Scaffold, Q+, and Q+S Release Notes

Scaffold Bug fixes

Fixed the X! Tandem subset database checkbox. Previously it was not registering unless it was actively set during the run. The resulting full database searches failed for large datasets or searches against large databases and returned extraneous results.

Fixed radio buttons for selecting scoring method. Previously, saved settings were displayed but were not registered unless the control was actively set during loading.

Set the correct Display Option when reopening a file.

Corrected an error in generating Peptide and Spectrum reports.

Fixed the Print and Print Preview operations.

Corrected an error in the clustering algorithm.

Updated the column names in reports to correspond to the new Display Option names.

Corrected an error in saving of table preferences that could cause score columns to disappear.

Allow reading of spectra from a single MGF file for multiple samples in a single mzIdentML file. This corrects an error that resulted in missing spectra when loading PEAKS files with multiple samples.

Fixed a null pointer error in mzIdentML exports.

Changed the text regarding recommended memory settings in the memory preferences dialog.

Corrected URL-encoding of file paths containing spaces in loading of MaxQuant files.

Trimmed the reporting of probability model for multiple samples in the Publish View and exports.

Restored the option to permanently install Scaffold as a viewer without repeatedly prompting for a key.

Scaffold Batch Bug fixes

Corrected parsing of the 'tag 3xScoring="false"'.

Scaffold Q+/Q+S Bug fixes

Corrected Display Options in the Samples View and exports in Q+/Q+S.

Added "Show Hidden Proteins" option to View menu.

Scaffold Features

Added support for Proteome Discoverer 1.4 and its new Sequest HT search option.

Improved the upgrade notification interface.

Made tooltips more user-friendly.

Scaffold Bug fixes

Changed the method of calculating NSAF.

Corrected a bug that could produce empty excel exports.

Corrected problems in protein grouping when both clustering and independent sample grouping are selected.

Fixed a null pointer error during regrouping with clustering.

Made the Export Current View report show clusters as expanded or collapsed depending on how they are displayed in the GUI.

Added units to retention time in the Spectrum Report.

Do not change views when a BioSample is deleted.

Fixed a bug in loading Sequest zip files.

Corrected the spectrum counts in the Load Data View for MSF files containing Sequest searches.

Added a wait panel that appears when checking and unchecking peptides in the Similarity View.

Prevented launch of X!Tandem if no spectrum files have been loaded.

Corrected the behavior of the X!Tandem checkbox in the loading wizard.

Pick up decoy sequences from all PLGS files.

Corrected an error that could cause loss of spectra when loading Mascot mzIdentML files with decoys.

Prevented rebuilding of FDR landscape in frozen files.

Improved interaction of FDR landscape and NTT in cache.

Added a dialog so user can choose whether or not to reapply FDR filtering when changing the Req Mods filter.

Corrected the rendering of the index numbers in the Samples View on Mac.

Added information about FDR criteria to the Publish View.

Corrected the behavior of protein ambiguity stars.

Automatically select the first protein when a file is opened.

Corrected the scaling of axes in the Search Engine Comparison Scatterplot.

Scaffold Bug Fixes

When installing Scaffold, confirm that the necessary files can be written, and if not warn the user to close any running copies of Scaffold.

Corrected an error in reading certain Unimod files.

Expand all clusters in the initial display of data after loading.

Scaffold Features

Modified the Similarity View to display a single MS Sample when Independent Sample Grouping is on. The MS Sample can be selected from a dropdown.

Added clustering information to the Protein Name Accession Report.

Scaffold Bug Fixes

Corrected an error that caused some of the Display Options to display the wrong counts when the legacy grouping model was used.

Corrected an error in the mzIdentML export that caused loss of data when files were loaded into Scaffold PTM. PTM users should also update their versions of Scaffold PTM.

Modified the category-level fold-change calculation to use sample averages within each category rather than raw sums.

