Chumash is Torah Shebiksav. When we speak of Mesora, we mean Torah Sheb'al Peh. Interestingly, there is a Mesora of the proper text of our Sifrei Torah. Unfortunately I do not have time to discuss this is detail; I can only give a brief introduction at this time.
The last Rashi in Parshas Noach (11:32) says that the nun in the word Charan is turned over (think of the nuns around vayehi binso'a in Beha'aloscha; but see Minchas Shai there about how the nun looks). The Minchas Shai asks that none of our sifrei Torah have an inverted nun. Are our sefarim kosher? Short answer: yes. He quotes a Teshuvas HaRashba (meyuchasos LeRamban, 232) quoted by Beis Yosef, Y"D 175 who discusses that there are several instances where a word has (or doesn't have) a yud or vav to make it "malei" but we have drashos in Gemara or Midrash that have the word spelled the other way. Many quote from Kiddushin 30a that we (already in the time of the gemara) are not experts in malei and chaser spellings. (About this, see Tosfos, Shabbos 55b s.v. Maaviram, and Gilyon Hashas there, by Rabi Akiva Eiger, who goes through many cases in Tanach were there is a discrepancy). Note that none of these spellings changes the meaning of the word. An answer which has been suggested to explain these differences have to do with the spellings of words in Ksav Livnai as opposed to their spellings in Ksav Ashuri (which we've used since the time of Ezra. See Sanhedrin 21b-22a, and Tosfos Megilla 2b s.v. ve'od).
The small Koren Tanach in the back has a list of differences between texts; there are three in Chumash. One is in this week's Parsha (9:29): Vayehi Bnei Noach or Vayihyu bnei noach.
There are also minor discrepancies where a parsha (blank space in the Torah, almost like a new paragraph) is different in our Torah versus what the Gemara says: In Lech Lecha - by the Bris Bein Habesarim. Se Tosfos Brachos 7b s.v. Lo haya. (About that, see Tzlach there; Netziv in Harchev Davar Breishis 15:8; also my uncle's friend Leesh showed us that Chadashim gam Yeshanim by R' Yehonasan Steif, and Birkas Yitzchak by R' Yitzchak Bernstein of England in Brachos briefly discuss this issue.) The Koren Tanach also lists a discrepency of whether a parsha is at Vayikra 7:28 or 7:22
Rambam, Sefer Torah 8:4 discusses that there are discrepancies in these matters; many of them are machloksim between Ben Naftali and Ben Asher. Rambam found a Torah fixed by Ben Asher in Egypt and lists the locations of all the parshios based on that Torah in Mishna Torah.
Another point which is probably more minor is the idea of Tagin - little "crownlets" on letters. Rabi Akiva made drashos on letters based on how many tagin they have. Some have none, some have one, and the letters "Shatnez Gatz" have three. See Meiri Kiryas Sefer Maamar 2 Cheilek 1 who only discusses Shatnez Gatz. But there are exception - som have four, and some letters sometimes have more than usual. See Ramban Devarim 27:3, that the tagim were copied from the avanim. (See Griz Stencils Menachos 29b.) The ArtScroll Baal Haturim (Davis edition) goes into some depth about tagim because the Tur sometimes discusses them. See there, Vayikra 23:43 (p. 1257) and footnote 138: Sefer Tagin "lists 55 instances where Kof is embellished with 4 tagin and 74 where the final kof has 4 tagin. Basukos in our pasuk isn't on the list, but basukos in pasuk 42 is...either he had a different text or the Raal Haturim has a different mesorah than Sefer tagin."