Version Release Updates

VERSION 5.4 | December 2023

Top features available in Byos 5. 4
  1. New Intact Reconstruction workflow to correlate peptide level PTM information with intact protein analysis
  2. New Charge Variant analysis with reconstruction workflow to correlate isoelectric point (“pI”) - based analysis results such as iCIEF data with peptide mapping data
  3. New Digested Oligonucleotides workflow now extends oligo analysis of digested samples – DNA and mRNA
  4. New MS1 isotope envelope confidence value for peptide mapping workflows
  5. Enhanced in-source artifact detection to distinguish between sample analysis artifacts from actual sample degradation
  6. XIC enhancements for more consistent AUC calculations and detection of peptide isoforms
Top features available in Byosphere 5. 4
  1. Dashboards with reporting across analysis methods: Template for monitoring Glycosylation at peptide and intact levels
  2. New Intact Dashboard Template for monitoring intact proteins
  3. New File Inspection tool for Dashboard visualizations to review contributing data files
  4. Enhanced Job status notification and reports in Byosphere
  5. CSV Export for file search results from Byosphere

VERSION 5.3 | October 2023

Top features available in Byos 5.3
  1. Enhanced features for simultaneous editing of XIC start and end times
  2. Stacking XIC plots available for all charge states
  3. Multiple charge states available simultaneously in MS1 plot zoom
  4. Improved signal processing for XIC boundaries for in silico peptides subject to interference (including deamidated peptides)
  5. Improved Click-to-click performance during peptide selection in stacked plots mode
  6. Ability to save and load custom protein annotations
Top features available in Byosphere 5.3
  1. Job history available to view within the job queue tab
  2. Traces available in Feature Finder mode within Web Analysis
  3. Enhanced Trace manipulations for all Web Analysis applications allowing overlaying trace plots
  4. Introduction of Baseline Anchors for traces within Web Analysis applications
  5. Allowing merging and splitting peaks for traces within Web Analysis applications
  6. Enhancements to modification target settings allowing termini designation within Web Analysis

VERSION 5.2 | August 2023

Top features available in Byosphere 5.2
  1. Redesigned Byosphere Home page and several updates on the Web Client – including a new Resources page
  2. Introduction of a configurable auto processing portal in the administrative interface
  3. Direct results view of completed jobs from the Desktop Client
  4. Expansion of Protein Characterization data processing in Peptide web analysis application with Feature Finder capability
  5. Several enhancements to Intact web analysis application – improvements to plot annotations and deconvolution preset use
  6. Mass matching improvements for Intact web analysis – Monoisotopic mass matching enabled
  7. Updated Modification Settings harmonized across web analysis applications
  8. Exporting of plots from Web Analysis applications to CSV or to clipboard
  9. Exporting Web Analysis reports to PDF
  10. New visualizations added to Dashboards powered by Deep Query – Scatter plots, Pie Charts and new Gauges

VERSION 5.2 | June 2023

Top features available in Byos 5.2
  1. Improved Glycan Fragmentation Logic – annotate and score tandem MS spectra to aid in Released Glycan characterization
  2. Charge and Monoisotope Checks – Glycan Fragment annotation improvements are available for profile scan data
  3. Implementation of MsReaderMzml – scans and chromatography data from mzML files are now supported
  4. Excel Reports enabled – Excel workbooks can now be generated from Byonic workflows in Byos
  5. Enzyme specificity improved in Peptide Manager – residue specificity of multiple enzymes is now recognized
  6. Input sample names displayed in Byologic projects – actual sample name is now displayed in the protein coverage table
  7. Mass matching improvements – Monoisotopic (vs Average) mass matching now enabled for Intact / Oligo workflows
  8. Enhanced fragment filtering – MS2 fragments assignments below the given threshold can be filtered out

VERSION 5.1 | March 2023

Top Features available in Byos 5.1
  1. Users now can display deconvolution settings in reports for samples processed with the oligo workflow.
  2. Updated PTM Report – All Peptide PTM Quant report tab now displays multiple modifications on the same peptidoform.
  3. Updated ADC report – improved annotation of mixed modifications with same Drug load.
  4. Users can now take advantage of isobar score filtering for significantly accelerated O-glycopeptide searches.

