Scaffold DIA Release Notes

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Scaffold DIA 1.3.1 Release Notes (2019-03-13)

Scaffold DIA Bug Fixes

Fixed issue caused by protein that lacks exclusive peptides.

Scaffold DIA 1.3.0 Release Notes (2019-03-08)

Scaffold DIA Features

Updated EncyclopeDIA version to 0.8.1.

Added a Tools Menu to allow access to EncyclopeDIA utilities.

Changed the Protein Score calculation and FDR thresholding algorithm to provide more accurate FDR thresholding.

Added a Peptide-Profile Correlation metric to the Peptides Table in the Proteins View.

Added a Fragment Consistency score to the Peptides Table in the Proteins View.

Trimmed file paths in the Publish View.

Updated demo files.

Scaffold DIA Bug Fixes

Corrected an error in naming modifications with the same mass on different residues.

Corrected an error in loading workflow files for library searches with modifications.

Corrected an error in displaying the Protein Level Charts bar chart.

Scaffold DIA 1.2.1 Release Notes (2018-12-14)

Scaffold DIA Bug Fixes

Corrected an error in applying GO terms with filters in effect.

Added tooltips to headers in lower table Proteins View.

Fixed broken Help links in Edit > Preferences > System dialog.

Created a warning message to appear if a newer file attempts to open in an older version.

Scaffold DIA 1.2.0 Release Notes (2018-11-20)

Scaffold DIA Features

Added a Heatmap to the Visualize View.

Added the option to change the sample clustering method for Heatmap to the Edit>Preferences menu.

Added support for MSP, TRAML and some SPTXT libraries.

Modified the Workflow Dialog to display modifications that will be used in library searches, and allow editing for annotation purposes.

Added new display types.

Add the ability to save DIA files to a specified location as part of a regular Scaffold DIA run.

Added an option to the File menu to convert files to DIA format for later use in searching.

Added the ability to save custom modifications for re-use.

Added violin plots to the Proteins View and the Visualize View.

Added a chart showing peptide quantities across samples.

Expanded the list of selectable digestion enzymes.

Added a mechanism to specify a custom digestion enzyme.

Applied sorting to file names in the workflow dialog.

Added a tooltip to display full file name when hovering over a file in the Workflow Dialog.

Changed the fragmentation table to display three decimal places.

Added a message indicating successful addition of stars through the Volcano Plot.

Added the option to display quantitative values in intensity or log intensity form.

Added a tooltip to the cells in the Precursor M/Z column.

Added the program version number to the beginning of each session in the error log.

Added support for Agilent raw files.

Added the ability to specify window size in the Workflow Dialog.

Added the ability to register the program without an internet connection.

Scaffold DIA Bug Fixes

Ensured that values are displayed for protein groups even when exclusive quantitative display types are selected.

Changed to using only Y ions for identification when ion type is HCD and enzyme is trypsin.

Corrected an error that could prevent proteins meeting the threshold from displaying.

Corrected an error in updating the display when the summarization hierarchy is updated.

Corrected an error that sometimes prevented building of the PCA display.

Adjusted EncyclopeDIA parameters to use the number of processors specified by the user for Scaffold DIA.

Fixed the Print Protein Sequence option.

Ensured that charts update when proteins are starred or unstarred.

Improved regular expression handling in search fields.

Ensured re-creation of already existing DIA files in the same directories as selected raw files.

Corrected an updating issue in Publish View when Protein FDR is adjusted.

Corrected a logging error.

Disabled all exports when no file is open.

Trimmed white space from the ends of peptide search strings in the Peptide Sequence filter.

Modified the Workflow Dialog to allow the samples pane to expand.

Ensured that a save location is specified before enabling "Create Reference Library".

Corrected window type terminology in the Experimental Data Search Parameters pane of the Workflow Dialog.

Corrected window type terminology in the Publish View.

Improved input validation in the modification dialog.

Scaffold DIA 1.1.1 Release Notes (2018-06-12)

Scaffold DIA Bug Fix

Repaired start action on Load Data button for ELIB experiments.

Scaffold DIA 1.1.0 Release Notes (2018-06-01)

Scaffold DIA Features

Implemented an option, now the default, to quantify only on exclusive peptides.

Added a Quantitative CVs chart to the Visualize View.

Added a warning message to discourage resource-intensive FASTA searches.

Split fixed and variable modifications into two columns in the Proteins View.

Improved the method of imputing missing values.

Added precision to the log10 intensity values exported in reports.

Scaffold DIA Bug Fixes

Corrected the modification creation dialog to allow specification of protein terminal modifications without specifying a specific amino acid.

Ensured that peptides which are not quantifiable do not have the "Quantified" box checked in the Proteins View.

Corrected summarization behavior upon deletion of an attribute or attribute group.

Corrected an error in loading when “No Bound” is selected as the Target FDR option.

Inactivated the Peptide Match Report option when no file is open.

Inactivated the SQL Export option when no file is open.

Re-enabled the ability to navigate between panes using tabs in multi-pane views through the View > Navigate menu option.

Scaffold DIA 1.0.2 Release Notes (2018-05-18)

Scaffold DIA Features

Modified file browser used in selecting raw files to accept *.d directories.

Changed terminology of "multiplexed windows" to "staggered windows" for clarity.

Added the ability to process DIA files with no precursor scans.

Updated the code-signing certificate.

Scaffold DIA Bug Fixes

Corrected a file-handling error during combined experimental data search and reference library creation from an existing library.

Accommodated duplicate lines in FASTA files.

Corrected problem in over-writing reference library files.

Protected against invalid specification of a modification through the CLI.

Scaffold DIA 1.0.1 Release Notes (2018-03-12)

Scaffold DIA Bug Fixes

Fixed bug in which program deleted DIA files prematurely.

Scaffold DIA 1.0.0 Release Notes (2018-03-09)

Scaffold DIA Released!

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