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 |
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