VERSION 5.0 | December 2023

Top features available only in Byosphere 5.0
  1. The Byosphere Web client has a brand-new homepage.
  2. New Byosphere Intact Web Analysis application is available to perform intact protein analysis directly within the web client.
  3. Several intact web analysis workflow templates are available: Intact, Isotope-Resolved, Mass Check, Native and Reduced.
  4. Intact web analysis uses an improved molecular model to assign deconvoluted masses.
  5. New Dashboards powered by Deep Query is available allowing users to collate data across several projects.
  6. Users can create customized dashboards based on system dashboard templates for PTM analyses review and System suitability visualization.
  7. Users can now upload mass spec raw data directly from the web client.
  8. Associated metadata information can be edited for several files in a batch.
  9. New File History Report download options available in the web client, which includes detailed Byos Audit Logs for projects on the Byosphere server.
  10. In the Byosphere Desktop client users can now view and search files by Metadata.
  11. Quick access links are available for User directories from the Local navigation tab of the Desktop Client file browser (Desktop, Downloads, Documents).
  12. New Product Manuals are available for Intact Web Analysis, Dashboards and Virtual Client admin (installed with desktop client or available upon request).
Top Features available in Byos 5.0
  1. A Byonic only workflow is now available as one of the default system workflows.
  2. Intact workflows now support the import of sample data via CSV file import.
  3. In the Oligo workflow, users have the ability to directly associate separate MS2 data with MS1 data.

VERSION 4.6 | September 2022

  1. The ability to view a summed MS1 is now available in Peptide analysis workflows!
  2. Peptide projects now have a feature to overlay theoretical isotope distributions on the observed distribution
  3. The "Score" column in peptide projects displays the 'max' value among all its child rows, instead of a min-max range
  4. A new feature in Intact will allow you to change the m/z dots to stars that will show the relative contribution of a given mass to the observed m/z
  5. Oligo MS2 fragment spectra are now annotated based upon the most likely charge state for a given peak
  6. Additionally, Oligo MS2 annotation labels can be made on an integral that shows the intensity of the entire isotopic cluster
  7. A new advance command helps load Oligonucleotide projects more quickly
  8. Oligonucleotides now have a candidate column showing the full mass sequence
  9. Configurable titles are now available in Intact MassXIC plots
  10. In peptide analysis reports you may now render the mass error plot

VERSION 4.5 | June, 2022

  • In intact workflows modification masses, like those for glycosylation, can now be localized to chains with validated N-linked glycosylation sites.
  • MassXIC feature enabled for Intact Workflows – allow easy comparison of elution profiles of different deconvolved species.
  • Intact and oligo workflows – can now annotate closely spaced peaks with overlapping isotopic envelopes.
  • Oligo Workflow – score column added and can now be used to assess MS2 data quality.
  • Fine control of the glycan cartoons in released glycan and peptide workflows.
  • Glycan structures not available in the default library can be added by IUPAC code input.
  • Report for Released Glycans now includes glycan cartoons.
  • Fold Change Calculation tab for peptide workflow reports – compare inter-sample peptide levels.
  • Adjusting integration limits individually in stacked/multi-sample plots affecting only certain traces and samples is now possible.
  • Improvements to the legend detection in the “Protein Map” have been made in the HDX report allowing the X-Axis to scale on both sides.

VERSION 4.4 | March, 2022

Only Byos

  1. A new feature for retention time calibration using internal reference glycans is now available for more confident released glycan assignments.
  2. Peptide Analysis workflows now include a feature to display glycan cartoons on glycopeptides in reports
  3. Chromatography workflows have been updated to allow manual candidate additions of glycopeptides
  4. Fast XIC options have moved from the advanced parameter section to the processing nodes tab in the graphical interface
  5. Peptide MS2 spectra now have optional annotation of internal fragments in the spectrum viewer
  6. Disulfide processing and annotation in chromatogram workflows are improved in several ways; allowing the import of validated peptide projects, allowing trace labelling of disulfides and new disulfide specific reports
  7. Delta masses in intact can now be assigned to selected samples for simplified Intact MS result generation
  8. There are several key improvements in our Oligonucleotide workflow – MS2 data validation by selecting or restoring best MS2 spectrum annotation; New building blocks added for improved coverage of assembled nucleotides; Sample input tab to import sample information via csv files; new Mass XIC widget; Improved impurity analysis for clipped sequence variants
  9. We have introduced the ability to generate Volcano plots in our reports; this feature is available in all workflows.
  10. Chromatogram comparison projects now enable direct input of MS samples as reference rather than reference projects

