Scaffold perSPECtives Release Notes

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Jacob Lippincott
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The following document provides a release note archive for Scaffold perSPECtives versions 3.1.0 and below.

Scaffold perSPECtives 3.1.0 Release Notes (2019-12-16)

Scaffold perSPECtives Features

Improved performance in opening large files.

Improved performance in building the protein sequence pane.

Prevented installation of new versions when support contract is expired.

Added TIC values to the Proteins View.

Added the calculated peptide mass to the PSM table in the Proteins View.

Updated the demo files.

Changed installer names.

Scaffold perSPECtives Bug Fixes

Ensured that the set of displayed GO terms is always saved with files.

Modified the display of e-value peptide scores.

Corrected an error in updating of the Publish View after thresholding.

Corrected the heading of the statistical test result column in the export of the Samples View table.

Improved the precision of the calculation of actual peptide mass.

Corrected an error in updating spectral counts upon manual invalidation of peptides in files without decoys.

Improved the calculation of masses and delta masses in the Proteins View.

Corrected the delta ppm value in the spectrum pane when delta value is adjusted.

Hide the precursor intensity column when opening file with no intensity values.

Restored functionality of the spectrum id filter in the Proteins View.

Corrected highlighting behavior of the filter controls on Mac.

Ensured that exports are inactive when no file is open.

Corrected behavior when saving files with pending peptide validation changes.

Removed an unnecessary warning when loading Byonic mzIdentML files.

Corrected an error when attempting to add a star color that was already associated with the protein.

Corrected the peptide sequence display in copied data from the PSM table in the Proteins View.

Added the software version to properties dialog of executable file in Windows.

Corrected display of version used for clustering and thresholding in the Publish View.

Scaffold perSPECtives 3.0.0 Release Notes (2019-06-01)

Scaffold perSPECtives Features

Implemented a new licensing system.

Redesigned the Organize View.

Implemented block editing of sample names.

Implemented a new Experimental Design dialog.

Added support for repeated measures, two-way ANOVA and randomized block experiments.

Updated the Publish View, including draft text for publications.

Added "gap filling" to allow proper experiment-wide protein grouping when combining experiments.

Added the ability to select primary peptide and protein score when combining data with different scoring information.

Implemented a system of protein grouping with parsimony.

Eliminated the Overview tab in the Samples View.

Made clustering of samples optional in the Heatmap.

Added a Similarity tab to the Proteins View.

Added the amino acid residue to the modifications in the Edit > Preferences > Colors dialog.

Created the perSPECtives Batch version of the program to be run through a Command Line Interface (CLI).

Allowed addition of data to an existing file via CLI.

Allowed the selection of a specific taxonomy when applying GO terms.

Enabled setting of memory limits from within program on Mac systems.

Removed the threshold control setting in the Proteins View, relying on the general settings instead.

Added an option to turn off the cursor in the protein sequence display.

Added a menu option to change the "Always as a Viewer" setting.

Added the protein molecular weight to the protein sequence coverage display.

Eliminated the separate perSPECtives Viewer program, allowing unlicensed copies of perSPECtives to operate in Viewer mode.

Added a warning that user should save files which have been converted from a previous version.

Recreated the demo files.

Updated the code signing certificate.

Scaffold perSPECtives Bug Fixes

Corrected a problem with the APFS on newer Mac operating systems.

Added the library searched to the sample information pane in the Organize View.

Changed the rendering of very small score values to scientific notation.

Changed "Filtering" to "Thresholding" in the Publish View.

Corrected behavior when all of a protein’s peptides are marked invalid.

Scaffold perSPECtives 2.2.0 Release Notes (2019-04-29)

Scaffold perSPECtives Features

Prevented opening of files created in a later version with a new schema.

Allowed export of quantitative values with full precision in the Samples Report.

Added validation of regular expressions to the search box in the Organize View.

Prevented allocation of too little memory to launch the program.

Added the corrected p-value to the tooltip in the statistical test results column when adjusted by a repeated measures test.

Scaffold perSPECtives 2.1.0 Release Notes (2017-03-07)

Scaffold perSPECtives Features

Upgraded the Java Version to Java 8.

Added Principal Component Analysis.

Added a Volcano Plot and a Quantitative Scatterplot.

Implemented the ability to select and star proteins from charts, such as the PCA Loadings Plot, Quantitative Scatterplot and Volcano Plot.

Replaced the p-value filter with a statistical significance filter.

