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New features

You speak, we listen. Mass Dynamics delivers features based on the needs of the community. New features are deployed regularly and can be accessed immediately. No annoying update installations or extra payments.

18th March, 2024

  • Improved performance when rendering Dose Response Visualisations
  • User can now create Dose Response Curves to Work across experiments
  • Change Search to work with protein metadata
  • User can now create Dose Response Volcano plots to work across experiments
  • User can now download all Dose Response visualisations for a tab
  • User can now upload Spectronaut data
  • User can now set dimensions of Dose Response visualisations
  • Introduce a peptide fold change plot

8th February 2023

  • Users can now provide Sample Metadata for driving Dose Response Curve Datasets
  • Users can now create multiple Dose Response datasets at the same time
  • Users can now render a Dose Response Curve from multiple datasets
  • Normalisation of data is now possible when creating a Dose Response Dataset
  • There is now a requirement for pg_matrix and pr_matrix when uploading a Dia-NN experiment
  • MaxLFQ for Dia-NN experiments are no longer used (except TIMS Dia-NN experiments)
  • Users can now view Dataset details that have failed to process
  • Caching between tabs has been improved

4th December 2023

  • Enhanced ability to edit account details
  • Introduced functionality to remove an account
  • Improved capability for downloading tabular data

20th November 2023

  • Allow users to download/export an output table from a Dataset

25th October 2023

  • Free, 30 minute, monthly live online Show Me How sessions launched. Bookings required
  • Rat (Rattus Norvegicus, Taxon ID: 4932) and E. coli (Escherichia coli, Taxon ID: 562) Species for Reactome ORA has now been included
  • Condition comparisons across experiments available to selected Organisations for Volcano Plot module.  Available on request.
  • The experiment name is displayed in emails when an experiment is shared
  • Module text search improvements for the enrichment modules
  • Module naming improvements for consistency across similar modules
  • Search bar now only appears once in the Enrichment Results module
  • Expanded bandwidth improvements to handle large experiments

25th July 2023

  • You can now share your experiment and manage collaborators all in one place.
  • Add all users from your organization (or just select a few)
  • Add any user from outside your organization
  • Remove collaborators from your experiment

3rd June 2023

  • Protein Tracer plot to allow you to trace a protein across all of your historical experiments

15th May 2023

  • Perform Protein-Protein Interaction via StringDB integration
  • Upload your own list of proteins to extend your analysis capacity 

4th February 2023

  • Improved upload experience to now support TIMS DIA-NN
  • Search your Experiment list for easier access to any experiment that you've created
  • Resolution of PNG exports are improved for plots including Differential Expression Volcano Graph, Enrichment Volcano Graph, Log Log Plot, Reactome ORA Bar and Reactome ORA Strip so they are ready for use straight after you export them

16th January 2023

  • Delete your own experiments and have full control over what is stored on the service

17th October 2022

  • Welcome Mass Dynamics V2.0! An improved modular web-based platform for accelerated proteomics insight generation and decision-making
  • Update Fold Change Ratio on Differential Expression Volcano Plots to enable more flexibility with how visualizations are presented
  • Improved upload experience to now support DIA-NN tabular format

16th September 2022

  • Intensity Heatmaps now available to show the log2 intensities of selected proteins across selected runs to enable grouping of proteins of interest
  • Correlation Heatmaps now available to show the protein-protein Pearson's correlations using log2 intensities of selected proteins. 

4th July 2022

  • Upset Plot now available to show the intersection of elements across user-defined protein lists
  • Create a Protein List from Upset Plots
  • Visualize Reactome ORA results with Strip plots 
  • Pairwise Comparison Log Log Plot now available show the signed adjusted p-values on the log scale for two sets of selected pairwise comparisons

30 June 2022

  • Show multiple volcano plots to allow multiple condition analysis
  • Add SVG export option for violin/dot plots
  • Create a protein list from found proteins in a Reactome ORA Pathway
  • Export Volcano plot as an SVG

3 May 2022

  • Protein list management made easier by removing controls for adding, updating and removing protein lists.
  • Select all significant proteins easier for a volcano plot by persisting up and down selections.
  • Speed improvements for creating demo data
  • Search feature for proteins to make it easier to find proteins of interest

24 April 2022

  • Discovery: Added Violin Plots which show protein intensity measurements for seeing protein expression across phenotypes
  • Discovery: Added Dot Plots which show protein intensity measurements for seeing protein expression across phenotypes
  • Discovery: Improved the navigation and usage of the Differential Expression Volcano Plot for easier interaction
  • Discovery: Improved upload experience of MaxQuant experiments and experiments in Generic Format so that we can accept more experiments

16 March 2022

  • Attribute Monitoring PPM Error Review
  • Peptide Mapping Advanced Parameters enabled
  • Peptide Mapping Sharing
  • Updated user experience for discovery
  • Protein lists have been made more prominent
  • For our enterprise customers, we have improved exports of Peptide mapping data

