Abstract
Label Free Quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web based analysis environment that can analyze and visualize LFQ data produced by software such as Maxquant. Unlike other tools, MD 1.0 utilizes cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardisation in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range.
The MD 1.0 platform is available globally via: https://app.massdynamics.com/.
Contact webb{at}wehi.edu.au
Competing Interest Statement
The authors Giuseppe Infusini, Aaron Triantafyllidis, Paula Burton and Andrew Webb declare that they are founders of Mass Dynamics, a for-profit enterprise, delivering software as a service in the processing, analysis and sharing of proteomics data. Joseph Bloom is an employee of Mass Dynamics.
