freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis

Figure 3

The data analysis pipeline with freeQuant. Three steps were involved. First, raw data were extracted to obtain spectral counts and total ion counts; functional profiling files were achieved through g:Profiler. Second, quantification coupled with biomedical knowledge was analyzed with freeQuant software toolkit using NSAF, MS/MS TIC, and shared peptides. Final, mitochondrial proteins were quantified and qualified by freeQuant. freeQuant software tool was appreciated by biologists, bioinformatics, and so forth.