manuscript on-line.
The corresponding author, through the web access, is responsible for actions with respect to each paper. E-mail prompts will be delivered only to the corresponding author. Articles can also be tracked by the corresponding author via the online system.
Name and affiliations of all other authors.
Cover letter is mandatory for all submissions and should address the novelty, significance of the work.
Order of filesManuscript should contain (in order) Title, Authors and addresses, Corresponding Author and address, Abstract, Keywords. In numbered sections: 1. Introduction; 2. Materials and methods; 3. Results; 4. Discussion; then Acknowledgements; References; Legends to Figures. Tables with their legends (in separate or combined files, numbered, in order). Figures (in separate files); preferred formats: JPEG, EPS or PDF. Supplementary and multimedia files.
FormatThe preferred format for the text is Microsoft Word. The title page, abstract and text should be formatted with line numbers. The manuscript should be formatted to A4 size paper, in English, double spaced and with 2 cm margins.
Further journal requirementsDuring submission you will also have to confirm that all authors have read the manuscript and accept responsibility for its contents and agree to an 'Ethics in Publishing' document.
Please submit, with the manuscript, the names, addresses and e-mail addresses of 3 potential referees. Note that the Editors retain the sole right to decide whether or not the suggested reviewers are used.
The text should be in single-column format. Keep the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. However, do use bold face, italics, subscripts, superscripts etc. When preparing tables, if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs, not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also the Guide to Publishing with Elsevier: http://www.elsevier.com/guidepublication. Note that source files of figures, tables and text graphics will be required whether or not you embed your figures in the text.
To avoid unnecessary errors you are strongly advised to use the "spell-check" and "grammar-check" functions. Subdivision - numbered sections
Divide your article into clearly defined and numbered sections. Subsections should be numbered 1.1 (then 1.1.1, 1.1.2, ...), 1.2, etc. (the abstract is not included in section numbering). Use this numbering also for internal cross-referencing: do not just refer to 'the text'. Any subsection may be given a brief heading. Each heading should appear on its own separate line. Material and methods
Provide sufficient detail to allow the work to be reproduced. Methods already published should be indicated by a reference: only relevant modifications should be described. Discussion
This should explore the significance of the results of the work, not repeat them. A combined Results and Discussion section is often appropriate. Avoid extensive citations and discussion of published literature. Appendices
This journal does not publish appendices. Information should be included within the manuscript text or provided as supplementary material.
Essential title page informationAbstract
• Title. Concise and informative. Titles are often used in information-retrieval systems. Avoid abbreviations and formulae where possible.
• Author names and affiliations. Where the family name may be ambiguous (e.g., a double name), please indicate this clearly. Present the authors' affiliation addresses (where the actual work was done) below the names. Indicate all affiliations with a lower-case superscript letter immediately after the author's name and in front of the appropriate address. Provide the full postal address of each affiliation, including the country name and, if available, the e-mail address of each author.
• Corresponding author. Clearly indicate who will handle correspondence at all stages of refereeing and publication, also post-publication. Ensure that phone numbers (with country and area code) are provided in addition to the e-mail address and the complete postal address. Contact details must be kept up to date by the corresponding author.
• Present/permanent address. If an author has moved since the work described in the article was done, or was visiting at the time, a 'Present address' (or 'Permanent 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. Superscript Arabic numerals are used for such footnotes.
A concise and factual abstract is required. The abstract should state briefly the purpose of the research, the principal results and major conclusions. An abstract is often presented separately from the article, so it must be able to stand alone. For this reason, References should be avoided, but if essential, then cite the author(s) and year(s). Also, non-standard or uncommon abbreviations should be avoided, but if essential they must be defined at their first mention in the abstract itself. The maximum length of the abstract is 300 words.
