Scaffold Elements Release Notes

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Jacob Lippincott
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The following document contains release notes for Scaffold Elements

Scaffold Elements 3.0.2 Release Notes (2022-01-14)

Upgraded Log4J version to 2.17.1 to address potential security vulnerability

Scaffold Elements 3.0.0 Release Notes (2021-03-18)

Implemented a new licensing system

Implemented a Command Line Interface (CLI) for Elements

Implemented block editing of sample names

Implemented a new Experimental Design dialog

Implemented automatic sorting to bring selected adducts to the top of the selection list.

Added a log intensity checkbox to the main window to toggle between display of intensities and log10 intensities in all views

Added the ability to display unidentified features without lowering the scoring thresholds

Added Quantitative Trend charts and an Intensity/CV chart to the Visualize View

Added violin plots to the Analyte Level Charts in the Analytes View

Added a supplementary data export to the Publish View

Added a Statistics table to the Analytes View

Added an option to copy only selected text in the Publish View.

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

Added the ability to copy chart data from the Volcano Plot and Quantitative Scatterplot.

Added labels to nodes representing analyte groups in the Volcano Plot

Redesigned the Organize View

Enhanced the Samples Report to allow the user to select various display options

Improved error reporting in import of CSV-formatted library files

Improved wait dialog messages

Improved the procedure for detection of ion charge

Adjusted the default file open and save positions

Changed the method of imputing missing values to QRILC

Changed the default location for saving indexed feature files

Changed the installer, launcher, desktop, and dock icons

Modified the wording relating to location of stored indexed feature files

Increased landing area for cursor to display tooltip in MS2 spectra

Reimplemented report generation to improve performance

Recreated the demo files

Altered the file signature to enforce licensing restrictions

Updated the Publish View, including draft text for publications

Updated the default version of msconvert to 3.0.19254 to support the Exploris

Updated the graphics, colors, and look and feel of the program

Corrected an error that allowed display of a single ion as both identified and unknown

Corrected a GUI error when moving the 3D plot tab

Corrected some minor textual issues in the GUI

Corrected a benign error in heatmap clustering

Ensured the text in the Publish View updates when the normalization method is changed

Ensured that the Samples View scrolls to make analytes selected through other Views visible

Fixed an error in hiding analytes in clusters

Fixed the display of a selected row in the Search Information table in the Organize View

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

Removed RT clustering unless the "Treat each MS1 peak group as a single analyte" option is selected

Removed internal borders in display panes

Disabled the copy/save/print options in the structure display in the Analytes View

Scaffold Elements 2.1.1 Release Notes (2018-12-17)

Scaffold Elements Features

Added a ProteoWizard download option to the Edit > Preferences > ProteoWizard menu.

Added the option to allow use of the set of consensus features of all unlabeled samples as the reference in flux analysis.

Scaffold Elements 2.1.0 Release Notes (2018-11-06)

Scaffold Elements Features

Changed the terminology of "MS1 spectrum" to "MS1 peak group".

Changed default setting of "Treat each MS1 peak group as a single analyte" to false.

Added re-extraction of labeled isotopic peaks during flux analysis.

Added the ability to analyze Deuterium-labeled samples in flux analysis.

Added the library containing the MS2 which was used to identify an in-source fragment to the Features Table.

Added an option to ignore all MS2 information in an input file.

Recreated the demo files.

Scaffold Elements Bug Fixes

Ensured reproducibility of results in repeated runs.

Corrected an error in cluster value suppression.

Changed the Flux Analysis dialog to accommodate MSE files by obtaining the lock mass correction of a labeled sample from its corresponding unlabeled sample.

Corrected an error that prevented calculation of mass accuracy scores for some ions.

Corrected an error in updating of the XIC Overlay tab when switching between Samples and Ions.

Renumbered retention time sets of analytes to reflect filtering.

Corrected the reporting of the option to retain unknown analytes in the Publish View.

Added display of libraries which produce no identifications to the Publish View.

Removed an empty tooltip in the Experiment menu.

Scaffold Elements 2.0.0 Release Notes (2018-06-01)

Scaffold Elements Features

Added support for metabolic flux experiments.