Only Byosphere

  1. Byosphere Virtual Client – Byosphere Byos client is installed on a server VM in the Byosphere data center and accessed by the end user via remote desktop
  2. Users can now view other file types in directly in the Byosphere browser, e.g., pdf, png, jpeg, etc., as well as custom rendering for certain csv files
  3. For improved data processing and job manipulation a new feature enables cancellation of running or queued jobs from the desktop Jobs tab
  4. Advanced option to import metadata information from files or added during project creation
  5. Chromeleon CDS generated data can now be accessed directly from the biosphere client file browser

Top 10 Combined

  1.  A new feature for retention time calibration using internal reference glycans is now available for more confident glycan assignments.
  2. Fast XIC options moved from advanced parameter section to processing nodes tab allowing users to enable this feature in the graphical interface
  3. Annotation of internal fragments in spectrum viewer for peptides
  4. Features to handle disulfides in chromatogram workflows by importing projects, allowing trace labelling for involved peptides and specific disulfide reports
  5. Several improvements for our Oligonucleotide workflow – MS2 data validation by selecting or restoring best MS2 spectrum annotation; New building blocks added for improved coverage of assembled nucleotides; Sample input tab to import existing information via csv files; new Mass XIC widget; Improved impurity analysis for clipped sequence variants
  6. New reporting feature for the ability to generate Volcano plots for all applications is now available
  7. Byosphere Virtual Client – Byosphere Byos client is installed on a server VM in the Byosphere data center and accessed by the end user via remote desktop
  8. For improved data processing and job manipulation a new feature enables cancellation of running or queued jobs from the desktop Jobs tab
  9. Advanced option to import metadata information from files or added during project creation
  10. Chromeleon CDS generated data accessed from the File Browser – Byosphere now takes data directly from the Chromeleon Server

VERSION 4.3 | December, 2021

Version 4.3 Release Now Available

New workflows and continued improvements at every level – from Byonic to Byos to Byosphere!

Some highlighted enhancements include (but are not limited to):

Across Products

  • Intact projects now support the ability to switch to an alternate match
  • Intact also now supports the ability to select scan type (MS1, MS2) for all vendors
  • Mass XICs available in the Oligonucleotide workflows allow you to accurately represent the elution profile of a molecule
  • Oligonucleotide software will now process and display MS2 only oligonucleotide data and can average MS2 scans if multiple rows are selected
  • HRIM ease of use enhancements
  • Released glycan projects have an updated “Add Candidate” interface to simplify glycan entry
  • Peptide workflow summary row grouping methods now show all values for ppm, Obs m/z, and Obs. M from child rows are listed in the parent row
  • Byonic now has new options for resolving homologous protein issues
    • Byonic can now exclude homologous peptides when calculating the protein score
    • Customers can choose to prioritize the assignment of a homologous peptide to a specific protein
  • Direct export of peptide data in the Chromeleon Import format
  • Many reporting improvements such as the ability to show both project creation and report generation software versions; an ability to sort pivot values within an existing grouping level; added an average option to the “Normalize” aggregator and many others.
Top features available only in Byosphere

  • Simplified Byosphere Byos Client File Menu Navigation
    • The file menu “Open Project” option can now be used to directly open projects from the server or local saved copies
    • Similarly, when saving an updated project, there is now a “save to server” option
    • if you close a local project without saving to the server, you will now see a reminder that you have not saved to the server yet
    • Other file types can still be uploaded and downloaded through the relocated “Upload” and “Download” options in the file menu
  • Automatic download and association of supporting files.  The Byosphere Byos desktop client will now identify and associate any missing resources and prompt the customer to download them.
  • Superusers and Administrators can now cancel jobs from the web client
  • Administrators can now change job priorities from the web client
  • Byosphere now allows customers to add tailored Metadata tags to their files
    • Administrators can define metadata for the organization
    • Metadata can be added automatically during data uploads
    • Customers can add or edit metadata for any file at any time
    • Some file metadata can be mapped to project setup options
  • New Enhanced web query facilities. A new  ‘Advanced’ query feature that allows much more complex queries based on new metadata fields.
    • Large queries can also be narrowed by means of ‘facets’ that will allow dynamic refinement of searches
  • Queries can be saved and shared with teammates
  • New notification options allow customers to be notified directly in the client as well as by email
  • The Byosphere application server is now capable of supporting auto scaling of analysis server capacity in Amazon, Azure and Google cloud implementations
  • The desktop client now provides better error messages if file downloads fail