Fixed an error that occurred when combining sample independent grouping with clustering.

Update FDR Landscape immediately when a custom peptide threshold is activated.

Corrected a protein grouping error that occasionally resulted in display of a protein with only 0% probability peptides.

Optimized building of the FDR landscape.

Optimized resetting of NTT calculations for proteins when regrouping occurs.

Perform an integrity check on FASTA index files and indicate if the index needs to be updated or repaired.

Made Edit > Edit FASTA Database and Experiment > Apply New Database displays consistent.

Display a warning message if user attempts to merge a non-Scaffold file.

Limited the size of tooltips. The full text can be seen by pressing F2.

Prevented editing of the peptide threshold in frozen experiments.

Scaffold Features

Implemented a new scoring method based on Local False Discovery Rate.

Calculate discriminant score using a Naïve Bayes approach to incorporate all available scoring information.

Made LFDR the default option for all data from decoy searches. If an insufficient number of decoy matches are found, Scaffold falls back to PeptideProphet.

Added new graphs to illustrate LFDR analysis to Statistics View.

Changed default minimum peptide probability for peptide validation from 50% to 0%.

Changed the maximum PeptideProphet probability from 95% to 97.25%.

Calculate the percent of decoys in a fasta database for use by the LFDR algorithm. Provide a manual over-ride for the percentage of decoys in the search.

Changed the format of the fasta index file name. This will require re-indexing of existing fasta files.

Provide LFDR criteria in the Publish View.

Added FDR filtering.

Users can now specify a maximum peptide and/or protein FDR and protein thresholds will be determined automatically.

Added an FDR Browser, a heat map in which the color indicates the number of non-decoy proteins that would pass the probability thresholds indicated by a certain point. The probability thresholds may also be set through this browser.

Made threshold dropdowns editable, allowing for any value to be input.

Introduced a new protein grouping option.

Cluster proteins based on shared peptides.

Modified protein grouping to allocate peptides among all matching proteins using a weighting system if Protein Clustering is enabled.

Modified the Samples View to allow expanded or condensed display protein clusters.

Made accession number field in Samples View into a dropdown for selecting primary accession number for protein groups and clusters.

Allow regrouping of proteins with different options without reloading data.

Replaced the “assigned” column in the Peptide table in the Proteins View with the “weight” when weighted grouping is used.

Added a column showing the number of other proteins sharing a peptide to the Peptide table in the Proteins View.

Added an option to View menu to display all proteins in clusters even if they do not meet current thresholds.

Changed the Similarity View to accommodate the new protein clustering.

Added quantitation options to the Quantitative Analysis Setup.

emPAI.

NSAF.

Weighted spectrum count.

Fold-change by sample category.

Expanded the list of file formats and search engines supported by Scaffold.

Added precursor intensity quantitation for MaxQuant results.

Added support for MS-Amanda searches run through Proteome Discoverer.

Added support for loading data from mzIdentML files.

LFDR or PeptideProphet support for mzIdentML files from Mascot, PEAKS, Myrimatch, SQID, MS-GF+

LFDR support for any search engine, including unknown, through mzIdentML files.

Enhanced GO Annotation support.

Implemented filtering of proteins upon double-click in GO pie chart.

Added a bar chart to compare GO annotations across sample categories.

Added an "Edit GO Term Options" selection to the Edit Menu.

Created a GO Database Setup Interface to allow user to index multiple GO sources and select from among them.

Added support for various GOA file formats including GAF 1.0, GAF 2.0, and TAIR.

Allow download of GOA files from any website through Scaffold.

Allow user to specify location of downloaded GOA files and Scaffold’s GOA databases.

Added the source of GO information to the Publish View.

Disallowed addition of GO terms through the free viewer.

Improved advanced filtering capabilities.

Added the option to filter on combinations of GO terms.

Added a protein sequence motif search to the advanced filters. Proteins containing the search motif are displayed, and the matching string in the protein sequence pane is highlighted in blue.

