As a main approach for disease related biomarkers discovery, quantitative research has become a hot topic in proteomics. With the development of experimental methods, the quantitative data processing methods are updated and improved constantly. Two categories of label-free quantitative algorithms are introduced at first, including database-free methods and database searching-based methods. Then, the analysis strategies and the details of the two kinds of methods are described, the advantages and disadvantages are also investigated, the frequently used tools and the corresponding internet resources are summarized. At last, some suggestions for improving the data processing of label-free quantitative proteomics are proposed.