Modified the format of the star filter.

Added parsing of Accession Numbers to allow GO annotation with more complex Accession Number format.

Added Pie and Bar charts for GO terms.

Added a molecular weight column to the Samples View.

Added an Export Attributes File button to the Organize View.

Added a sample information pane to the Organize View.

In the Organize View, added highlighting of samples that will be excluded from the experiment because they do not have Attributes selected for Attribute Groups that are in the summarization hierarchy.

Updated the taxonomy.list, gene_ontology.obo and unimod.xml files included in the installer.

Added a spectrum counting demo file.

Scaffold perSPECtives Bug Fixes

Modified the method of downloading and parsing GOA databases.

Made creation of new experiments faster.

Restored the functionality of the Apply Changes button in the Proteins View when validation changes are made.

Restored functionality of the heatmap detail pane.

Restored functionality of the heatmap report.

Ensured that the Samples Overview tab respond to changes in reference, normalization and summarization.

Corrected an error that prevented loading of very large files.

Reloaded the fold-change reference setting during file opening.

Made the Peptide Search feature case insensitive.

Preserved ordering of columns in Samples View when attribute names are changed.

Corrected an error that could cause display of empty Samples Table.

Corrected the behavior of the Clear All Filters button.

Added tooltips to the attribute bands in the heatmap detail display.

Modified the Mascot decoy mzIdentML reader to support Mascot 2.6.

Modified the warning message that appears when mzIdentML files with missing scores are loaded using the MZID-specified Thresholding option.

Ensured that any applied statistical test is updated when Attribute Group, Attribute or Sample names are changed.

Corrected an error in the Proteins View when a new file is created without closing the current file.

Corrected the default file name in Save As.

Made reporting of GO terms in the Samples Table Report more consistent.

Added thresholding, filtering and summarization hierarchy information to the Samples and Heatmap exports.

Corrected an error that caused Accession Numbers to be repeated in the Peptides Table.

Eliminated a silent error when opening files.

Corrected behavior of the Cluster Proteins with Shared Evidence dialog upon closing.

Removed the Number of Annotations column in the GO Term Configuration table to improve performance.

Reformatted the EULA displayed through the Help menu.

Ensured that all Views are empty when no experiment is open.

Corrected a class casting error.

Scaffold perSPECtives 2.0.6 Release Notes (2015-04-24)

Scaffold perSPECtives Bug Fixes

Corrected issue with installation on newer Mac OS X operating systems.

Scaffold perSPECtives 2.0.5 Release Notes (2014-09-19)

Scaffold perSPECtives Bug Fixes

Corrected an error in normalization of quantitative values based on precursor intensity.

Scaffold perSPECtives 2.0.4 Release Notes (2014-08-08)

Scaffold perSPECtives Features

Updated the Help system and the Users' Guide

Added support for precursor intensity quantitation.

Added the ability to read precursor intensity values provided in the title lines of MGF files or intensities specified in mzIdentML files.

Added log2 fold change to the Display Types.

Replaced the modified heat map of the previous version with a Samples Table Overview.

Added a Visualize View containing a true Heat Map.

Removed the expression profile clustering option which was replaced by the Heat Map.

Removed the option to perform expression profile coloring.

Added the ability to filter based on the p-value of an applied statistical test.

Apply thresholding and protein grouping during data loading.

Allow user specification of customized default parameters for thresholding and protein grouping during loading.

By default, when first loading data, the thresholds are as follows:

  • If the data has no decoys, the minimum number of peptides selected under the FDR option in the preferences tab, or MZID thresholds if that is selected in the preferences tab.
  • If the data has decoys, the default FDR levels shown in the preferences tab, or MZID thresholds if that is selected in the preferences tab.

When adding data to an existing file the default thresholds are as follows:

  • For existing data with decoys and an FDR threshold: the FDR thresholds are reapplied at the same levels, with the same minimum number of peptides.
  • For existing data (with or without decoys) with MZID thresholds: MZID thresholds are reapplied.
  • For existing decoy-free data with a minimum number of peptides threshold: When new decoy-free data is loaded, the threshold is reapplied at the same minimum number of peptides; AND When new data with decoys is loaded, FDR thresholds with the same minimum number of peptides and unbounded protein and peptide FDR is applied.

Indicate with parentheses calculated values that depend on missing values.

Improved the Experimental Design interface in the Configure Quantitative Analysis dialog.

Added new export reports and improved existing reports in the Export menu and in the right-click context menus.

