Protein Metrics Product Updates

Version 5.7 brings new features and functionality across all workflows and products including new Multi-Protein Quantitation and Multi-Protein Identification workflows in Byos and Byosphere.

Version 5.6 brings new features and functionality including a Native intact deconvolution workflow, a new Report Template for UV purity assessment, and a new Traffic Light Sample Status review feature in Byosphere.

Version 5.5 brings new features and functionality including a new default report generated for Byonic workflows in Byos, ability to export theoretical peptide lists from peptide and chromatography project results and a new System Suitability report template.

Version 5.4 brings new features and functionality including a new Intact Reconstruction workflow, a new Charge Variant analysis with reconstruction workflow and a new Digested Oligonucleotides workflow.

Version 5.3 brings new features and functionality including enhanced features for simultaneous editing of XIC start and end times, stacking XIC plots available for all charge states, and job history available to view within the job queue tab in Byosphere.

Version 5.2 brings new features and functionality including Improved Glycan Fragmentation Logic, Charge and Monoisotope Checks, and introduction of a configurable auto processing portal in the administrative interface in Byosphere.

Version 5.1 brings new features and functionality including:

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

Version 5.0 brings new features and functionality including a Byonic only workflow in Byos, a new Byosphere Intact Web Analysis application and new Dashboards powered by Deep Query available in Byosphere.

Version 4.6 brings new features and functionality including updates to the Peptide, Intact and Oligo workflows:

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

• 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.

• A new feature for retention time calibration using internal reference glycans is now available for more confident glycan assignments.
• Fast XIC options moved from advanced parameter section to processing nodes tab allowing users to enable this feature in the graphical interface
• Annotation of internal fragments in spectrum viewer for peptides
• Features to handle disulfides in chromatogram workflows by importing projects, allowing trace labelling for involved peptides and specific disulfide reports
• 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
• New reporting feature for the ability to generate Volcano plots for all applications is now available
• 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
• For improved data processing and job manipulation a new feature enables cancellation of running or queued jobs from the desktop Jobs tab
• Advanced option to import metadata information from files or added during project creation
• Chromeleon CDS generated data accessed from the File Browser – Byosphere now takes data directly from the Chromeleon Server

New workflows and continued improvements at every level – from Byonic to Byos to Byosphere! Some highlighted enhancements include (but are not limited to):

• 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.

Version 4.2 Release Now Available with Powerful New Functionality. New workflows and continued improvements to digestion options, HDX parameters, Byonic annotation, file reading, tutorials, reporting, and more

Version 4.1 Release Now Available with Powerful New Functionality. 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!

Version 4.0 Release Now Available with Powerful New Functionality. 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.

Version 3.11 Release Now Available with Powerful New Functionality. 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!

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!

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!

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!

Version 3.7 Release Now Available with Powerful New Functionality. We continue 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!