A graphical abstract is mandatory for this journal. Authors should supply a thumbnail image for all types of manuscripts. Articles accepted for publication will be featured via a copy of the article abstract together with a thumbnail image to direct people to the manuscript. An image that serves to illustrate the theme of the paper is desired. It can be a figure from the paper or a related image that typifies the content of the paper. Authors must supply the thumbnail image separately as an electronic file. The maximum final dimensions of the thumbnail image will be 5 cm x 5 cm. Please consider readability after reduction, especially if using one of the figures from the article itself.
Highlights are mandatory for this journal. They consist of a short collection of bullet points that convey the core findings of the article and should be submitted in a separate file in the online submission system. Please use 'Highlights' in the file name and include 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point). See http://www.elsevier.com/highlights for examples.
Immediately after the abstract, provide a maximum of 6 keywords, using British spelling and avoiding general and plural terms and multiple concepts (avoid, for example, 'and', 'of'). Be sparing with abbreviations: only abbreviations firmly established in the field may be eligible. These keywords will be used for indexing purposes.
Avoid the use of abbreviations, but if necessary, authors should use the list (click here to see list) as a guide to those terms that need not be given in full, or define each abbreviation on first use.
Authors should provide confirmation of consent from persons acknowledged in manuscripts for example personal communications. This can be provided in a covering letter or by e-mail to the editorial office.
Follow internationally accepted rules and conventions: use the international system of units (SI). If other units are mentioned, please give their equivalent in SI.
Elsevier encourages authors to connect articles with external databases, giving their readers one-click access to relevant databases that help to build a better understanding of the described research. Please refer to relevant database identifiers using the following format in your article: Database: xxxx (e.g., TAIR: AT1G01020; CCDC: 734053; PDB: 1XFN). See http://www.elsevier.com/databaselinking for more information and a full list of supported databases.
Footnotes should only be used in tables. Indicate each footnote in a table with a superscript lowercase letter. Electronic artwork
• Make sure you use uniform lettering and sizing of your original artwork.
• Embed the used fonts if the application provides that option.
• Aim to use the following fonts in your illustrations: Arial, Courier, Times New Roman, Symbol, or use fonts that look similar.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Provide captions to illustrations separately.
• Size the illustrations close to the desired dimensions of the printed version.
• Submit each illustration as a separate file.
A detailed guide on electronic artwork is available on our website:
You are urged to visit this site; some excerpts from the detailed information are given here.
If your electronic artwork is created in a Microsoft Office application (Word, PowerPoint, Excel) then please supply 'as is' in the native document format.
Regardless of the application used other than Microsoft Office, when your electronic artwork is finalized, please 'Save as' or convert the images to one of the following formats (note the resolution requirements for line drawings, halftones, and line/halftone combinations given below):
EPS (or PDF): Vector drawings, embed all used fonts.
TIFF (or JPEG): Color or grayscale photographs (halftones), keep to a minimum of 300 dpi.
TIFF (or JPEG): Bitmapped (pure black & white pixels) line drawings, keep to a minimum of 1000 dpi.
TIFF (or JPEG): Combinations bitmapped line/half-tone (color or grayscale), keep to a minimum of 500 dpi.
Please do not:
• Supply files that are optimized for screen use (e.g., GIF, BMP, PICT, WPG); these typically have a low number of pixels and limited set of colors;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.
Color ArtworkIllustration services
Illustrations of all kinds should be listed together under ′ Legend to Figures′ numbered consecutively and their positions indicated in the text. Figures should be high quality, of an adequate size to ensure clarity, and letters and numbers should be at least 4 mm in height. Magnification should be indicated by inclusion of a scale bar in the figure and its value should be indicated on the figure or in the legend. Each figure should be obvious from its file name. If images have been altered, describe the nature of changes made and software used. This information should be included in the ′ Materials and methods′ section of the manuscript.
Elsevier's WebShop (http://webshop.elsevier.com/illustrationservices) offers Illustration Services to authors preparing to submit a manuscript but concerned about the quality of the images accompanying their article. Elsevier's expert illustrators can produce scientific, technical and medical-style images, as well as a full range of charts, tables and graphs. Image 'polishing' is also available, where our illustrators take your image(s) and improve them to a professional standard. Please visit the website to find out more.
