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

Figure 2

The functional analysis workflow. Gene name of each protein from IPI FASTA database was extracted by freeQuant. The list of gene name were inputted into g:Profiler via http://biit.cs.ut.ee/gprofiler/gconvert.cgi. A list of functional annotation results for each identified protein in Excel format were then generated by g:Profiler. Each functional annotation result was labeled with value using Benjamini-Hochberg statistic method to show its statistical confidence. Next, the output of g:Profiler in Excel format was analyzed by freeQuant to automatically obtain functional annotation for complex proteomes. Especially in case of g:Profiler generating multiple functional annotation results for a single protein, the annotation result with smallest value was finally selected to annotate the corresponding protein.