In almost all cases you should transcribe a quotation exactly as it appears in the source. However, you may occasionally want to italicize words in a quotation to call special attention to them. If you add italics for emphasis, indicate that you’ve altered the quotation by using the phrase emphasis added (or my emphasis), like this:

Lincoln specifically advocated a government “for the people” (emphasis added).

To include an in-text citation with a quotation you’ve altered, put the citation first, followed by a semicolon, and then the words emphasis added:

Lincoln specifically advocated a government “for the people” (Brown 512; emphasis added).

For more on permissible alterations to quotations, see the MLA Handbook, eighth edition, section 1.3.6.