I am currently working on a research paper in Computer Science which involves quite a few math equations. I am using MS Word currently to write the paper. I haven't yet included the equations. I am planning to send it to a journal.
I have a previously published paper in IEEE Digital Xplore for which I used LibreOffice Writer in Ubuntu to specify the equations and the content. I thought it wouldn't matter what platform I used because I would later convert the document into PDF format. But in the actual paper available on the website, the equations all look pixelated and downright illegible.
My question is, what is the standard way of specifying equations for a research paper? Should I convert the whole document to LaTex and specify equations there? If so, should I look up on the particular journal format to use before including the content?
[EDIT: this answer refers to contexts in which the publisher is responsible for the typesetting. In contexts in which the author is supposed to produce directly a "ready-to-upload" pdf file, what I write is inappropriate, as correctly noted in the comments.]
Your only responsibility is making sure the equations are readable and understandable to the referees. I assume that the equations looked better in the manuscript that you first submitted, so you are clear.
It's the typesetters'/copy editors' job to make sure that the final pdf looks good, and they should be professionals who know the functioning of the software tools they use and the basic things to check when they convert from one format to another. They should have caught this problem before the paper went online, and fixed it themselves or asked you for a copy of the equations in a different format. They completely failed at doing their job.
You should complain with the publisher and request a change. In addition, you should also let the scientific board of the conference know informally, possibly by contacting the editor you have interacted with. The panel deserves to know that the publisher they use did such a bad job, because they are the ones that can complain at a higher level and change things.