VERSION 4.2 | September, 2021

Version 4.2 Release Now Available with Powerful New Functionality

We continue to focus on your success:

New workflows and continued improvements to digestion options, HDX parameters, Byonic annotation, file reading, tutorials, reporting, and more!

Some highlighted enhancements include (but are not limited to):

  • New Byos workflow: Oligonucleotide analysis. MS1-based analysis with MS2 Fragmentation viewer
  • New Byos workflows: HRIM Intact, HRIM Peptide, and HRIM Glycan for MOBILion High-Resolution Ion Mobility (HRIM) analysis
    • HRIM Intact workflow to support intact analysis of MOBILion HRIM data
    • HRIM Peptide workflow to support peptide analysis of MOBILion HRIM data
    • HRIM Glycan workflow to characterize released glycan analysis of MOBILion HRIM data
  • Support for simultaneous C-Term and N-Term specific enzymes (e.g., LysC and AspN)
    • Peptide and Chromatogram Analysis can now support a combination of C-Term and N-Term proteases
  • Advanced feature for grouping in-silico peptides from CSV file with MS/MS peptides
    • In the previous releases, peptides from MS/MS identification and peptides imported from a CSV file (in-silico assignments) were grouped separately. These peptides are now grouped together if the retention times of the peptide from MS/MS and in-silico assignments are same
  • HDX – New signal processing parameters to improve the sensitivity of HDX analysis
  • MS/MS annotation
    • Improved oxonium ion annotation for ECD MS/MS spectra
    • Improved MS/MS annotation at lower m/z regions ( < 500 m/z )
  • Processing – File Reading
    • Bruker – improved analysis with newer chromatogram acquisition of Total Ion Current (TIC) and Base Peak Intensity (BPI) traces
    • Thermo Scientific, Waters, and SCIEX instruments – metadata information such as Vendor, Model, Run date and other fields such as liquid chromatography (LC) setup used for the experiment can now be accessed in Byos
    • Shimadzu – Byos software can now read, parse and analyze the Shimadzu *.lcd SP2 data
  • Reporting – Visualization
    • Add images to reports – drag and drop an image into the free text in a report or the template editor in the summary tab
    • Add a predefined pivot table within a new plots tab
    • Undetected peptides – now annotated in Peptide and Chromatogram Analysis reports through a new label “ND” in the Peak Comment column
    • Duplicate pivot table headers on every page
    • Export images in SVG format
    • Enhanced Excel exporting – merge pivoted rows and columns, display every row and column for each record, and show report details
  • Reporting – Plots and Charts
    • Stacked plots – ability to show/hide stacked plots in the report
    • Show correlation percentage in PCA plot
    • Rotate labels in error bar and line charts
    • Add multiple pie charts in the same window/page
  • Reporting – Disulfide linkages
    • Improved Xlink Class column ordering of disulfide linkages – the Xlink Class column “Expected” will now be ranked higher than other alternatives for the same peptide
    • Improved reporting for disulfide linkages within the same protein – the Xlink Partner Peptide Protein Name now reports the Protein name for disulfide linkages within the same protein
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com

VERSION 4.1 | June, 2021

Version 4.1 Release Now Available with Powerful New Functionality

We continue to focus on your success:

Improvements to stacked plots, Byos project creation usability enhancements, customized filtering in heatmaps, Venn diagrams, plots resizing options, ability to report modifications through antibody CDRs, display features for totals in tables and graphs, and more!

