Proteomics is the global analysis of proteins, with mass spectrometry (MS) one of the most prevalent technologies that can characterise and quantify proteins in biological and clinical samples. More recently, affinity platforms such as the Olink proximity extension assay (PEA) are becoming popular due to their ability to analyse small sample volumes with high specificity and sensitivity. As these technologies become more common, the breadth of software algorithms (often called search engines) and packages developed to analyse MS data and quantitative results are often too complex for many researchers to interpret without extensive training or experts’ help. Moreover, various types of proteomic datasets can be generated for different research needs and/or exported from different search engines, which further complicates the matter. There is a clear gap for easy-to-use tools for data pre-processing and analysis, and especially the visualisation of information-rich proteomic datasets.
To cater for this unmet need, 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”. These tools work directly with output files from the most popular search engines, including MaxQuant, FragPipe, Spectronaut (Biognosys), DIA-NN and Proteome Discoverer (Thermo Scientific). The packages support data-dependent acquisition (DDA), data-independent acquisition (DIA) and Tandem Mass Tag (TMT) data, as well as Olink Normalised Protein expression (NPX) data. Each individual web application (LFQ-Analyst, DIA-Analyst, TMT-Analyst, FragPipe-Analyst, Phospho-Analyst, NPX-Analyst) is compatible with output from different software engines and provides a wealth of user-analytical features and publication-quality output graphics to facilitate exploratory and statistical downstream analysis and interpretation. Additionally, each web application will seamlessly tie into a novel module entitled Pathway-Analyst to easily perform pathway and network analyses using various databases (e.g. Gene Ontology, KEGG, String) and tools (e.g. g:Profiler, GSEA). To date, these sites have helped people complete more than 170,000 sessions across 83 countries and have received highly positive feedback. Despite their simplicity, the Proteomic Analyst Suites use state-of-the-art bioinformatic pipelines, and we have made numerous expansions and updates, which will be highlighted here, and they are freely accessible at https://analyst-suites.org/.