Cancer is one of worldwide diseases at the present time. Therefore, scientists are performing intense efforts to prevent and early detection of cancer types. One of the most common types of cancer is colon cancer. In this regard, on time diagnosis paves a new avenue for the treatment process resulting in a healthy individual. Femtosecond (fs) laser desorption ionization mass spectroscopy “LDI-MS” methods offer pioneering opportunities in all areas in science from chemical to biological material analysis. When laser beam is focused on a biological tissue in a high vacuum environment in the sampling chamber, an ion cloud or ion plasma are created by a focused laser beam. This plasma is pumped to the interaction zone of a high resolution mass spectrometer and detected after mass analyser separation according to their mass to charge ratios (m/q). Although all biological molecules have a very similar fragmentation pattern when they are exposed to laser radiation, the intensities of the basic mass components are quite different. The main subject of this work is to open up a path to discrimination analyses and interpretation of spectral data obtained from LDI-MS using principal component analysis (PCA) and factor analysis (FA). In this study, the difference between healthy colon tissue and cancerous colon tissue by using fs LDI-MS methods and PCA as well as FA statistical method skills are presented and a comparison of the performance of methods for the same data is concluded. The analysis of the tissue and the obtained statistical results are given in detail.