Bitter pit is a physiological disorder occurring in apple, pear, and quince and has been associated with calcium uptake or lack thereof. Studied for over a century, little is known regarding the development of bitter pit, what triggers its occurrence, and why there are no completely effective preventative treatments to reduce fruit loss. In the present study, Malus domestica proteins were extracted, injected, and analyzed on a LC Q Exactive mass spectrometer. More than 1500 proteins were identified between bitter pit and healthy samples. To establish quality markers of bitter pit, proteins were filtered using p<0.05 (95 % significance). A total of 170 proteins were identified as quality markers for bitter pit (Whether significantly greater or lower). This study is first to report the bitter pit protein profile in Malus domestica and identify significantly different markers between bitter pit and healthy samples that indicate the occurrence of bitter pit.Peer Reviewe