Replaced the identification, scoring, grouping and clustering algorithms to rely on formation and characterization of MS1 spectra.

Adjusted scoring to take advantage of annotation of ion forms as in-source fragments in MS1-only data.

Revised retention time alignment algorithm.

Added load-time identification thresholding with a configurable score threshold.

Improved GUI performance.

Updated search parameter defaults.

Changed all uses of the term "metabolite" to "analyte".

Updated the code-signing certificate.

Scaffold Elements Bug Fixes

Ensured that ion forms do not match library entries with different charge states.

Improved feature finding.

Scaffold Elements 1.4.2 Release Notes (2018-02-23)

Scaffold Elements Bug Fixes

Corrected an error in saving unidentified metabolites.

Scaffold Elements 1.4.1 Release Notes (2018-02-12)

Scaffold Elements Features

Changed the program name from Elements for Metabolomics to Scaffold Elements.

Improved performance in metabolite grouping.

Scaffold Elements Bug Fixes

Removed requirement for TIC in MS2 scans to support a wider variety of raw files.

Scaffold Elements 1.4.0 Release Notes (2018-01-05)

Scaffold Elements Features

Added the ability to download and search the METLIN libraries. License fee is included in the Elements purchase price.

Allowed evaluators access to the evaluation version of the NIST library through the Library View.

Included isotopically labeled library entries in LIBDB.

Adjusted the isotopic distribution scoring algorithm to better distinguish lipid isotopologues.

Discontinued assessment of isotopic distribution scores when [M+2] isotope is not found to improve identification of lipids.

Created a dropdown menu in the Library View to provide access to current and additional library functions.

Added a dialog to allow copying of multiple library entries based on search queries.

Added match information to the export of the MS2 spectrum.

Added the m/z values of previously encountered unknown compounds identified by searching personal libraries to the molecular weight field in the Samples View.

Added an explanatory tooltip to Minimum RT Between Scans setting.

Recreated the demo files.

Updated the Java version to 1.8.

Scaffold Elements Bug Fixes

Improved performance when performing searches with multiple libraries.

Corrected an error that occurred when searching libraries with different identifiers for the same metabolite.

Improved loading speed of large libraries.

Improved the function of the threshold controls.

Corrected behavior in Samples View when an attribute is renamed.

Allowed inclusion of empty columns for optional data when loading a library from a TSV file.

Changed coloring method to provide different colors for different Waters MSE samples.

Restored functionality of the memory settings in the Elements Viewer.

Corrected an error that could interfere with normalization to an internal standard.

Corrected rendering of collision energies of 0 eV in Library View.

Scaffold Elements 1.3.4 Release Notes (2017-03-24)

Scaffold Elements Features

Added the ability to add or change a chemical structure associated with a metabolite in an editable library by entering a SMILES or reading the structure from a file.

Changed the default selection for performing RT Alignment to OFF.

Scaffold Elements Features

Added the missing RT Match column to the Expanded Samples Report.

Adjusted the tooltip in the Molecular Weight column header.

Allowed deletion of duplicate records in a library.

Ensured that isotopic distrubution scores are computed and reported for matches against metabolites added to a library after being reported as unidentified in a previous search.

Allowed searches with fragment mass tolerance above 0.5 Da. New cutoff is 10 Da.

Adjusted calculations in the Volcano Plot.

Corrected problems when reopening files after adjusting the summarization hierarchy.

Ensured that the PCA tab updates when normalization is changed.

Corrected an error that occurred when creating a new file after closing the Configure Quantitative Analysis dialog without applying any changes.

Improved progress indication when loading files.

Corrected an error in coloring the Feature Intensity Heat Map to ensure that the highest intensity points are visible.

Added a helpful message when WIFF files are missing their corresponding SCAN files.

Corrected duplicate opening of browser when clicking on an Accession Number.

Inactivated weblinks upon right-click.

Corrected an error in the Metabolite Feature Export when Unknowns are included.

Scaffold Elements 1.3.2 Release Notes (2017-01-26)

Scaffold Elements Features

Allowed copying of chart data from charts in Visualize View through right click menu.

