Physicochemical properties of proteins/peptides are often used to separate proteins/peptides from complex biological samples in proteomics research, which is necessary for the further proteins/peptides identification. So, the analyses of these properties are very important for the design of proteomic experiments and the further analyses of identified results. Current available web-based tools are difficult to analyze large-scale datasets. Here we provide a standalone software ProPAS (Protein Properties Analyses Software) to calculate these properties in local computers. ProPAS could be used to calculate several physicochemical parameters of proteins/peptides, including the isoelectric point (pI), hydrophobicity (Hy) and mass weight (MW). Additionally, ProPAS provides the statistic results to get the number distribution along the parameter values. The results could be copied to other software such as Excel to get the distribution chart. The amino acid composition of all the input proteins/peptides could also be calculated from all input sequences. Detail description, updates and download link for ProPAS could be found at the website of http://bioinfo.hupo.org.cn/tools/ProPAS/propas.htm.