Ensure that each illustration has a caption. Supply captions separately, not attached to the figure. A caption should comprise a brief title (not on the figure itself) and a description of the illustration. Keep text in the illustrations themselves to a minimum but explain all symbols and abbreviations used.
Number tables consecutively in accordance with their appearance in the text. Place footnotes to tables below the table body and indicate them with superscript lowercase letters. Avoid vertical rules. Be sparing in the use of tables and ensure that the data presented in tables do not duplicate results described elsewhere in the article.
The references in the reference list should be in alphabetical order. References to journal articles should contain names and initials of all author(s), year of publication, article title, abbreviation of the name of the journal, volume number and page numbers.Unpublished data, personal communications and papers ′ in preparation′ or ′ submitted′ , abstracts (whether published or not) and these should not be listed in the references (but may be incorporated at the appropriate place in the text); work "in press" may be listed only if it has been accepted for publication. Personal communications must be accompanied by a letter or e-mail from the named person(s) giving permission to quote such information. References to books should also include the title (of series and volume), initials and names of the editor(s) and publisher and place of publication.
Examples:Combes, C., 2001. Parasitism. The ecology and evolution of intimate interactions. University of Chicago Press, Chicago and London.
Kumar, N., Cha, G., Pineda, F., Maciel, J., Haddad, D., Bhattacharyya, M.K., Nagayasu, E., 2004. Molecular complexity of sexual development and gene regulation in Plasmodium falciparum. Int. J. Parasitol. 34, 1451-1458.Pettersson, E.U., Ljunggren, E.L., Morrison, D.A., Mattsson, J.G., in press. Functional analysis and localisation of a delta-class glutathione S-transferase from Sarcoptes scabiei. Int. J. Parasitol.
Sangster, N.C., Dobson, R.J., 2002. Anthelmintic resistance. In: Lee, D.L. (Ed.), The biology of nematodes. Taylor and Francis, London and New York, pp. 531-567.Citation in text
Please ensure that every reference cited in the text is also present in the reference list (and vice versa). Any references cited in the abstract must be given in full. Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list they should follow the standard reference style of the journal and should include a substitution of the publication date with either 'Unpublished results' or 'Personal communication'. Citation of a reference as 'in press' implies that the item has been accepted for publication.
Web referencesJournal abbreviations source
As a minimum, the full URL should be given and the date when the reference was last accessed. Any further information, if known (DOI, author names, dates, reference to a source publication, etc.), should also be given. Web references to published articles can be included in the reference list. Other web references such as software programs, databases and individual web pages, should have the reference details included at the appropriate place within the text.
Journal names should be abbreviated according to the NLM catalogue: http://www.nlm.nih.gov/tsd/serials/lji.html.
Video dataSupplementary data
Elsevier accepts video material and animation sequences to support and enhance your scientific research. Authors who have video or animation files that they wish to submit with their article are strongly encouraged to include these within the body of the article. This can be done in the same way as a figure or table by referring to the video or animation content and noting in the body text where it should be placed. All submitted files should be properly labeled so that they directly relate to the video file's content. In order to ensure that your video or animation material is directly usable, please provide the files in one of our recommended file formats with a preferred maximum size of 50 MB. Video and animation files supplied will be published online in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com Please supply 'stills' with your files: you can choose any frame from the video or animation or make a separate image. These will be used instead of standard icons and will personalize the link to your video data. For more detailed instructions please visit our video instruction pages at http://www.elsevier.com/artworkinstructions.
For non-integrated supplementary files, a footnote should be typed on the title page of the manuscript: ′ Note: Supplementary data associated with this article. A copy of supplementary material should be submitted at the same time as the manuscript. Preferred formats are Microsoft Office for text or graphics and AVI for movie files. Maximum size of files is 10 MB. If files cannot be reduced to 10MB, authors should contact the IJPDDR Editorial Office at IJPDDR@elsevier.com.
