Journal Proofs

What to do when the journal sends your accepted paper back for a final check.

fact_check What a proof is

After a paper is accepted, the journal lays it out in its final style and sends it back once more. That is the proof. It carries the journal's own small edits (a comma, a capital letter, "Conclusion" made "Conclusions"), words they highlighted, and questions for you, usually numbered AQ1, AQ2 and so on. They expect answers within a few days. Journals send proofs in three shapes, and TeXpress reads all three:

folder_zip A ZIP with their LaTeX files (MDPI does this). Their edits are in the file, and their questions sit next to the highlighted words.
picture_as_pdf A PDF with comments on it (Elsevier, Springer Nature, Wiley, IEEE, Taylor & Francis). Highlights, sticky notes, crossed-out words with a replacement, and an author query form at the front or back. The answers go into the publisher's own website.
description A Word file with tracked changes (some journals and most copyediting services). Every change is marked, and questions are comments in the margin.

Whatever the shape, you do not need to open the file. TeXpress lines it up with your manuscript and shows one card per thing the journal did or asked. No AI is involved at any step: the comparison is exact, so nothing is invented.

lock Before you start: the button is locked until you have generated once

The Journal proof button sits in the editor header, next to Generate TeX / ZIP. It stays locked, with a small padlock, until the manuscript has been generated and compiled at least once. That is not a formality: a proof is compared with the version of your manuscript that went to the journal, and there is nothing to compare with before that. Click the locked button and it tells you exactly this. Finish the manuscript, press Generate TeX / ZIP, wait for the compile, and the button opens.

upload_file Step 1: import what the journal sent

Open Journal proof and upload the file exactly as it arrived: the ZIP (or the single .tex file inside it), the PDF, or the .docx. TeXpress works out which shape it is and, for a PDF, which publisher it came from.

1 LaTeX ZIP. Every paragraph, heading, caption and declaration is matched with yours. Only real differences become cards, and every comment the journal wrote becomes a question card attached to the paragraph it is about.
2 Annotated PDF. Every comment, highlight and query marker on the pages is read, together with the author query form, and each one is found in your manuscript by the words it sits on. Cards show the page number and the publisher's own label (AQ3), so you can check against the PDF if you want to.
3 Word with tracked changes. Each changed paragraph becomes an edit card, each comment a question card.

Nothing changes yet. Importing only creates the cards. Your manuscript is untouched until you accept an edit, and the first time you do, TeXpress saves a snapshot you can go back to from the Activity panel.

A PDF with nothing on it? Some publishers put their questions only in an email or in their website. TeXpress tells you when a PDF carries no comments or queries, and then those are answered where they were asked.

edit_note Step 2: go through the cards

Cards are grouped by section, in the order they appear in the paper. A counter at the top shows how many are still to review, and the filter buttons show only the edits, only the questions, only what is left, or only what is done.

edit_note Journal edits show the changed words: removed words struck through in red, added words in green. Use the journal's wording writes the change into your manuscript at once. Keep my wording leaves your text as it is. Undo puts things back either way. If a paragraph has changed since the proof was made, TeXpress says so instead of guessing, and offers I did it in the editor for when you make the change by hand.
info Journal queries show the question and the words it is about. Type your answer in the reply box and save it; the card is then marked answered. If you changed the text instead of replying, click Mark as answered. Reopen brings a card back.
edit Open in editor on any card jumps to that exact place in the editor and highlights the words in question, so you can read the surrounding paragraph or make a bigger change than the card suggests.
group Names and affiliations are always shown as questions, never changed automatically. Every journal writes that block differently, and a wrong guess there is the one mistake that would follow you into print. Make those changes on the Metadata tab.

Two questions journals ask so often that the editor answers them for you

groups "Please provide an author contributions statement." On the Declarations tab, the CRediT builder is a grid of the fourteen standard roles against your authors. Tick the boxes, watch the sentence build itself in the journal's preferred wording (role first with initials for MDPI, author first for Elsevier), and press Insert. You can still edit the sentence afterwards.
segment "Section 3 has only one subsection; we have removed the numbering." Most journals do this, and then ask you to confirm. The Content tab points out a section with a single subsection before you submit, so you can fold it in or add a second one yourself.

download Step 3: send it back

What you send depends on what the journal sent. Once every card is decided, the page tells you which download to use.

folder_zip LaTeX proof: the updated ZIP

Compile preview first. It builds a PDF of the journal's own files with your decisions applied, so you read the result the way the journal will. The journal's original PDF is never sent back, because it was made before your corrections.
Download updated ZIP gives you the journal's bundle: their files unchanged, their LaTeX with your decisions and your replies written under their comments, the compiled proof PDF under their own file name, a fresh references file, and a plain-text list of every query and answer.
Anything you fixed yourself in the editor, a typo, a sentence, a new reference, is picked up too. Each one is marked as an author change in the file and listed for the journal's editors. A reference you add goes into the journal's list at the position where it is first cited, so it gets the right number.
Upload the ZIP wherever the journal asks for the corrected proof.

picture_as_pdf PDF or Word proof: the reply list

These publishers keep the source, so there is no file to patch. Download reply list gives you a plain-text file: every query with its page, its label and your answer, then your decision on every edit they proposed. Paste the answers into the publisher's website, query by query.
For a PDF proof, Annotated PDF is the publisher's own PDF with each of your replies attached to the comment it answers. Some portals ask for exactly that file.
Edits you accepted are already in your manuscript. Corrections you made on your own are for your copy; tell the publisher about them in the portal, where most let you edit the text directly.

Generate TeX / ZIP and the updated ZIP are two different things

Generate TeX / ZIP builds your manuscript in the TeXpress layout for your chosen journal: your own copy, for reading, sharing and archiving. The updated ZIP and the compiled proof PDF on the proof page are the journal's files, laid out their way, with your decisions applied. They will not look identical, and they are not meant to: the journal's version has their page design, their running heads and their comments. The content is the same once you have gone through the cards. Send the journal their files; keep using the editor for yours.

history Good to know

A second proof is imported as a new round. The earlier round stays in the list, and the header badge counts what is still to review in the newest one.
Removing a round removes its cards only. Edits you already accepted stay in your manuscript, and the snapshot taken before them stays in the Activity panel.
Table contents are not compared, only captions. If the journal edited numbers inside a table, check the table yourself.
Collaborators with view access can read the cards and download the response; only editors can import, decide and reply.

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