During the last decades, several label-free and label-based proteomic workflows and acquisition strategies have been developed to comprehensively interrogate the proteome of virtually any biomedical sample. As mass spectrometry data is highly complex, software algorithms – often called search engines – are used to convert mass spectrometric raw files into data matrices containing qualitative and quantitative information on peptides and proteins. Postprocessing and further downstream analysis usually requires additional software (such as Perseus) and/or R-based statistical packages, which are exceptional in their ability to visualise and interpret the results, but their general usability is limited by the fact that only highly skilled individuals proficient in proteomics, mass spectrometry and/or bioinformatics are able to use them appropriately. As mass spectrometry-based proteomics gains more and more traction across many different disciplines, this often poses an insurmountable challenge for researchers whose expertise lies elsewhere.
To cater this unmet demand, we have developed the Proteomic Analyst Suites, which is a collection of easy-to-use, interactive web applications to analyse and visualise proteomic datasets with ‘one click’ (encompassing DDA, DIA and TMT data) based on output files from the most popular software packages including MaxQuant, FragPipe, Spectronaut (Biognosys) and ProteomeDiscoverer (Thermo Scientific). Each individual web application (LFQ-Analyst, DIA-Analyst, TMT-Analyst, FragPipe-Analyst, Phospho-Analyst) provides a wealth of user-analytical features and publication-quality output graphics to facilitate exploratory and statistical downstream analysis and interpretation. A novel module entitled Pathway-Analyst is integrated into each web application to easily perform pathway and network analyses using various databases (e.g. Gene Ontology, KEGG, String) and tools (e.g. g:Profiler, GSEA). Despite their simplicity, the Proteomic Analyst Suites use state-of-the-art bioinformatic pipelines, and they are freely available at https://analyst-suites.org/.