Scaffold Elements Bug Fixes

Corrected an error that could cause failure of saved METDB files to open.

Corrected an error in deleting metabolites from preview dialog before saving to a spectral library.

Corrected a null-pointer that could occur during file loading.

Corrected an error that occurred when changing the preferred metabolite with filtering applied.

Corrected an error that occurred when changing attribute names with a statistical test applied.

Corrected the behavior of the Remove All Filters button.

Corrected the tooltip in the Volcano Plot.

Ensured that all Views are cleared upon File>Close operation.

Improved progress indication when loading files.

Corrected an error in coloring the Feature Intensity Heat Map to ensure that the highest intensity points are visible.

Added a helpful message when WIFF files are missing their corresponding SCAN files.

Corrected duplicate opening of browser when clicking on an Accession Number.

Inactivated weblinks upon right-click.

Corrected the display of missing collision energies in Library View.

Corrected an error in the Metabolite Feature Export when Unknowns are included.

Scaffold Elements 1.3.1 Release Notes (2016-12-13)

Scaffold Elements Features

Dramatically enhanced the responsiveness of the GUI for large files.

Improved progress listeners.

Added the ability to import MSP library files, such as those from Mass Bank of North America.

Added the ability to create personalized spectral libraries.

Created a dialog, accessible through right-click in the Samples View or through the Experiment menu, to allow addition of a selected group of metabolites to a personalized library.

Added the option to add individual spectra to a personalized library, accessible through the MS2 Spectra tab in the Metabolites View.

Added the ability to specify chromatographic information when loading data, to store this information in personalized libraries, and to use it in subsequent searches.

Allowed editing of certain fields in the Library View for editable libraries.

Added a Notes tab in the Library View to display record notes and comments.

Added columns for RT and Chromatographic System to the Records table in the Library View.

Added a notation to the Isotopic Distribution Tab to indicate whether it is a theoretical or experimental distribution.

Modified the buttons in the Library Manager to provide an Import button for reading libraries from files and a Create button for creating new personal libraries.

Added the ability to create subset libraries by copying library entries to a personal library.

Added new features to the Visualize View:

Added a Quantitation Tab to the Visualize View containing a Volcano Plot and a Quantitative Scatterplot.

Added PCA capability to Elements.

Added the ability to tag metabolites with stars through charts.

Added the ability to label points in charts.

Added an XIC Overlay tab to the Metabolites View.

Added a transition list export for Skyline.

Added new search options

Modified the Workflow dialog to accommodate additional search parameters and chromatographic information.

Added an option in the Search tab to retain only identifications with MS2 spectral matches.

Added the option to search based on mass only or on a combination of mass and RT.

Modified the scoring algorithms to allow matching against previously observed isotopic distributions for unidentified metabolites in personalized libraries.

Updated the Publish View to reflect all of the new options.

Perform noise thresholding through msconvert when the user elects not to save MZ5 and index files and sets an absolute noise threshold.

Modified the p-value filter to allow filtering based on significance with or without FWER correction.

Added a filter based on the library used to identify metabolite.

Added a dropdown to allow sample switching in the Feature 3D Viewer when using manual bounds.

Added a checkbox to toggle the display of the legend in the Chromatography View.

Added an option to allow the user to select the preferred database for weblinks.

Added a column to the Samples View table to indicate whether RT was used in matching the metabolite.

Added a column to the Features Matching Selected Ion table in the Metabolites View to indicate the library to which a feature was matched.

Added the collision energy to the MS2 spectra display.

Added MS Sample information to the Publish View.

Improved the MetaboAnalyst export.

Added an Export Attributes File button to the Organize View.

Added a dialog inviting the user to organize data after loading multiple samples.

Added a warning when importing a new library might overwrite an existing one.

Colored sample names in red in Organize View if they are missing attributes included in the current display hierarchy.

Blocked the ability to set the ProteoWizard source from the Elements Viewer.

Updated the required version of ProteoWizard.

Rebuilt the library files of all libraries downloadable from our website and included KEGG information.

Regenerated the demo files.

