MD 2.0 unleashes next level MSP insight generation (Part 2)

MD 2.0 unleashes next level MSP insight generation


In my opinion, MSP is one of the most exciting areas in biological research. By allowing us to accurately model and predict any possible biological outcomes, we can begin to envisage a tomorrow in which human disease does not exist.

The explosion in the use of MS-based proteomics has highlighted the need for robust, user-friendly automation in proteomics, including hardware and software to ensure high levels of quality control, data integrity and reproducibility for proteomic analyses.


Data processing is essential to the success of proteomics and subsequent knowledge generation. To address these issues, Mass Dynamics was established to create a modular web-based platform for accelerated proteomics insight generation and problem solving.

Mass Dynamics was established to create a modular web-based platform for accelerated proteomics insight generation and problem solving.

The original platform, MD 1.0, has been adopted across the globe since its introduction in 2019, with members spread across academic, government and industry settings. 

The new Mass Dynamics 2.0 platform (MD 2.0) gives users the next iteration of functionality, user-friendliness and analytics power. It extends the analytic and collaboration functionalities available in MD 1.0 to support more bottom-up proteomics workflows, improve data import options, integrate with external knowledge bases and facilitate more collaboration.

MD 2.0 simplifies, customizes and templates complex proteomics analysis for rapid insight generation and decision-making from complex proteomics datasets.

Bigger and better data interrogation, analysis and storage

Large-scale studies yield massive data sets that hold the secrets to life, yet our ability to analyze and interpret it is limited and presents a bottleneck in the discovery process.


To create the large data sets required, MS must be coupled with hardware for robust, fast, and automated sample preparation and data acquisition and powerful software to process the datasets reliably and accurately and interpret the data produced. 


And herein lies the rub. The tools that automate highly complicated tasks inevitably end up comprising large amounts of code that must be available for reproducibility. 

Mass Dynamics 2.0 balances the competing needs of reliability, automation (user-friendliness), reproducibility and transparency.


Data can be interrogated and visualized in the form of various plots (dot plot, list table, volcano plot, violin plot, protein expression log log plot) to show the abundance and differential expression of proteins or peptides. 

More importantly, this occurs in real-time and with a bi-directional feedback loop, offering several advantages for experimentation.

The Mass Dynamics platform makes data analysis and storage simple with a user-friendly web interface and secure cloud storage.

Greater user-friendliness

MD 2.0 improves the experience for users, from beginner to expert.

It supports a wider variety of import options, including the direct upload of DDA Thermo *.raw files, processed files from MaxQuant or via a Generic Format upload, and upload of data-independent analysis (DIA) via the integration of DIA-NN.


MD 2.0 also offers the ability for users to drag and drop files for upload and move them to different conditions for each experiment design.

Finally, MD 2.0 offers users both a modular and a flexible system of templates to support a diverse and growing field of users, from newcomers to proteomics to seasoned experts.


Selecting templates automatically populates the tab workspace with pre-determined sets of analysis modules, which may be preferred by beginner users to help speed up analysis and reporting, or those who prefer more rigidly defined experiment analysis flows.


And for more experienced users, MD 2.0 allows the customisation and personalisation of templates and modules to better suit their needs and interrogate data in new ways.


Proteomics calls for a skill set mash-up and greater multi-disciplinary collaboration

Researchers are often super-specialised in their field with limited knowledge and training across other disciplines. Until recently, experimental data would be generated and then moved along the research pathway to a bioinformatics team, with years of specialized training and expertise in computational analysis.


The advent of advanced algorithms, scalable cloud-based computing, standardization of statistical methods (in particular moving toward more objective outcomes in statistics analysis) are set to change this.

MD 2.0 places the power of proteomic analysis back into the hands of researchers. It allows even greater user-friendliness and functionality through drag and drop analysis and visualization modules and templates to create personalized reports.


Using MD 2.0, any user can directly upload pre-processed data with the click of a button. In this way, users across all scientific fields are empowered with user-friendly but powerful bioinformatics tools to interpret data to unlock the power of proteomics, regardless of their level of bioinformatics training.


This means that a company or research lab can use its limited resources effectively, without needing to hire or pass on data to bioinformatics experts. Mass Dynamics analyses are immediately accessible to all collaborators, ensuring that knowledge is rapidly shared – without huge learning curves for new users.

Unlike other available tools, the Mass Dynamics platform utilizes a safe and secure cloud-based architecture to store, manage and rapidly share data analysis with collaborators. 

Web browser access to multiple users enables real-time data sharing with seamless discussions, enabling remote and multi-disciplinary collaboration. 

In this way, MD 2.0 provides better viability to problem solve in corporate environments and research institutes and eliminate the silos that often exist. 

Enrichment analysis with external knowledge integration

The increased functionality in MD 2.0 enables enrichment analysis, a bioinformatics method which identifies enriched or over-represented gene sets to discover their biological meaning.


MD 2.0 seamlessly links LC-MS data to differential expression analysis. It identifies enriched terms from external databases based on comparing protein intensity measurements using the Bioconductor package LIMMA.


Enrichment analysis allows interrogation of data to construct “gene and protein set libraries”, which are groups of genes or proteins defined by common functionality or being on a common pathway (Bloom et al., 2021), from publicly available knowledge bases including UniProt, Gene Ontology (GO) and Reactome. MD 2.0 allows users to make rapid knowledge gains from these integrated database banks.


With greater analytic power and functionality, MD 2.0 is a valuable and powerful tool to enable scientists unpick the very fabric of life, proteins, and this is where truly amazing discoveries of how life exists are possible. 




Bloom, J., Triantafyllidis, A., Burton (Ngov), B., et. al. 2021.Mass Dynamics 1.0: A streamlined, web-based environment for analyzing, sharing and integrating Label-Free Data. bioRxiv 2021.03.03.433806; doi:


MD 2.0 can be accessed at, and the source code for the workflows and knowledge integration is accessible at

Join us our community Slack channel

This is the place to chat about Mass Spectrometry, Proteomics, -omics or anything else you think the #massgeek community would like to hear about.