Added a Taxonomy filter to the advanced filters.

Added the ability to filter on stars.

Save advanced filtering settings with a file.

Enhanced mzIdentML export options.

Added an mzIdentML export formatted for compatibility with the PRIDE converter.

Support export of data to Skyline through mzIdentML format.

Added options to perform bulk operations in the Samples View through Edit menu and right-click context menu in Samples View.

Added ability to select multiple proteins at once for bulk operations.

Enhanced the starring feature in the Samples View. Added a second color of star providing the ability to classify proteins into four categories.

Allow filtering of proteins based on star status.

Added an export of starred proteins available through the right-click context menu in the Samples View.

Added option in bulk operations to hide or show decoy proteins.

Added ability to hide multiple proteins with a bulk operation.

Improved handling of modifications.

Added an option through the Edit > Preferences > Paths menu to configure sources of modification metadata, such as unimod or customized modification files.

Add information about the source of modification information to the Publish View.

Streamlined file loading.

Improved the loading wizard.

Moved Queue Structured Directories to the Load Data View.

Added capability to search in Mascot Search log when loading data directly from the Mascot server.

Enabled loading of files from the Mascot server by double-clicking on the file name.

Retain the last setting of the Load Condensed option.

Added a warning message about correct use of the MuDPIT option.

Enhanced Fasta database handling.

Added ability to specify decoy parse rule when using Auto-parse.

Indicate Fasta databases that need maintenance. Highlight fasta databases that are no longer found in the specified location in pink, and those with outdated indices in gray.

Changed options for exporting a subset database to allow either export of all displayed proteins, respecting all filters in place, or only the starred proteins.

Added the option to export a subset database consisting only of starred proteins.

Improved the Scaffold Graphical Interface.

Changed the FDR dashboard display. It now shows in pink for decoy searches and blue for non-decoy. It also displays the peptide and protein thresholds used as well as giving the FDR values.

Changed terminology for display options in Samples View and in exports for clarity in light of the new grouping algorithm.

Added Display options Total Unique Peptide Count and Total Unique Spectrum Count if clustering is on.

Save column sizes and positions with a file, and retain the settings when a new experiment is opened.

Show the quantitative method when displaying Quantitative Value.

Added indicators in corner of display to indicate which display setting options are currently selected.

Highlight samples being compared in a quantitative analysis with different colors.

Changed default sorting of peptides table in the Proteins View. Now orders on start/stop position.

Consolidated the Export > To Excel menu and added new reports to it.

Added option to set a default selection for display option.

Hyperlinked the points in the scatterplot to the corresponding proteins.

Enhanced exports.

Included cluster information in the Protein Report when clustering is turned on.

Added a new Protein Cluster report.

Added TIC, Retention time, precursor intensity to the Peptide Report.

Added GO information to the Spectrum Report if “Show GO annotations” is enabled.

Provided option to export mzIdentML files in either 1.0.0 or 1.1.0 format.

Provided option to gzip mzIdentML files on export.

Added weighted spectrum quantitative value to the Peptide Quantitative Report.

Enabled copying of all chart data from the Quantify and Statistics views.

Place exported mzIdentML and mgf files into their own folder.

Provided easier access to program information.

Added Show Log Files option to Help menu.

Made the Scaffold version in About Scaffold able to be copied.

Added a link to the Q+ User's Guide under Help which is active only if a quantitative license is in effect.

Regenerated some demo files and added new ones.

Added welcome dialog with option to permanently disable.

Added a Welcome to the Wizard page to load wizard with an option to permanently disable.

Added an automatic check for updates of Scaffold.

Made an editable configuration file for Scaffold parameters such as FASTA and GOA indices, alternate unimod files, etc.

Implemented new key system.

Scaffold Bug Fixes

Improved performance in merging files.

Changed the distributions in PeptideProphet.