Some highlighted enhancements include (but are not limited to):

  • Read about everything new in the Release Notes. Just go to Help -> Open User Guides menu to find this important document
  • Chemical noise affecting your peptide map or released glycan analysis in Chromatography workflows? Don’t forget you can sum scans to reduce noise! And now time ranges are displayed in the plot
  • Did you like stacked plots but wished for more options? We listened to your feedback and now you can annotate all plots, display your sample name as the plot label, and control the order
  • We are always looking to increase usability. Now Byos project creation defaults to the last used path and there are new workflow upgrade options
  • Beat the heat(maps)! Were you looking for more heatmap customization options? We have added the ability to set thresholds, complete with additional coloring
  • Did you want to include Venn diagrams? Now you can!
  • Plots need to be ready for publication? Now you can resize them
  • Did you want to report the presence of modifications within antibody complementarity determining regions (CDRs)? You can now detail “CDR Start”, “CDR Stop”, and “Is Modification within CDR” in the reports
  • Did you wish you could report totals in tables and graphs? This is now available.
  • Did you want to include your Byos project creation options in the report? Now this important information is present by default
  • We have continued to expand upon the “Conditional fixed modifications” options supported in searches, for any amino acid
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com

VERSION 4.0 | March, 2021

Version 4.0 Release Now Available with Powerful New Functionality

We continue to focus on your success:

Scan summing and noise reduction in Chromatography workflows, HDX with ion mobility, digest enzyme aware protein coverage, more flexible fixed modifications in Byonic, plot labels and reporting capabilities.

Of special note is a default workflow to enable finding your features from MS1 rather than UV. Combined with an updated report template, it will make your MAM life easier.

Some highlighted enhancements include (but are not limited to):

  • Read about everything new in the Release Notes. Just go to Help -> Open User Guides menu to find this important document.
  • Have you struggled with noisy data in the Chromatography workflows and wished you could help make your peaks of interest more visible? Now you can with scan summing and noise reduction.
  • Do you prefer finding your features from MS1 rather than UV? We now have a default workflow to support this, along with an updated report template. Please let us know what you think!
  • You had feedback and we listened, including processing of ion mobility data. Please review the updated User Guide to learn more about our HDX progress.
  • Did you wish you could control how homologous peptide sequences were annotated in the Protein coverage table? This is now available in both Peptide and Chromatography workflows.
  • Were you looking to set custom digests, add the same digest entry to multiple files, etc? We have now simplified this step for you.
  • We have continued to improve upon usability when working with duplicate peptides. We have additions to both Peptide and Chromatography workflows to help you understand your results more quickly.
  • Were you looking to specify fixed peptide-specific modifications? This is now possible for fixed NGlycan, Protein NTerm, and Protein CTerm modifications.
  • We are excited to present to you an enhancement to our plot labeling. Collisions are minimized and you have more control over the amount of labels present in your plots. We are looking forward to your feedback!
  • We have acted upon your feedback and enhanced our exporting capabilities. You will now be able to export the exact image as viewed in your analyses and reports.
  •  As usual, we acted upon several reporting requests including filtering by modifications plus corresponding WT, protein coverage font sizes, line charts can now show slope and intercept, and more!
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com.

VERSION 3.11 | December, 2020

Version 3.11 Release Now Available with Powerful New Functionality

We continue to focus on your success: HDX workflow, review duplicated peptides through Protein summary table and corresponding report, adjust for chromatography variation across samples, free thiol filter in disulfide projects, improved Intact chromatogram annotations, reporting capabilities, and more!

Some highlighted enhancements include (but are not limited to):

  • Read about everything new in the Release Notes. Just go to Help > Open User Guides menu to find this important document.
  • Have you always wanted to complete hydrogen deuterium exchange (HDX) analysis in Byos? Well, good news, because we have a new HDX workflow.
  • Have you heard about the new Intabio Blaze system? We now natively support this with the new iCIEF-MS with Blaze from Intabio workflow.
  • If you wished for a simpler multi-protein interface, we have added a new Protein summary table and corresponding report. This further facilitates the review of duplicated peptides and multispecifics and HCPs.
  • Do you wish you could adjust for chromatography variation? We listened and now changing XICs across multiple files adjusts for chromatography variation across samples.
  • Were you looking for more filtering options in disulfide reports? Good news, we have a new Free Thiol filter for you to give a try.
  • Did you find yourself often updating the Intact chromatogram annotations? We heard you and have updated them to highlight the peak number and most abundant mass name by default.
  • Were you looking to filter protein coverage? This is now available in the Summary table.
  • Do you want to select a scan type (MS1, MS2 or both) and mass range in Intact? This is available through advanced commands.
  • Have you wanted to add numeric labels to the X-axis for Line Charts and Bar Charts? Now you can, even as logscale.
  • As usual, we acted upon several reporting requests including adding colored dots and labels in plots, new exact include mode filters in Plots, short code searches, and more!
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com.

