Mass spectrometry has emerged to be one of the most powerful high throughput techniques for protein analysis, and iTRAQ labeling technique is the one of the newest techniques for protein identification and quantification in this field. Here, we display a new protein abundance analysis software for iTRAQ technique called MassTRAQ that can analyze up to four sets of samples at the same time. We have analyzed two samples with expression level 1:1, and have the result of 1:1.007 with standard deviation 0.004. Thus, Mass-TRAQ provides a good interpretation of the protein analysis. 1
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