Scaffold Software Release Notes

added Implemented a new license key system
added Implemented custom peptide thresholds for MSFragger scores
added Bundled Percolator into the Scaffold installer
added Created a new set of demo files
added Incorporated new graphics and colors to update the look and feel of the program and installers
added Added the ability to link already installed X! Tandem and MSFragger executables to Scaffold
added Added support for MSFragger searches of raw data through Scaffold
added Added support for using either MSFragger or X! Tandem for supplementary searches through Scaffold
added Added a dialog to the Loading Wizard for specification of search parameters for MSFragger
added Added the ability to run MSFragger or X! Tandem supplementary searches through Scaffold Batch
added Added the option to use Percolator to assess peptide probabilities during data loading
added Added a Properties dialog to allow adjustment of axes and other graph properties to Scatterplots and Volcano Plot
added Added support for reading FragPipe results
added Added the ability to read precursor intensity values from PEAKS results
updated Changed the way modifications on peptide termini are annotated in the Proteins View
updated Changed the wording of the SFDB and mzIDentML to reflect move from perSPECtives to Scaffold LFQ
updated Changed the wording of the warning when loading large data sets
updated Changed the wording in the custom peptide threshold dropdown list
updated Updated the wording in the Memory Preferences dialog
updated Improved performance of the search box
updated Realigned the headers and columns in the Spectrum Report
updated Adjusted reading of modifications and peptide sequences from Comet to accommodate different coding in newer versions
updated Adjusted the Comet file reader to accommodate Comet's changes in naming of its scores
updated Allowed duplication of spectrum identifications in mzIdentML files loaded into Scaffold
fixed Fixed an error that occurred with very long sample names
fixed Fixed a problem with labeling modified peptides when a modification applies to more than one amino acid
fixed Fixed a problem with adding multiple star colors through Scaffold Batch
fixed Corrected calculation of PeptideProphet with High Mass Accuracy adjustment when delta masses are very large
fixed Corrected an error in labeling modifications from MaxQuant
fixed Corrected an error in computing the charge state of peptides
fixed Corrected an error that sometimes prevented export of SFDB files
fixed Corrected an error in counting protein clusters
fixed Corrected a problem with incorrectly saved thresholds causing inconsistent values on file reopening
fixed Corrected an error in counting the number of spectra loaded from mzIdentML files with LFDR as the probability model
fixed Corrected an error that produced duplication of input file names when loading newer PEAKS files
fixed Corrected the behavior of the Batch setup GUI for handling of prefiltered data
removed Eliminated 32-bit installers
removed Deprecated the LFDR scoring system in the Loading Wizard
removed Removed the option to condense during loading
removed Stopped bundling X! Tandem into the Scaffold installer

added Added a "clear" button to the advanced filter dialog
added Added tooltips to the column header in the Proteins view peptides table
added Added support for FDR thresholding of MZID data using Percolator PEP or Byonic scores
added Added a helpful message when an already-expired key is activated
added Added drag-and-drop in the license entry dialog
added Allow pasting or dropping License ID and Password at the same time in the license entry dialog
added Allow assigning attributes by dragging an attribute folder onto a sample
added Added feature to include current License ID when reporting errors
added Show more detailed messages in the progress dialog
added Added ability to copy selected text from the publish view
added Added tooltips to violin plots
updated Updated colors, icons and GUI look-and-feel for Scaffold LFQ
updated Improved functionality of the volcano, quantitative scatter and PCA scores plots
updated Improved performance for internal utility methods
updated Improved some error messages when reading an invalid MZID file
updated Improved handling of file paths in an MZID when they are URL-encoded or contain special characters
updated Switched to bundling Java 11 JRE in installers
updated Improved GUI behavior in the bulk edit sample names dialog
updated Replaced "MZID-specified" with "externally-specified" in grouping and thresholding UI
updated Updated default locations for some image exports and attribute file export
updated Updated the Samples view color legend when switching "log intensities"
fixed Fixed "No Clustering" optimization that could cause some groups that passed thresholds to not display
fixed Fixed an infinite loop when trying to draw a box plot with few underlying items
fixed Properly display percentage values in the color options dialog
fixed Fixed incorrect scrolling to selected peptides in very long protein sequences
fixed Fixed graphical artifacts in the protein sequence panel when resizing the window
fixed Prevent the Proteins view from displaying filtered-out proteins
fixed Report the cutoff for decreasing scores unambiguously in the publish view
fixed Fixed bug in the summarization combo box that could prevent editing summarization
fixed Corrected typo in installation error message
fixed Fixed protein selection dropdown options after double-clicking a protein in the volcano plot
fixed Fixed a bug causing the GO Term Filter to not appear when first applying GO terms
fixed Fixed a bug that could cause incorrect normalization of counts for the selected protein after changing summarization or statistical test
fixed Fixed a bug that could cause GO term clustering to randomly fail
fixed Fixed a bug which could cause an error while recomputing heatmap clustering; improve performance of heatmap rebuilds
fixed Fixed a bug that prevented proper opening of files when an attribute category's name contained leading or trailing whitespace
fixed Fixed issues with cut-off text and keyboard focus traversal in the license entry dialog
fixed Ensure that tooltips in quant trend charts correctly respect the "Log Intensities" option
fixed Fixed a hang when copying an EMF image from the PCA scores plot
fixed Fixed resizing of the Organize view when deleting a category; ensure buttons are consistently sized
fixed Fixed a bug when imputing quantitative values with certain sample counts
fixed Fixed an error when sample names contained long sequences of digits
fixed Display group names in volcano plot tooltips instead of "null"
removed Do not show multiple rows for a protein group in the heatmap details
removed Do not display GO Terms that are associated with a protein with the "NOT" qualifier