Set a lower bound of 0.0001 for p values in Scaffold.

Improved the process of downloading NCBI annotations to prevent timeouts and network interruptions.

Fixed the NCBI download cancel button.

Changed the name of the automated peptide checkbox setter to "Reset Peptide Validation."

Changed the title of the "Good?" column in the Proteins View to "Valid."

Read modifications from the Spectrum Mill smconfig.custom.xml file.

Strip byte order marks from Spectrum Mill configuration files.

Corrected reporting of Spectrum Mill scores in mzIdentML export.

Pick up decoy sequences from Spectrum Mill files.

Fixed a null pointer error in loading certain MaxQuant files.

Changed PLGS parser to use the accession element rather than the entry as the Scaffold accession number.

Corrected a bug in the NTT filter.

Added right-click paste ability to the Search box.

Added right-click copy ability to the protein tooltips.

Changed the notation for decoy hits recorded by search engines that create their own decoys from -R to -DECOY.

Changed notation in annotated spectra for consistency.

Updated the Phenyx parser.

Corrected a scaling problem in the spectrum/model error graph.

Retain protein selection when Peptide Validation reset.

Corrected GO ontology column title "Cellular Component."

Made "Edit Biological Sample" automatically update the Samples View.

Corrected the tooltips for the high mass accuracy and PeptideProphet graph selection buttons in the Statistics View.

Corrected an error in handling hidden proteins during calculation of Quantitative Values.

Made digestion enzyme codes correspond to Mascot's.

Truncated protein names in the Similarity View. Full names appear in the tooltip.

Adopted consistent use of the term BioSample in place of Biological Sample and Quantitative Sample.

Corrected display of peptide tolerances correctly when samples searched with different tolerances are loaded together.

Fixed the cancel option upon quitting Scaffold on a Mac.

Eliminated redundant and flawed option to Save As a JPG file from GO Pie Chart. Save JPEG Image functions correctly.

Fixed an error in updating percent coverage when applying a new database.

Added a spinner to indicate progress during file queueing.

Fixed tooltips in the Samples View under Linux.

Removed extraneous information from the tooltip for quantitative test values.

Improved performance in scanning PLGS files for loading.

Allowed loading of PLGS data from folder containing both zipped and unzipped versions of the same data.

Changed focus of wait dialog during loading to prevent accidental cancellation.

Prevent creation of custom peptide thresholds with the duplicate names.

Updated splash screens to correspond to the product license.

Scaffold Batch Features

Load and organize labeled or label-free quantitative data for Scaffoldd Q+.

Added new tags to Scaffold Batch for new options.

Select LFDR or PeptideProphet Scoring.

Select protein clustering or legacy protein grouping.

Added ability to pre-fill the Publish View information from Batch.

Added precursor intensity as a quantitative method for Scaffold Q+.

Accepts files containing precursor intensity data from Mascot Distiller, MaxQuant, Proteome Discoverer and Spectrum Mill.

Added an option to choose statistical blocking at the spectrum, peptide, or sample level in the random permutation test.

Load SILAC data analyzed with Spectrum Mill

Scaffold Bug Fixes

Changed the method of performing the permutation test and switched to using F-statistic for evaluation of significance.

Corrected report names in Scaffold Q+.

Changed the Bonferroni correction to use the number of proteins meeting thresholds, regardless of filters applied.

Increased the number of significant digits for quantitative values in Q+ peptide and spectrum reports.

Changed the export options in the Publish View of Scaffold Q+.

Improved the Q+ sample organization dialog.

Q+/Q+S Bug Fixes

Improved the Mean/Median Density Chart.

Corrected number of assigned spectra display for proteins with protein grouping ambiguity.

Matched the spectra exported in SQML file to those exported in MZID file for quantitation in Scaffold PTM.

Scaffold Features

Support loading of PLGS 3.0 files.

Scaffold Batch Features

Added option to specify format of mzIdentML exports, either 1.0.0 or 1.1.0.