Upgraded to Java 8.

Scaffold Elements Bug Fixes

Corrected an error that could cause failure of saved METDB files to open.

Corrected an error that could result in formation of composite features with more than one feature from the same sample when loading large numbers of samples.

Ensured that metabolites would be correctly displayed when opening a file with log10 intensity filtering applied.

Required that the polarities match when matching MS2 spectra.

Corrected an error in navigating the metabolites in the Metabolites View after disabling the Feature 3D Plot.

Rescaled spectra in the Library View.

Adjusted the order of attributes in Metabolites View Features Matching Selected Ion Table to force consistency.

Retained all file information when reanalyzing.

Changed display of missing MS2 scores from "?" to blank.

Stopped deleting mz5 files if they were explicitly selected for loading, even if the option to save mz5 and index files is not checked.

Report any searched library even if it identifies no metabolites.

Adjusted the method of choosing the representative metabolite name when merging metabolite entries in a library to prefer the shorter name.

Included the minimum acceptable version of msconvert in the installer messages.

Corrected behavior of the Edit>Preferences tab to select ProteoWizard version when the previously selected version is no longer found.

Adjusted the count of peaks in the reference spectrum in the MS2 Spectra pane to not include the precursor peak.

Corrected a GUI update error in the MS2 Spectra pane of the Metabolites View.

Ensured that metabolite retention time groups would not be numbered if only a single instance of the metabolite remains after filtering.

Blocked the loading of files with the same name but different file extensions.

Blocked the use of non-ASCII characters in file paths.

Removed the mass label from precursor ion peak in MS2 spectra.

Corrected the behavior of the Cancel button when importing a library file.

Corrected default location for importing an Attributes File.

Corrected a silent error when loading files.

Corrected errors that occasionally occurred while loading large data sets.

Corrected an error that occasionally prevented the References tab in the Metabolites View from being populated.

Corrected a null pointer error that could occur when calculations were canceled.

Corrected an error that occasionally resulted in failure to display data in the Quantitative Charts.

Corrected an error that occurred when changing preferred metabolites while columns are hidden.

Streamlined updating of Retention Time units when changed in GUI.

Corrected a threading error.

Improved performance when editing the summarization hierarchy.

Corrected an error in linking out to the KEGG database.

Prevented editing of file name in browser when loading a LIBDB file.

Corrected an error that prevented printing from unsaved files.

Corrected an error that marked newly opened files as modified.

Improved progress indication when loading files.

Corrected an error in coloring the Feature Intensity Heat Map to ensure that the highest intensity points are visible.

Added a helpful message when WIFF files are missing their corresponding SCAN files.

Corrected duplicate opening of browser when clicking on an Accession Number.

Inactivated weblinks upon right-click.

Corrected the display of missing collision energies in Library View.

Corrected an error in the Metabolite Feature Export when Unknowns are included.

Scaffold Elements 1.2.1 Release Notes (2016-06-02)

Scaffold Elements

Fixed issue with in-program help searching

Scaffold Elements 1.2.0 Release Notes (2016-06-01)

Scaffold Elements Features

Dramatically enhanced performance during file loading and processing.

Added support of analysis of Waters MSE data using an implementation of the DIA Umpire algorithm and a dialog for verification of specification of lock mass for MSE data.

Ensured that the msconvert option to sum intensities across drift times is used for HDMSE data.

Enabled 3D viewing of features when viewing METDB files even when mz5 and index files are not present.

Added a menu option to connect mz5 and index files to allow viewing of the full data landscape.

Modified the re-extraction process for isotopic peaks to search the raw data rather than noise- thresholded data.

Improved the responsiveness of the GUI during thresholding and filtering.

Changed the format of feature finding index files to improve performance and limit disk usage. The new file format, the PFDB file, replaces the mz5.index file.

Implemented an improved MS2 feature finding algorithm.

Refined the MS2 scoring algorithm.

Marked the precursor intensities in MS2 spectra.

Added a polarity setting to the manual bounds control in the Feature 3D Viewer Control.

Updated the minimum acceptable ProteoWizard version number.

