Mass spectrometry-based quantitative proteomics plays an increasingly important role in -omics research because it helps researchers to obtain accurate protein abundances and their changes in a high throughput way. As the experimental strategies of quantitative proteomics are improving rapidly, many quantification algorithms and tools have been developed. However, the community still needs free and flexible software tools with high accuracy and precision. Here, we summarize some novel free tools and algorithms for both relative and absolute quantification, as well as post-processing of the quantification results. The user manuals for these tools are described in step-by-step detail.