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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.

A. Siliqua-N

Silique-N was programmed to analyze LC-MS data from completely 15N-enriched inorganic nitrate and/or ammonia metabolic labeled peptide samples. The labeling strategy is convenient and economical to autotrophic organisms. As all nitrogen-contained molecules, specifically proteins, are labeled, the 14N- and 15N-coding peptides derived from two groups of separately treated organisms can be distinguished in the MS1 data by the isotopologue difference between the two samples.

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Stable isotope metabolic labeling

B. Silique-D

Silique-D focuses on the quantification of mass spectrometry data from multiple isotope-coded dimethyl-labeled peptide samples. Similar to Silique-N, mass shifts in MS1 data caused by distinct stable isotope dimethyl labeling are used to distinguish peptides from various biological samples. The chemical labeling occurs at the peptide level, so this approach is theoretically applicable to proteomics studies of any living organism, including humans.

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Multiplex stable isotope dimethyl labeling