VERSION 3.10 | September, 2020

Version 3.10 Release Now Available with Powerful New Functionality

We continue to focus on your success: update chains in saved sequence combinations for easy bispecific screening, accelerate XIC processing, better handle duplicated peptides in multispecifics and HCPs, generate in-silico peptides for disulfide linkages, customize peaks scoring and annotation, and more!

Some highlighted enhancements include (but are not limited to):

  • Read about everything new in the Release Notes. Just go to Help > Open User Guides menu to find this important document.
  • Did you find yourself having to update file paths after saving customized workflows? We heard you and the paths are now automatically updated.
  • Did you wish it were easier to prepare filing-ready images? We agreed and label dots in the Chromatogram, Deconvolved Mass, and MS1 plots can now be removed.
  • Everyone wants to process more quickly. We have a new tool to accelerate XIC generation – FastXIC.
  • Did you find yourself struggling with bispecifics? Intact wflws now enable the user to update chains in saved sequence combinations, allowing easy screening.
  • Have you been challenged by duplicated peptides in multispecifics and HCPs? These can now be viewed in a new column “Protein summary list”. Inconsistent protein assignments between samples can be corrected to assign to the highest ranking protein to all samples.
  • Have you wanted to enter custom peaks in Byonic? Now you can through user-specified custom peaks scoring and annotation.
  • Did you already love our validators? Well, now there is more to love with further improvements to the Mod Validator a new Wildtype Validator.
  • Did you wish you could select alternative peptide assignments? Good news – the Peptide workflow now includes the new “Replace” button.
  • Were you trying to associate sequence combinations with individual samples? Now you can in the updated Traces table.
  • Were you confused why all non-MS traces were reported as UV? Now you will see UV, FLR, DAD, etc correctly in the Samples tab.
  • We of course have new reporting capabilities including glycan groups to better support glycopeptide analyses, additional columns and tabs for enhanced usability, new color options, and more!
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com.

VERSION 3.9-7 | June, 2020

Version 3.9 Release Now Available with Powerful New Functionality

We continue to focus on your success: extensive customer requests addressed across all Byos® workflows and reporting including generating zoomed plots around observed masses, new “Clipped” status and “Expected Type” column, enhancements to Feature Finder, and more!

Some highlighted enhancements include (but are not limited to):

  • Read about everything new in the Release Notes. Just go to Help > Open User Guides menu to find this important document.
  • Thanks to customer feedback, we have an extensive set of new functionalities for you!
  • Did you always want to automatically generate zoomed plots around observed masses? Good news, we added it! This is set up at project creation.
  • Want to do more in Byos? We added new database options, parameters including Wildcard Search and Custom Crosslink, and the ability to add additional Byonic nodes.
  • Did you find yourself updating many default parameters in Byos? We listened to your feedback and made several updates – Byos is easier to use for more types of analyses.
  • Want to include clips in your recognized modified species? Now you can – the new  “Expected type” column includes a “Clipped” status.
  • Want to view the m/z baseline subtraction in MS1 plots? This is a new option in the Render and zoom options!
  • Are you enjoying the benefits of Feature Finder for MS2 feature matching? We made it even better with two additional parameters.
  • We of course have new reporting capabilities including add free text, edit fonts, filter in the plots tab, and more!
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com.

Version 3.8-11 | March, 2020

Version 3.8 Release Now Available with Powerful New Functionality

We continue to focus on customer success: usability focus for elution peaks and traces, new Peptide Manager for enhanced in-silico capabilities, Sample-protein tab added to Byos, diagnostic peak filtering, pI values, enhanced support for UNIFI integration, new reporting capabilities, and more!

