Scaffold Quant Release Notes

The following document contains release notes for Scaffold Quant

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

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