SILIQUE™ is a highly accurate and efficient proteomics quantification software package for MS data mining and analysis. It was designed for mass spectrometry (MS) based quantitative proteomics and quantitative post-translational modification (PTM) proteomics. With the assistance of stable isotope labeling, SILIQUE™ is able to provide quantitative proteomics/PTM proteomics results of high confidence using raw MS data, which provide a convenient method of investigating the vast amount of proteomic and metabolic data generated by mass spectrometers. SILIQUE™ utilizes both peptide chromatography data and mass spectrometry data to calculate the relative difference of each peptide in two independently stable isotope-labeled samples. It can be used to quantify MS data generated from either metabolically or chemically stable isotope-labeled peptide samples. Silique-N and Silique-D are two programs currently offered through online services, which are able to quantify the MS data derived from the stable isotope metabolic labeling using 15N-enriched salts, and from stable isotope dimethyl labeling.