IsoQuant: A software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation

Zhongping Liao, Yunhu Wan, Stefani N. Thomas, Austin J. Yang

Research output: Contribution to journalArticle

17 Scopus citations


Accurate protein identification and quantitation are critical when interpreting the biological relevance of large-scale shotgun proteomics data sets. Although significant technical advances in peptide and protein identification have been made, accurate quantitation of high-throughput data sets remains a key challenge in mass spectrometry data analysis and is a labor intensive process for many proteomics laboratories. Here, we report a new SILAC-based proteomics quantitation software tool, named IsoQuant, which is used to process high mass accuracy mass spectrometry data. IsoQuant offers a convenient quantitation framework to calculate peptide/protein relative abundance ratios. At the same time, it also includes a visualization platform that permits users to validate the quality of SILAC peptide and protein ratios. The program is written in the C# programming language under the Microsoft.NET framework version 4.0 and has been tested to be compatible with both 32-bit and 64-bit Windows 7. It is freely available to noncommercial users at

Original languageEnglish (US)
Pages (from-to)4535-4543
Number of pages9
JournalAnalytical chemistry
Issue number10
StatePublished - May 15 2012
Externally publishedYes


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