The following list will be useful during the final checking of an article prior to sending it to the journal for review. Please consult this Guide for Authors for further details of any item.
Ensure that the following items are present:
One Author designated as corresponding Author:
• E-mail address
• Full postal address
• Telephone and fax numbers
• All figure captions
• All tables (including title, description, footnotes)
• Manuscript has been "spellchecked" and "grammar-checked"
• References are in the correct format for this journal
• All references mentioned in the Reference list are cited in the text, and vice versa
• Permission has been obtained for use of copyrighted material from other sources (including the Web).
Use of the Digital Object IdentifierProofs
The Digital Object Identifier (DOI) may be used to cite and link to electronic documents. The DOI consists of a unique alpha-numeric character string which is assigned to a document by the publisher upon the initial electronic publication. The assigned DOI never changes. Therefore, it is an ideal medium for citing a document, particularly 'Articles in press' because they have not yet received their full bibliographic information. The correct format for citing a DOI is shown as follows (example taken from a document in the journal Physics Letters B):
Ifyou use the DOI to create hyperlinks to documents on the web, they are guaranteed never to change.
One set of page proofs (as PDF files) will be sent by e-mail to the corresponding author (if we do not have an e-mail address then paper proofs will be sent by post) or, a link will be provided in the e-mail so that authors can download the files themselves. Elsevier now provides authors with PDF proofs which can be annotated; for this you will need to download Adobe Reader version 7 (or higher) available free from http://get.adobe.com/reader. Instructions on how to annotate PDF files will accompany the proofs (also given online). The exact system requirements are given at the Adobe site: http://www.adobe.com/products/reader/tech-specs.html.
If you do not wish to use the PDF annotations function, you may list the corrections (including replies to the Query Form) and return them to Elsevier in an e-mail. Please list your corrections quoting line number. If, for any reason, this is not possible, then mark the corrections and any other comments (including replies to the Query Form) on a printout of your proof and return by fax, or scan the pages and e-mail, or by post. Please use this proof only for checking the typesetting, editing, completeness and correctness of the text, tables and figures. Significant changes to the article as accepted for publication will only be considered at this stage with permission from the Editor. We will do everything possible to get your article published quickly and accurately – please let us have all your corrections within 48 hours. It is important to ensure that all corrections are sent back to us in one communication: please check carefully before replying, as inclusion of any subsequent corrections cannot be guaranteed. Proofreading is solely your responsibility. Note that Elsevier may proceed with the publication of your article if no response is received.
The corresponding author, at no cost, will be provided with a PDF file of the article via e-mail (the PDF file is a watermarked version of the published article and includes a cover sheet with the journal cover image and a disclaimer outlining the terms and conditions of use). For an extra charge, paper offprints can be ordered via the offprint order form which is sent once the article is accepted for publication. Both corresponding and co-authors may order offprints at any time via Elsevier's WebShop (http://webshop.elsevier.com/myarticleservices/offprints). Authors requiring printed copies of multiple articles may use Elsevier WebShop's 'Create Your Own Book' service to collate multiple articles within a single cover (http://webshop.elsevier.com/myarticleservices/offprints/myarticlesservices/booklets).
Submission of sequence data to databasesGenBank/DNA sequence linking. In order for automatic links to be made between papers and GenBank, authors should type the accession number in bold, underlined text. Letters in the accession number should always be capitalised. (See the example). When published they will appear in normal type.
Novel nucleotide or protein sequence data must be deposited in the GenBank™ , EMBL or DDBJ databases and an accession number obtained before the paper can be accepted for publication. Submission to any one of the collaborating databanks is sufficient to ensure entry in all. The accession number should be included as a footnote on the title page of the manuscript: 'Note: Nucleotide sequence data reported in this paper are available in the GenBank™ , EMBL and DDBJ databases under the accession number(s)'. If requested the database will withhold release of data until publication. The usual method for submitting sequence data is by the World Wide Web to either GenBank (via BankIt: http://www.ncbi.nlm.nih.gov/BankIt/), EMBL (via WebIn: http://www.ebi.ac.uk/subs/allsubs.html) or to DDBJ (via SAKURA: http://sakura.ddbj.nig.ac.jp/). Special types of submissions, such as genomes, bulk submissions, segmented sets, and population/phylogenetic/mutation studies, can be more easily prepared with the Sequin programme (available from the above Web sites). Authors are encouraged by the databases to update their entries as the need arises.
