What's New in Byos and Byosphere 5.7

Byos and Byosphere 5.7 Feature Overview

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.

Top features available in Byos 5.7

• New Multi-Protein Quantitation and Multi-Protein Identification workflows
• New Automatic Match Between Runs algorithms
• New Multi-Condition and Replicates report template
• New %RSD and Peptide Quantitation Curation filters
• New Merged Multi-Input File Identification results
• Search Large Proteomes with New Multi-Protein Preview workflow
• New Automatic Charge State Balancing for PTM analyses
• Enhanced in-silico Peak Alignment for Peptide workflows
• Enhanced Chromatographic Peak XIC Bounding for peptide workflows
• FAST XIC default for all Peptide Analysis workflows
• New Trace peak integration option for Intact workflows
• Enhanced HRIM, Oligo and Empower tools and workflows
• New Oligo internal fragment annotations

Top features available in Byosphere 5.7

• New Multi-Protein Quantitation dashboard template for HCPs
• New Chromatogram dashboard template
• New data source for biophysical data correlation to MS analysis data
• New Biophysical data correlation dashboard template for Peptide MS vs Biophysical data
• Recent Dashboards accessible on the Dashboard homepage
• New visual normalization function and error bar features available for Dashboard visualizations
• New Custom Column feature for metadata use in Web analysis
• New filtering function for Web analysis tables
• Capability to edit numerical setting for Tables, Plots and Spectra within Web analysis
• Byosphere Desktop and Web client enhancements

New Multi-Protein Workflows

As of Byos v5.7 there are three new Multi-Protein Analysis workflows available:

These workflows are applicable to:

• Users who analyze Host Cell proteins from Bioreactors in the early phases of development
• Users who analyze mixtures of proteins in a complex matrix
• Users who need to investigate protein mixtures and quantify proteins in that mixture
• Users who need to monitor levels of specific proteins in a complex mixture (tens of thousands of proteins) across each step of the purification process

Multi-Protein Preview

The Multi-Protein Preview workflow provides a rapid overview of the data and indicates analysis parameters that are likely to be optimal. The Multi-Protein Preview provides the user with the capability to:

• Preview the 'top hits' (proteins) in their data
• Measure the accuracy and precision of their mass spec calibration
• Assess the efficiency of their protein digestion
• Understand the modifications and artifacts in their data

Multi-Protein Identification

The Multi-Protein Identification workflow has been optimized for analyzing mass spectrometry data which is expected to have thousands of proteins, and tens of thousands of peptide identifications. This analysis workflow is available from the default System Workflows.

Multi-Protein Quantitation

The Multi-Protein Quantitation workflow provides a mass spectrometry-based assessment of many proteins at the same time, with features such as:

• Protein Quantitation: Allows the user to provide Label-Free quantitation without the need to cope with complex sample preparation by using information from precursor extracted ion chromatograms (XICs).
• High-throughput analysis: Allows users to study datasets with a large number of proteins (tens of thousands) and quantify proteins from a subset of a database searched (thousands of proteins) at a time.
• Rapid Results: Automatically curates peptide-level data from enzymatic digests to provide quantitative information rapidly, automatically, and report relative quantitation levels.
• Instant Reporting: The interface allows users to rapidly review data generated, as well as interact with the data to produce templated, or customized reports.
• New algorithms: The Multi-Protein Quantitation workflow can automate the following tasks:
  • Check which proteins are quantified across an entire sample set
  • Match between runs to ensure that the same peptides are used for quantitation across the entire study
  • Choose peptides that are consistent across a sample set
  • Automatically curate raw data to ensure that appropriate peptides are used

Oligo Workflow

Internal fragments can now be shown in the MS2 plot for the Oligo Deconvolution workflow

Users can enable internal fragment annotation from the MS2 fragment annotation options dialog

Improvement in stacked plots arrangement in Oligo workflows

The Trace plot now renders plots in the order they appear in the Peaks table, reflecting any active sorting or filtering. This aligns Trace plots with MS1 and Deconvolved plots, ensuring consistent curve display order across all plots and making it easier to compare samples.

Peptide Workflow

A new advanced command to aid XIC generation for MS2 identified peptides by assuring same charge states between peptides is now available

When using this advanced command, in-silico peptides will be added to the project so that any version of a peptide (unmodified and modified species) will all contain XICs for the same charge states, in order to allow for fair relative quantitation calculations across different species of the same peptide:

[Byologic]

FillMissingChargeStates=true

True:

False:

FastXIC is now enabled by default for all Peptide workflows

Improved behavior for generating in-silico charge state XICs in Peptide projects

Add Missing Peptide Charges has been updated to proceed automatically.

If this option is selected, a dialog will ask if the user would first like to make a copy of the document prior to adding in-silico peptide charge states.

If the user selects “Yes”, the software will automatically begin the XIC additions once the project copy has been saved. In-silico peptides will be added to the project so that any WT/Variant peptide pair will have the same charge states available.

Byonic

Workflow switch has been added for merging Byonic results

A Merge results into a single project option has been added to the Byonic node in the Multi-Protein Identification workflow and it is enabled by default.

If set to Yes, then the results are merged. Otherwise, multiple .byrslt files are created.

New advanced command for enabling InSilicoAlign for Byonic results

A new option for XIC bounding and peptide quantitation is available with the following advanced command:

[MSFeatureFinderSeg]

UseInsilicoAlign=true

Improvements include improved bounding of noisy peaks, alignment of charge state variants, consistent split proposal across samples, and the preservation of split proposals from distantly eluting isoforms that are indistinguishable by MS2.

Intact Workflow

Ability to set a window for integration around the apex of a peak

A new option was added to the trace peak options in Project Creation to limit the width of peaks to a fixed value relative to the peak apex.

Intact Analysis now supports very high mass peaks

The selection of high masses above 2MDa by the software is now possible in Intact, and these values will be available in both the Masses table and plots.

Chromatogram Workflow

New columns for electropherogram trace support in chromatography workflows to reflect unit pI values

Start pI, End pI, and Apex pI columns have been added to the Peaks table in Chromatography projects that contain electropherograms. The values from the new columns are used to display correct annotations/labels on the Traces plot.

HRIM Workflows

Three new values available in all three HRIM workflows

Three new values are available in all three HRIM workflows (Intact, Peptide, Glycan) -- Start Mobility, End Mobility, and Apex Mobility, all in milliseconds (ms).

Byos and Byosphere

.arw files from Empower are now supported for use in both Byos and Byosphere

Users can now upload .arw exported trace files from Empower to their analysis.

Reporting in Byos

New MPQ_Replicates_and_RSDs.rptc available as default report present for Multi-Protein Quantitation workflow

Full Release Notes

Read detailed release notes directly from the software. Just go to the Help menu > Open User Guides for release notes and up-to-date user guides on all workflows.