Modified the installation dialog to allow easier installation of and linking to the msconvert executable.

Provided the option to turn off retention time alignment.

Provided the option to turn off re-extraction.

Provided the ability to limit the RT range over which data should be processed.

Provided an option to set the minimum time between scans to improve performance when processing data from instruments with very high sampling rates.

Included new demo files.

Eliminated support for loading mzXML files because msconvert does not reliably report the collection mode (i.e. profile or centroided)

Added the ability to copy and paste information from the Publish View in both HTML and plain text modes.

Scaffold Elements Bug Fixes

Modified the method of calculating the isotopic distribution to combine intensities arising from C13 and N15 in the same ion.

Improved the behavior of the Progress Bar.

Ensured that re-extracted metabolite features associate only to metabolites within mass tolerance.

Changed the default adduct selection.

Corrected the Elements version displayed in the Publish View to indicate the version in which the file was created.

Improved the FWHM calculation to eliminate a potential source of error.

Improved the behavior of the spinner controls for mass tolerances in the Search parameters tab.

Scaffold Elements 1.1.2 Release Notes (2016-04-19)

Scaffold Elements Features

Expanded the tab-delimited spectral library file reader to support additional columns.

Adjusted the SDF library file reader to accommodate files generated by PubChem.

Added an "Apply" button to the manual bounds controls for the 3D feature viewer.

Added a title to the raw files section of the loading wizard.

Scaffold Elements Bug Fixes

Adjusted the reading of mz5 files during indexing to properly use the "deltaMZ" flag.

Corrected a potential inconsistency in the assignment of re-extracted features to composite features.

Corrected an error in the maximum intensity displayed in the isotopic distribution plot.

Corrected an error that interfered with viewing of the 3-D plots in the demo files by multiple users on a system.

Corrected an error in parsing file names containing unusual characters.

Updated the Users Guide.

Scaffold Elements 1.1.1 Release Notes (2016-02-01)

Scaffold Elements Features

Added a Reanalysis feature to allow addition of files or modification of search parameters from within an existing experiment.

Added a radio button to reposition tables in the Metabolites View to allow a larger viewing area for graphics and charts.

Added an auto-generated description of the analytic methods to the Publish View.

Added a warning when the Fragment Tolerance is set too low and might limit identification of metabolites.

Adjusted the XIC splitting criteria to better resolve structural isomers.

Adjusted the Isotopic Distribution scoring algorithm to consider both peak heights and areas.

Improved the performance of the peak-picking algorithm.

Improved the performance of the Feature 3D Viewer.

Factored out internal parameters into a configuration file.

Modified the installer to delete old versions of demo files during upgrades.

Updated the demo files.

Scaffold Elements Bug Fixes

Corrected an error in the Expanded Samples Report.

Corrected an error when loading workflow files that refer to inaccessible library files.

Allowed loading of WIFF files with no associated MTD files.

Modified the peak picking algorithm to better identify one-sided peaks.

Adjusted the re-extraction algorithm to better handle overlapping peaks.

Ensured that MS2 spectra are associated with re-extracted features when available.

Corrected an error in loading of certain attribute files.

Corrected an error in calculation of the m/z FWHM column.

Changed the default setting so that unknown metabolites will not be reported.

Corrected a rendering problem in the Feature 3D Plot for Mac OS X.

Adjusted the default setting for the Parent Tolerance in Daltons.

Adjusted the Isotopic Distribution analysis to better identify ions with higher charge states.

Ensured that the MS2 Spectrum tab is properly refreshed when displaying an unknown metabolite.

Ensured that retention time mapping from previous runs is removed prior to reloading of a single file.

Adjusted the Metabolites View to always provide the option to load data for Feature 3D Plot.

Removed the publication-sized image export from the MS2 spectrum context menu.

Scaffold Elements 1.1.0 Release Notes (2015-12-15)

Scaffold Elements Features

Changed the peak picking algorithm from msInspect to an in-house point clustering-based algorithm.

Created files to store peak information, which may be used for reanalysis and 3D visualization.

Created two linked tabs in the Metabolites View to visualize peaks: a 3D plot and a 2D heat map, with numerous visualization controls.