Added the ability to export an Attributes file through the right-click context menu.

Display additional information in the Publish View including the perSPECtives version in which the data was thresholded or filtered.

Added the ability to hide columns through the right-click context menu.

Added failure notification to the Find function.

Added colors to indicate statistical significance levels.

Added colors to the View > Summarization menu.

Modified the display of spectral counts in the Peptides Pane to indicate if the count has been adjusted by invalidating peptides.

Renamed the Display Options control Color Options, removed the dropdown for selecting the coloring method. Each Display Type now has its own coloring method and the color options last selected for a specific Display Type become the default color selections for that Type.

Provide an informative message about available updates.

Added a warning about clustering on "any shared evidence".

Removed the Undo and Redo controls.

Activate and display the "clear all filters" icon when data is filtered on protein/accession number.

Made the program compatible with Java 7. Include Java 7 JVM in Mac Installer for compatibility with OS 10.9.

Scaffold perSPECtives Bug Fixes

Improved default file loading and saving locations.

Fixed the automatic download of the "All Proteomes" GOA database.

Allow longer names in imported attributes.

Adjusted the behavior of dialog boxes for queueing files during loading.

Corrected an error in loading files with q-values as scores.

Made the permutation test deterministic.

Allow loading of mzIdentML files containing no threshold information.

Fixed an error that prevented proper loading of certain Scaffold-generated mzIdentML files.

Fixed an error that prevented reloading of the same file during the same perSPECtives session.

Improved the interface for specifying experimental design for quantitative analysis.

Improved performance in populating the GO Annotation Databases table.

Corrected an error that could prevent data from displaying in the Samples View after loading large datasets.

Fixed an error that prevented newly created attributes from appearing in the dropdown for assigning attributes to samples.

Corrected the sort order in the delta PPM column in Proteins View.

Retain protein selection when: performing a sort operation in the Samples View, changing the Display Type in the Samples View or applying a quantitative test.

Removed incorrect tooltip text from the Normalization checkbox. When normalization is not appropriate for the selected Display Type the checkbox is not shown.

Allow proteins to be unstarred and removed from the proteins list when a star filter has been applied. Provide a warning message.

Improved treatment of missing values in quantitative tests.

Scaffold perSPECtives 1.0.3 Release Notes (2013-1023)

Scaffold perSPECtives Features

Added the Benjamini-Hochberg method (a FDR control) to the Statistical Test Coloring Method in the Display Options.

Added the Fisher’s Exact Test to the Quantitative Analysis.

Added the ability to go to a previous match in the Find dialog.

Scaffold perSPECtives Bug Fixes

Updated the protein order in the Proteins View to reflect the order from the Samples View.

Improved the tool tips in the Summarization menu to include attribute names.

Disallowed selecting the Fisher’s Exact Test with normalized data.

Changed default file name when saving a new file.

Scaffold perSPECtives 1.0.2 Release Notes (2013-1015)

Scaffold perSPECtives Features

Added a Heatmap tab in the Samples View.

Added the ability to hide columns in the Samples View with a right click in the table header.

Added the ability, in the Display Options, to save a customized color scheme within a single file.

Scaffold perSPECtives Bug Fixes

Updated statistical coloring when switching between quantitative tests.

Increased the area for the header legend so all text lines are visible.

Fixed a null pointer exception when applying expression profile clustering.

Scaffold perSPECtives 1.0.1 Release Notes (2013-0924)

Scaffold perSPECtives Bug Fixes

Corrected an error which could interfere with the opening of new files.

Corrected a null pointer error when opening a new file in the Proteins View.

Corrected an error in applying the modification filter in the Proteins View.

Made the color of the corresponding column change in the Organize View Table when an attribute group color is changed.

Improved the PNG export of tabular data.

Corrected a typographical error in the license key validation dialog.

Improved performance when switching to the Proteins View.

Ensured that the Proteins View would refresh after clearing user validations.

Adjusted the spacing of the Protein Sequence Panel.

Retain the divider position in the Protein Sequence Panel while switching between proteins.

Close extended tooltip windows on entry of ESC character.

Accommodate longer protein group identifiers when reading mzIdentML files.

Scaffold perSPECtives 1.0.0 Release Notes (2013-09-06)

Scaffold perSPECtives 1.0 Release

Scaffold perSPECtives is still new, so release notes aren't yet available. As soon as version 1.0.1 or higher is released, you will see release notes.

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