+ What is the aim of the Alpha Trial?

We are working with a small group of Mass Spec experts to validate that Mass Dynamics works as expected. Once we know that the results are better than today's benchmark, we will start rolling out access to the masses.

We are looking for feedack and validation in the following areas:

  • Are the results better than what you have achieved with your existing workflow?
  • Were you pleased with the experience? Was it easy to use?
  • What features would you like to see next?
  • On completion of the workflow, what would you typically do next and what can we build to support this?
  • Was there anything that confused you?
  • Would you use Mass Dynamics again?

We thank you for your support in helping us through the Alpha Trial.

+ How do I get started with the Alpha Trial?

The Alpha Trial is a closed activity, therefore you will need get the ok from a Mass Dynamics team member. You will then need to sign up here which will secure your spot. On completion of the form, we will get you started by sending you an invitation to Slack (our communications tool of choice). It's here that we will setup your username and password, send you the Mass Dynamics URL and also answer any questions that you may have.

+ How long does the Alpha Trial go for?

The Alpha Trial will close at the end of April.

+ What data do I need to get started?

At Mass Dynamics, we've made it simple to get started. If you have raw or converted files that have been produced using a ThermoFisher Mass Spectrometer instrument, you're good to go.

For the Alpha Trial, we will require that you upload a FASTA file so that we understand the context of your experiment. If you don't have one, you can download one from the Uniprot website.

+ What types of experiments can I use Mass Dynamics for?

The Alpha Trial is limited to Data-Dependant Acquistion, Label-Free Quantitative (DDA LFQ) methods and we will be introducing additional methods in the future.

We recommend the first experiment that you run on Mass Dynamics is one that is:

  • a DDA LFQ experiment
  • Limited to 24 runs
  • Has been created using ThermoFisher mass spectrometers
  • Has been analysed previously (to ensure a more efficient and easier comparison)

+ How does Mass Dynamics handle Missing Values?

Historically, a drawback of the Data-Dependant Approach (DDA) has been the number of missing values (MV) that are generated. Inspired by DeMix-Q, Mass Dynamics uses a novel quantification-centred scoring approach resulting in better dataset completeness (ie less missing values). This involves a hydrid Peptide Identity Propagaton (PIP) method, with a scoring function for quality control, and takes into account deviations from Retention Time, m/z and peptide abundance.

+ Is it compatible with all Mass Spectrometry instruments’ raw data?

Mass Dynamics will be compatible with all instruments, and for the Alpha Trial we are focussing on ThermoFisher.

+ How much does it cost?

Use of the Alpha Trial is free. In exchange for the free results processing, we ask users to provide feedback via a survey at the end of the 2 month Alpha Trial

+ Why are there so few parameters needed?

We have intentionally built the Alpha Trial for simplicity as we want Mass Dynamics to be a tool for the masses. We have limited the number of parameters required, and can activate particular parameters on request.

+ What does the Mass Dynamics workflow do?

Starting with the upload of your raw or converted MS files, Mass Dynamics automates the following steps in the Proteomics Data Analysis workflow:

  • Feature Detection
  • Deconvolution
  • Consensus Mapping
  • Quality Control
  • Database Searches
  • Data Analysis

Mass Dynamics is made possible thanks to clever cloud computing, machine-learning algorithms and exceptional Proteomics expertise.

+ How long should I expect to receive my results?

While your results should be available to you within a few days, the Alpha Trial may uncover unexpected issues which may cause delays. We’ll keep you up to date on Slack.

+ What results files will Mass Dynamics create for me?

When Mass Dynamics has finished processing your files, you will be notifed. Once you log in, you will be given access to your results files that you can download. This includes:

  • A Quality Control (QC) report
  • Feature Tables
  • Peptide Intensity
  • Peptide Table
  • Protein Intensity
  • Protein Table
  • Features Identified
  • Features All
  • MS2

+ Can I share the results with my peers or team leaders?

You sure can. And if you would like to use the results for any other purposes outside of the Alpha Trial, please get in contact with us so the results can be validated.

+ What will happen with my data during and after the Alpha Trial?

All results files that are produced by Mass Dynamics are owned by the submitter of the experiment (researcher). If the workflow’s results wish to be used for any other purposes outside of the Alpha Trial, please get in contact with MD so the results can be validated.

Ingested raw data and results files will only be stored for the duration of the Alpha Trial. It will then be deleted and not accessible by Mass Dymamics or the submitter of the experiment (researcher). Files can be downloaded and saved locally at any given during the Alpha Trial.

+ Slack and MD

Slack is a platform that connects teams with apps, services, and resources they need to get work done. This will be the main channel that the MD team will communicate with you throughout the Alpha Trial.

If you don't yet have an account:

  • Sign up for one - it's free
  • Email the MD team on hello@massdynamics.com and let them know which email address you use for Slack
  • Wait to receive an email adding you to the Mass Dynamics Community Slack workspace
  • Follow the Slack instructions in the email