added Added support for unique peptide counting
added Added context menu option for showing only certain fragment ion series in the fragment chromatogram chart
added Added an exclusivity column to the Samples view
added Added a count of data and reference files in the workflow dialog
added Added a "clear" button to the advanced filter dialog
added Added peptide π₀ to the Publish view and the dashboard tooltip
added Added tooltips to the column header in the Proteins view peptides table
added Added tooltips to violin plots
updated Improved functionality of the volcano, quantitative scatter and PCA scores plots
updated Improved GUI behavior in the bulk edit sample names dialog
updated Improved performance for internal utility methods
updated Improved workflow GUI to simplify library selection, use clearer terminology and link to downloadable public libraries
updated Updated colors, icons, and GUI look-and-feel for Scaffold DIA 3
updated Updated error reporting to include current license ID in reports sent to Proteome Software support
updated Updated the default locations for some image exports and attribute file export
updated Updated Proteins view peptide table mass column presentation to match Scaffold LFQ
updated Updated terminology used for libraries in Publish view
updated Updated EncyclopeDIA from 0.9.6 to 1.2.2
updated Updated the Samples view color legend when switching "log intensities"
updated Changed the bottom pane of the Proteins view to show two tabs side-by-side; allow dragging tabs from side to side
updated Changed the bundled JRE to Java 11 in installers
updated Fragment chromatogram chart now scales vertically to optimally show quantified fragments
updated Only show searchable ELIBs when picking a library
updated Display more detailed messages in the progress dialog
updated Samples view now sorts proteins by total identified peptide count instead of protein score
updated Replaced usages of the plural "data" in the Publish view
updated Capture the Percolator version when searching only a single sample
updated Allow importing attributes files with a first column containing raw file names
updated Allow CLI workflows to override the default expected peak width used by EncyclopeDIA
updated Allow assigning attributes by dragging an attribute folder onto a sample
updated Allow copying selected text from the publish view
updated Allow the CLI to perform library searches with a workflow that doesn't specify modifications
updated Allow updating the msconvert location used for raw file conversion without restarting the program
fixed Fixed incorrect scrolling to selected peptides in very long protein sequences
fixed Fixed a bug that could cause incorrect normalization of counts for the selected protein after changing summarization or statistical test
fixed Fixed a bug that could cause GO term clustering to randomly fail
fixed Fixed a bug which could cause an error while recomputing heatmap clustering; improve performance of heatmap rebuilds
fixed Fixed a bug that prevented proper opening of files when an attribute category's name contained leading or trailing whitespace
fixed Fixed issues with cut-off text and keyboard focus traversal in the license entry dialog
fixed Fixed a hang when copying an EMF image from the PCA scores plot
fixed Fixed resizing of the Organize view when deleting a category; ensure buttons are consistently sized
fixed Fixed a bug when imputing quantitative values with certain sample counts
fixed Fixed bug in the summarization combo box that could prevent editing summarization
fixed Fixed a bug causing the GO Term Filter to not appear when first applying GO terms
fixed Fixed a bug that prevented loading searches with long mod names
fixed Fixed an error when sample names contained long sequences of digits
fixed Ensure that the currently-selected protein is visible when switching to the Samples view
fixed Ensure that settings that won't affect the current search type are not written to workflow files
fixed Ensure that the fragmentation table matches the fragment annotations provided by EncyclopeDIA when fragment masses are ambiguous
fixed Ensure that the Samples view table header reflects renaming of attributes in all cases
fixed Ensure that tooltips in quant trend charts correctly respect the "Log Intensities" option
fixed Prevent potentially-lengthy threshold recomputation when the threshold hasn't changed
removed Do not attempt to launch the GUI after running the installer in headless mode
removed Do not show multiple rows for a protein group in the heatmap details
removed Do not display GO Terms that are associated with a protein with the "NOT" qualifier

