IsoQuant: A Software Tool for Stable Isotope Labeling by Amino Acids in Cell Culture-Based Mass Spectrometry Quantitation

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 http://www.proteomeumb.org/MZw.html.