Provided the option to specify the location to which peak information files are written.

Added a file check when loading raw files with a notification of missing files at the beginning of the loading process.

Added a noise threshold parameter to the search parameters dialog.

Improved the process for identification of isotopic peak clusters.

Replaced the XIC score with the new isotopic distribution score.

Revised the isotopic distribution plot to reflect the new isotopic scoring method.

Refined the MS2 scoring algorithm.

Replaced the XIC score threshold with a log10 intensity threshold.

Explicitly label re-extracted features in the XIC score column in the Metabolites View.

Added a Publish Report export.

Updated the demo files.

Included a running file count in the loading wait dialog.

Updated the End User License Agreement (EULA).

Added an option to view the EULA to the Help menu.

Scaffold Elements Bug Fixes

Adjusted the intensity calculations to use a trapezoidal approximation of peak area.

Removed duplicate entries from the Adducts table and rearranged the common and uncommon lists.

Removed the option to select or deselect all adducts with a single click.

Allowed recognition of *.wiff.mtd and *.wiff.scan files with or without the string "wiff" in the name.

Corrected an error in loading certain WIFF files.

Corrected the sorting order of the intensity column in the Features table.

Ensured that the Publish View is closed when a file is closed.

Corrected an error that occurred when changing the summarization hierarchy in files with many samples.

Added the memory options tab to the preferences dialog on Mac OS X.

Scaffold Elements 1.0.3 Release Notes (2015-09-16)

Scaffold Elements Bug Fixes

Fixed missing DLL issue on some Windows system.

Scaffold Elements 1.0.2 Release Notes (2015-08-28)

Scaffold Elements Features

Created a new evaluation version that can analyze raw data with the NIST evaluation library.

Heatmap export can annotate the columns and rows in the image.

Added a link to PubChem from a CAS registry number.

Scaffold Elements Bug Fixes

Updated link to BiGG database (due to a new version of BiGG).

Scaffold Elements 1.0.1 Release Notes (2015-07-24)

Scaffold Elements Features

Replaced the Log10 Intensity Threshold with an XIC Score Threshold.

Added summarization information to the header of the Samples Report.

Created a Metabolite Features Report.

Added an Expanded Samples Report showing each metabolite in a metabolite group on a separate line.

Created a report suitable for uploading to the MetaboAnalyst Statistical Analysis or Time Series/Two Factor Analysis tools.

Added a Peak List Export.

Changed to CSV format for exports rather than tab-delimited text files.

Changed the default settings to hide the Isotope Traces in the XIC tab of the Metabolites View.

Added columns to the Heatmap Export.

Changed the title of the second table in the Metabolites View.

Scaffold Elements Bug Fixes

Adjusted the isotopic distribution display to correctly account for adducts and neutral losses.

Improved performance in searching and filtering.

Eliminated slowdowns upon repeated opening and closing of files.

Adjusted the format of the adducts.tsv file to allow easier editing.

Adjusted the Color Legend to display only two decimal places.

Standardized the number of significant digits displayed in various views.

Corrected the Scan Start Time for MS2 spectra.

Reorder metabolites in a metabolite group when the preferred metabolite is changed.

Adjusted tooltips in Metabolites View.

Changed the display format of intensity values to scientific notation.

Ensured that all views respect the Accession Number preference setting.

Corrected errors in saving summarization and quantitative testing information to METDB files.

Save preferred metabolites when saving a METDB file.

Corrected handling of settings changes made when no file is open.

Slightly adjusted the normalization algorithm in cases in which samples are fractionated.

Corrected program name in tooltip displayed by Desktop Icon.

Added a scroll bar to the Details View of the Heatmap.

Added Help buttons to various views.

Always display p-value filter control but deactivate it when no quantitative test is applied.

Disable the controls for Quantitative Tests and Display Dropdowns when no file is open.

Corrected wrapping behavior in the GUI display of the Threshold controls.

Adjusted the behavior of the default file save location.

Scaffold Elements 1.0.0 Release Notes (2015-06-29)

Scaffold Elements

Released Scaffold Elements version 1.0.0

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