The following document contains release notes for Scaffold Quant
- Scaffold Quant 5.0.3 Release Notes (2022-01-14)
- Scaffold Quant 5.0.2 Release Notes (2021-12-17)
- Scaffold Quant 5.0.0 Release Notes (2021-10-29)
Scaffold Quant 5.0.3 Release Notes (2022-01-14)
Upgraded Log4J version to 2.17.1 to address potential security vulnerability
Scaffold Quant 5.0.2 Release Notes (2021-12-17)
Upgraded Log4J to version 2.16.0 to address potential security vulnerability
Scaffold Quant 5.0.0 Release Notes (2021-10-29)
Add support for loading peaklists from mzML files referenced by mzIdentML files
Add support for labeled quantification types and the ability to switch between labeled and label-free samples
Support extracting reporter ion intensities from iTRAQ- and TMT-labeled spectra, including configurable purity correction
Add iTRAQ/TMT intensity display type
Implement IRS normalization for iTRAQ and TMT display types, including the ability to specify which channels contained pooled samples, to normalize based on the intensity of a specified set of proteins, and to enable/disable IRS and TRL normalization independently
Display details of IRS calculations for each protein in the Proteins Pane
Visualize Pane now contains a chart showing the distribution of peptide intensities in each sample before and after normalization
When viewing labeled quant data, display the intensities for each channel in the Proteins Pane Spectra table
Add TIC display type, calculation of TIC during file loading, and the ability to enable TIC quantification in existing files
Display gene names in the Samples Table. Parse gene names from protein descriptions during data loading and allow parsing gene names in existing files
Add an option to compute fold changes from the corresponding "aligned" reference sample instead of always using the same reference
Add an options to restore original sample names and for regex find/replace in the "Bulk Edit" dialog
Allow using channel name as an attribute for labeled quant samples in the "Bulk Edit" dialog
Add a "Spectra Report" containing all spectrum identifications in the experiment regardless of thresholds
Add a "Spectra by Protein Group" report containing all spectrum identifications associated with each protein group passing thresholds in the experiment
Allow copying data from Quantitative Trend, Protein Level, and Statistics charts
CLI now has options to allow writing spectra, spectra-by-protein, and peptides reports
Rewrite core application data structures to use multi-threading for many more calculations
Various changes to improve performance and GUI responsiveness
Re-implement the Peptides Report for a significant performance increase. Each peptide is now reported once for each protein group, and the protein name and peptide start/stop index columns have been removed.
Alter the display type menu to allow choosing between quantitative types
Allow choosing each display type's normalization in the Advanced Samples Report
When organizing labeled samples show the MS sample and channel in the Organize Pane
During data loading, do not modify any peaks within the mass range for iTRAQ or TMT reporter ions
Add an outline to GO term indications to aid visibility
Only display "hollow" GO term indications in the column(s) for terms that are not confidently associated with the protein, instead of affecting all indications in the row
Move NTT column to the upper table of the Proteins Pane
The Quantitative Trend and Intensity/CV charts always reflects the current display type
Charts do not include samples that are hidden from the Samples Table
Improve progress indication while building some charts
Improve formatting of error messages some charts
The summarization and statistical setup dialog is now centered in the main window when it's opened
Memory settings on macOS now match other platforms
Replace some hard-coded mass values with values read from the Unimod XML file in the program's installation folder
Use consistent terminology for protein clustering techniques
Replace occurrences of "quantitation" with "quantification"
Ensure that settings requiring a program restart are consistently described
Audit third-party dependencies for any versions with know security vulnerabilities and update them to avoid these versions. Note that no known vulnerabilities were found affecting previous releases of Scaffold LFQ
Update some dependencies to avoid warnings written to the console at startup
Switch to a new log output format and log file handling system
Write CLI output to log file
Fix precursor intensity normalization that previously did not reflect the summation of intensities across technical replicates
Don't allow choosing a summarization that excludes all samples
Block the creation of empty samples names in the "Bulk Edit" dialog
Fix truncation of long sample names in reports/exports from the Samples Pane
When a fatal error occurs during data loading the "Queue Files" dialog is not shown again
Ensure samples' statistical test category is indicated in Samples Report
The CLI and Publish Pane now report the same version string as the GUI's "About" dialog
Better respect the user-specified core count restriction
Address uncommon issues where some database operations would fail randomly due to conflicts between multiple threads