Example: ′ GenBank accession nos. AI631510, AI631511, AI632198, and BF223228), a B-cell tumor from a chronic lymphatic leukemia (GenBank accession no. BE675048), and a T-cell lymphoma (GenBank accession no. AA361117)′ .Additionally, any multiple alignments of nucleotide or protein data must be submitted to a recognised database and must also receive a unique accession number. The accession number can appear in the text in the relevant section of the Results, as: ′ Alignment files are available by anonymous FTP from FTP.EBI.AC.UK in directory/pub/databases/embl/align or via the EMBLALIGN database via SRS at http://srs.ebi.ac.uk; under accession(s)′ . The usual method for submitting alignments is by the World Wide Web to the European Bioinformatics Institute (via Webin-Align: http://www.ebi.ac.uk). Microarray data, in MIAME-compliant format, should be submitted to ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) or GEO (http://www.ncbi.nlm.nih.gov/geo/). Accession identifiers relating to the data should be provided in the manuscript text.
Policy on bioinformatics papers. In silico analysis: The following guidelines apply to papers that exclusively use in silico analysis or rely heavily on this approach for analysis and conclusions. Such papers should address a significant biological issue or issues. Bioinformatic data should be supported by novel or published biological data. Work would typically use information from a number of databases and even from a number of parasite or host species and use a number of analytical methods. Types of ′ metaanalysis′ are encouraged either across a wide range of parasites or, say, at a number of points in a metabolic or signalling pathway or an immune cascade. In silico analysis may be especially suitable for review articles.Guidelines for reporting of protein identifications using mass spectrometry
The following information should be provided for protein or peptide identifications using mass spectrometry:
1. The program, and version number, used to create peak lists and the parameters used in the creation of the list.Author inquiries
2. The program, and version number, of the program used for database searching. Parameters used for searching should be specified, including, but not limited to, precursor-ion mass tolerance, fragment-ion mass tolerance, modifications allowed for, missed cleavages and enzymes used in protein cleavage.
3. The name and version number of the sequence database used in searches. If a custom-made database is used then complete information on the origin of the sequences and database size should be disclosed. Given the dependence of scoring on database size, the use of a small database, or one excluding contaminants, should be justified. 4. A short description of the methods use to interpret the significance of search results, including any statistical analysis, confidence thresholds and other values specific to judging the certainty of the identification.
5. For large-scale experiments a false-positive determination should be reported. This may be the result of randomized database searches or other approaches.
6. Each protein identification should include the accession number, score generated by the search algorithm used, sequence coverage and the number of unique peptide sequences assigned in the protein identification.
7. Single peptide identifications should include an annotated MS/MS spectrum showing fragment assignments together with the peptide sequence, precursor mass, charge and error.
8. Identifications arising from peptide mass fingerprinting should include an annotated mass spectrum. The number of matched peaks, the number of unmatched peaks and the sequence coverage should also be reported along with all parameters and thresholds used to analyse the data. This includes mass accuracy, resolution, calibration methods, contaminant exclusions along with the scoring scheme used and measure of the false-positive rate.
For inquiries relating to IJPDDR please contact the Managing Editor of IJPDDR at: IJPDDR@elsevier.com. You can track accepted articles at http://www.elsevier.com/trackarticle and set up e-mail alerts to inform you of when an article's status has changed. Also accessible from here is information on copyright, frequently asked questions and more. Contact details for questions arising after acceptance of an article, especially those relating to proofs, will be provided by the publisher.