Mass spectrometry-based phosphoproteomics is a powerful method for investigating the detailed molecular events that occur in response to cellular stimuli. Although thousands of protein phosphorylation sites can be detected and quantified in a single experiment, processing and interpreting this data remains challenging. This is, in part, because utilization of many different websites, software packages and databases can be required for comprehensive analysis resulting in a complicated and iterative process that is difficult for new researches to grasp and cumbersome and time-consuming for those with experience. Here, we present a substantial expansion to our phosphoproteomics data analysis website - ‘Phosphomatics’ – that incorporates a suite of new tools and resources for statistical and functional analysis that aim to simplify the process of extracting meaningful insights from experimental results.
The latest update to Phosphomatics provides a range of new and upgraded features. For example, a significantly expanded data import wizard helps users to intuitively upload and pre-process quantitative phosphoproteomics data from a wide range of search engines including MaxQuant and Spectronaut without the need for manual editing of input files. New methodologies to assess patterns of quant value missing-ness have been introduced as well as additional value imputation and normalization methods. Improved statistical plots provide methods to assess the quality of quantitative data prior to downstream analysis. Methods have been incorporated that allow users to seamlessly track how phosphorylation site groups of interest have been created and combined. Interactive plots can be downloaded as high-resolution vector graphics and capabilities to share and reprocess datasets using downloadable study definition files have been incorporated. Taken together, these expanded features aim to provide a ‘one-stop-shop’ for phosphoproteomics data analysis.
Phosphomatics has achieved approximately 500 unique users, 1000 data analysis sessions and 5,500 page views from users in 40 countries and is freely available via the internet at https://phosphomatics.com/