18 February 2022

  • Protein Sequence Coverage map default prioritised choice when filtering
  • Absolute values provided when downloading quantitation data from the graph
  • Autocomplete feature for Naming Category names
  • On the PSM or Quantitation tabs, the Total Percentage coverage for each protein is visible
  • On the PSM Screening or Quantitation tabs, when an amino acid is selected it is then matched and to be reviewed identifications for the amino acid

December 2021

  • December 17th - MD+ Enterprise: Attribute Monitoring, enhanced Reporting and Client View to accomodate representation of results that are less than 1%
  • December 17th - Product Characterisation: A variety of Peptide Mapping experience enhancements including:
    • Total Percentage Coverage for a Protein so you can more easily quantify the total coverage
    • Filter options moved into a popup dialog so you can more easily use the Protein Sequence Coverage Map to navigate results
    • Legends options moved into a help dialog so you have more space to see the list of Identifications
    • Enhanced the exporting of visualisations

November 2021

  • November 21st - MD 1.0: CHO (Chinese Hamster Ovary) is now supported as species for Enrichment Analysis
  • November 16th - Product Characterisation: A variety of Peptide Mapping enhancements including:
    • Expanding and collapsing Identification items that have long sequences so you can view the full sequence string
    • Annotated sequences so you can easily see the position where a modification occurred on a peptide
    • Provide shortcuts to go directly to a Groups Quantitation visualisation so you can navigate faster and easier
    • Allow select all for Identifications when creating a Group so you can perform your work faster and easier
    • Improved spacing so you can have more screen space for PSM Screening and Quantitation Analysis
    • Introduce Retention Time comparisons in PSM Screening
    • Further internal benchmarking against public datasets so you can continue to have confidence in the results
    • Fixed a bug so the link to a peptide mapping study no longer shows an error

October 2021

  • October 21st - Product Characterisation: a new dataset has been added to our automated benchmarking suite to ensure the standardised quality of the Peptide Mapping workflow and service
  • October 14th - Product Characterisation: a variety of PSM screening enhancements to improve the overall Peptide Mapping service experience
  • October 2nd - MD 1.0: Improvement on generic format validation so you still process an experiment successfully even if you accidentally get your number/string format incorrect

September 2021

  • September 16th - Product Characterization: Peptide Mapping experiments using Demo Data "Probing the Sensitivity of the Lumos Mass Spectrometer using a Standard Reference Protein in a Complex Background"
  • September 11th - MD 1.0 'Papers from Journals' experiment added. "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine"
  • September 4th - MD 1.0 'Papers from Journals' experiment added. "Deep muscle-proteomic analysis of freeze-dried human muscle biopsies"
  • September 4th - MD 1.0: Surfaced workflow parameters for Generic Format and MaxQuant experiments so you can see how the workflow processed your data.

August 2021

  • August 20th - MD 1.0 'Papers from Journals' experiment added. "Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics"
  • August 20th - MD 1.0: Table in Enrichment Tab is now ordered by PValue so you can see the smallest PValues first.
  • August 11th - MD 1.0: Added the total number of quantified proteins shown when viewing volcano plot so you can navigate your data better.
  • August 5th - MD 1.0  'Papers from Journals' experiment added. "Label-free proteomic analysis of serum exosomes from paroxysmal atrial fibrillation patients"

July 2021

  • July 19th - MD+ Enterprise: Member can update Project Library meaning more control for the team
  • July 19th - MD+ Enterprise: Deamidation Substitution means deamidation handling can be turned on or off for greater control
  • July 19th - MD+ Enterprise: Trends Plot improvements means better visuals and easier interpretation
  • July 19th - MD+ Enterprise: Client JMP Download for Cross Studies means better and faster offline analysis of studies
  • July 16th - MD 1.0: Data uploaded to Mass Dynamics using a generic format means you can use Mass Dynamics - no matter what software you use to pre-process raw Proteomics Mass Spectrometry data.
  • July 3rd - MD 1.0 'Papers from Journals' experiment added. "TMT Demo: PXD019880: Isobaric matching between runs and novel PSM-level normalization in MaxQuant strongly improve reporter ion-based quantification"

June 2021

  • June 22nd - MD 1.0: In Enrichment, new columns and content for the size of the pathways and the number of proteins in the pathway that we observed means quicker insightsx
  • June 20th - MD 1.0: Identify significantly enriched or over-represented gene sets using Enrichment Analysis via GO and Reactome Databases means quicker and non-biased discovery. See #MassGeek Mastery Enrichment video here.
  • June 10th - MD 1.0: Table in the enrichment tab now ordered by P-Value, showing the smallest P-Values first means easier reviewing of data in the table
  • June 3rd - MD 1.0 Longer session times before being logged out means faster access to your experiments.

April 2021

  • April 23rd - MD 1.0: Improvements to Volcano Plot means easier navigation and usage
  • April 12th - MD+ Enterprise: Creation of custom sample variables means better and faster understanding of data trends
  • April 3rd - MD 1.0: Quality Control report now downloadable means better and easier offline usage with your QC Report. See #MassGeek Mastery QC Report video here

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