Relative label-free quantification (LFQ) of shotgun proteomics data is still the most frequently used approach to comprehensively identify and quantify phosphorylated peptides and their associated proteins across biological samples and conditions. One of the most popular software suites to analyse such (phospho)proteomic datasets is MaxQuant, whose primary output is a set of ‘tables’ in text format, which contains quantitative data on (phospho)peptides and proteins in addition to a variety of supporting information. Despite the popularity of MaxQuant and the increased utilization of phosphoproteomics in biomedical research, there is still a lack of simple and user-friendly tools to support downstream analysis and interpretation.
We have therefore developed Phospho-Analyst, which is an easy-to-use, interactive web application developed to perform differential expression analyses with “one click” and to easily visualize complex phosphoproteomic datasets. If quantitative (total) proteomic information is available for the same samples, Phospho-Analyst normalises all phosphoproteomic results to corresponding protein abundance levels thereby ensuring that only genuine changes in phosphorylation events are considered. Similar to its sibling LFQ-Analyst, Phospho-Analyst provides a wealth of user-analytical features and publication-quality output graphics to facilitate exploratory and statistical analysis and interpretation of quantitative phosphoproteomic datasets. Despite all this, Phospho-Analyst was designed for and can be used by researchers without any prior expertise in (phospho)proteomics, statistics or bioinformatics.