title: IsoQuant: a software tool for stable isotope labeling by amino acids in cell culture-based mass spectrometry quantitation.
abstract: 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 .
authors.affiliation: Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, United States.
authors.forename: Zhongping
authors.initials: Z
authors.lastname: Liao
authors.forename: Yunhu
authors.initials: Y
authors.lastname: Wan
authors.forename: Stefani N
authors.initials: SN
authors.lastname: Thomas
authors.forename: Austin J
authors.initials: AJ
authors.lastname: Yang
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D002478:Cells, Cultured; D002851:Chromatography, High Pressure Liquid; D030562:Databases, Protein; D006624:Hippocampus / Q000378:metabolism; D007553:Isotope Labeling; D011506:Proteins / Q000032:analysis*; D040901:Proteomics; D051381:Rats; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D000596:Amino Acids; D011506:Proteins