  • Read about everything new in the Release Notes. Just go to the Help > Open User Guides menu to find this important document!
  • Want to enter elution peaks parameters and add traces much more easily? We have done a major usability enhancement – the parameters have been moved to the Samples and Sample input tabs and traces are organized in a Traces table within the Samples/Sample input tabs.
  • Did you always want to use the Sample-protein input tab in Byos? Good news, we added it! The CSV template is created through File > Export > Generate MS path template CSV.
  • Want to intelligently search for distinct masses? Now you can with new MS/MS Filtering, particularly useful for glycans, antibody-drug-conjugates, etc.
  • Do you like our in-silico functionalities but wish everything were in one place? We have a new Peptide Manager providing a color-coded preview of project changes and enhanced control over which rows and columns are affected.
  • We also addressed your requests for Average Mass, Monoisotopic Mass, and Biopolymer Models – users can now designate peptide chain masses without sequences as average mass or monoisotopic mass.
  • Want to include pI values in the Peptides table? A new column was added to the “Peptides” table. This is also included in the report.
  • Interested in the Byos UNIFI Application Programming Interface (API)? We spiffed it up – sample results stored in the Waters UNIFI API can now be loaded directly into Byos. The integration requires installation of the Waters UNIFI API and configuration of both UNIFI and Byos.
  • We of course have new reporting capabilities including advanced color-by features in 3D reporting, multiple color assignments in heatmaps, and more!
  • Any queries? Don’t forget you can always ask for technical support at support@proteinmetrics.com.

Version 3.7 | December, 2019 

Version 3.7-32 | January, 2020

Version 3.7 Release Now Available with Powerful New Functionality

Version 3.7 continues to focus on customer success: enhanced support for oligonucleotide sequences, Feature Finder included in the UI, combinatorial calculations, Protein molecular weight column, additional columns and annotation for monoisotopic mass, new reporting capabilities, and more!

Bug fixes in version 3.7-32 :

  • Byologic: comment counting, in-silico alignment
  • Byomap: fractional minute offsets, label scripts
  • Batcher: File paths
  • I/O: Lumos and Velos Pro data reading
  • Byologic: Feature Finder processing of TOF data
  • Read about everything new in the Release Notes. Just go to the Help > Open User Guides menu to find this important document!
  • Want to enter your oligonucleotide sequences much more easily? We have a new “Oligonucleotide” radio button based upon your feedback on several items including naming conventions, ability to enter custom letters and symbols, and automated updates to the Sequences sub-tab.
  • Did you really enjoy our beta offering of Feature Finder but wished it were in the user interface? You are in luck – this new algorithm which allows the user to scan the MS1 domain for all existent peptides in a sample is now controlled in the UI.
  • Do you wish there was a way to add combinatorial delta masses in Intact Mass? You asked, we listened – this has been added via an “Add combinations” button.
  • We took your feedback on the additional items you wanted to see related to monoisotopic mass – additional columns in the Elution Peaks and Masses tables (Delta mass from most intense, Delta mono mass from most intense, Expected mono mass, Delta mono mass, and Delta mono mass (ppm)).
  • We also addressed your request to highlight the monoisotopic mass in the Deconvolved Mass Spectrum – you will now see an orange diamond at that mass.
  • Want to include the protein molecular weight in the Peptides table? A new column was added to the “Peptides” table in Byologic and Byos. Now you can report your HCPs in molar concentration or in mass concentration.

Version 3.6 | September, 2019  

Version 3.6 Release Now Available with Powerful New Functionality
Version 3.6 continues to focus on customer success: UI update in Intact, WIFF2 processing, stacked plots, support for in-source dissociation, peak evaluation logic, and more.
  • Read about everything new in the Release Notes. Just go to the Help menu to find this important document – it is 18 pages for this release!
  • Want to enter your protein details much more easily? We have taken your feedback on combining chains, defining the number of disulfide bonds, considering clipped species, setting commonly modified residues, specifying atomic weights, and selecting the biopolymer type (DNA, RNA, and the default protein). Yes, you can now use Byos to analyze oligonucleotides.
  • Want to process WIFF2 files from SCIEX? This is now fully supported.
  • Want to use your own PDB file in 3-D reporting? Now you can.
  • Want to quickly identify in-source dissociation (ISD)? A new column was added to the “Candidates” table in the detached glycan workflows.
  • Want to automatically inspect a degradation or sequence variant project for possible false positives without having to toggle between the project and report? Give the new “Mod Validator” and “SVA Validator” a try.