added Implemented a new licensing system
added Implemented a Command Line Interface (CLI) for Elements
added Implemented block editing of sample names
added Implemented a new Experimental Design dialog
added Added support for repeated measures, two-way ANOVA and randomized block experiments
added Implemented automatic sorting to bring selected adducts to the top of the selection list.
added Added a log intensity checkbox to the main window to toggle between display of intensities and log10 intensities in all views
added Added the ability to display unidentified features without lowering the scoring thresholds
added Added Quantitative Trend charts and an Intensity/CV chart to the Visualize View
added Added violin plots to the Analyte Level Charts in the Analytes View
added Added a supplementary data export to the Publish View
added Added a Statistics table to the Analytes View
added Added an option to copy only selected text in the Publish View.
added Added the ability to copy chart data from the Volcano Plot and Quantitative Scatterplot.
added Added labels to nodes representing analyte groups in the Volcano Plot
updated Redesigned the Organize View
updated Enhanced the Samples Report to allow the user to select various display options
updated Improved error reporting in import of CSV-formatted library files
updated Improved wait dialog messages
updated Improved the procedure for detection of ion charge
updated Adjusted the default file open and save positions
updated Changed the method of imputing missing values to QRILC
updated Changed the default location for saving indexed feature files
updated Changed the installer, launcher, desktop, and dock icons
updated Modified the wording relating to location of stored indexed feature files
updated Increased landing area for cursor to display tooltip in MS2 spectra
updated Reimplemented report generation to improve performance
updated Recreated the demo files
updated Altered the file signature to enforce licensing restrictions
updated Updated the Publish View, including draft text for publications
updated Updated the default version of msconvert to 3.0.19254 to support the Exploris
updated Updated the graphics, colors, and look and feel of the program
fixed Corrected an error that allowed display of a single ion as both identified and unknown
fixed Corrected a GUI error when moving the 3D plot tab
fixed Corrected some minor textual issues in the GUI
fixed Corrected a benign error in heatmap clustering
fixed Ensured the text in the Publish View updates when the normalization method is changed
fixed Ensured that the Samples View scrolls to make analytes selected through other Views visible
fixed Fixed an error in hiding analytes in clusters
fixed Fixed the display of a selected row in the Search Information table in the Organize View
removed Eliminated the separate Elements Viewer program, allowing unlicensed copies of Elements to operate in Viewer mode
removed Removed RT clustering unless the "Treat each MS1 peak group as a single analyte" option is selected
removed Removed internal borders in display panes
removed Disabled the copy/save/print options in the structure display in the Analytes View

updated Updated colors, icons, and GUI look-and-feel for Scaffold PTM 4.0
updated Updated to using new licensing system
fixed Fixed an incorrect warning about saved scores for multiply-modified peptides
fixed Fixed a bug that could result in using the wrong summarization level when switching tabs in the Quant view
fixed Fixed a bug where display type controls would sometimes not appear in the Quant view
fixed Disabled analysis of PTM sites without a known location in the protein sequence to prevent incorrect results and errors when viewing such sites in the Proteins and Quant views
removed Removed 32-bit installers
removed Removed support for PTM Batch/Console

fixed Fix a bug where a new installation of the program required Java on the system. All users should update to ensure that the correct version of Java is used