Allow OMSSA MSSpectrum_iscale values < 1.

Replace ambiguous amino acids in peptide sequences with appropriate specific amino acid where possible.

Corrected calculation of delta mass for modified peptides from MaxQuant files in the High Mass Accuracy Scoring adjustment.

Restored category to the Export Current View report of the Samples View.

Fixed error that created negative p-values from the Mann-Whitney test.

Modified the OMSSA parser to extract accession numbers in the format of the original fasta file, rather than in blast format.

Support GluC as enzyme for X! Tandem searches.

Fixed the web link to provide help in forming regular expressions in the Advanced Protein Filter configuration pane.

Better aligned spectrum labeling between Scaffold and Scaffold PTM.

Corrected merging of files with missing spectra.

Restored display of sequence information for decoy proteins.

Added the modifications automatically searched by X! Tandem to the list of searched mods when importing X! Tandem data.

Fixed the high mass accuracy scoring option for MaxQuant data.

Improved the Peptide Prophet distributions for PLGS data from searches of redundant databases.

Corrected a problem in reading charges of spectra in OMSSA files.

Corrected reading of modifications such as Gln -> pyro-Glu from MaxQuant's modifications.xml file.

Corrected calculation of delta mass for modified peptides from MaxQuant files in the High Mass Accuracy Scoring adjustment.

Corrected an error that prevented loading SILAC MSF files with both MuDPIT and "Condense During Loading" options selected.

Correctly read n-term modifications from MSF files.

Features

Digitally sign OSX installation package as Apple registered developer to support default Gatekeeper settings.

Added displayed GO terms to Export Current View report from Samples View.

Enhanced behavior of Auto Parse in parsing Uniref databases.

Bug Fixes

Corrected a null pointer error that occurred when performing condensed save of a file whose input included files with no data.

Corrected an error that caused incorrect calculation of cursor position in protein sequence display.

Corrected behavior of Export Current View report from the Publish View.

Scaffold Features

Support loading of MaxQuant files from versions through 1.3.0.5.

Updated the unimod.xml file.

Added password protection for 'Show Hidden Proteins'.

Scaffold Bug Fixes

Made Scaffold respect search engine modification choices where possible.

Retain name of searched database when files are merged.

Retain all GO terms during merge.

Retain label-free quantitative information during merge.

Preserve decoy-based FDR calculation while saving frozen and condensed.

Respect setting of 'Show lower scoring matches' option when moving between MS-Sample and Biosample mode in the Proteins View.

Corrected an inconsistency between peptides displayed in Proteins view and in exports.

Corrected an error in the taxonomy file that produced display errors in the Samples View.

Changed behavior of the Configure Database Parser display to update all rows according to current parsing even when first row fails.

Corrected an error that could overwrite accession numbers with decoys in fasta index files when accession numbers are longer than 80 characters.

Improved naming of biosamples during merge.

Scaffold Batch Bug Fixes

Added ability to toggle Quantify Pane in Batch.

Scaffold Features

Added a menu option in the Help menu to allow users to upgrade Scaffold keys.

Added an option for exporting unfiltered mzIdentML files for analysis by other software.

Scaffold Bug Fixes

Changed the method of storing IdentityE data to accommodate larger files and improved performance in GUI for large IdentityE files.

Modified the parser for MaxQuant modifications.xml file to handle mods with arrows in them.

Improved the progress listener for file loading.

Corrected MuDPIT loading of MSF files from same search engine.

Corrected peptide and spectral counts in Samples View to properly reflect the setting of the "show lower scoring matches" option when moving between biosample and MS-sample views.

Corrected an error that sometimes caused protein sequence information to be lost after applying NCBI annotations.

Corrected errors in saving condensed and frozen.

Correctly load non-Spectrum Mill zipped files.

Changed behavior of GUI in setting custom filter on Parent Mass Tolerance.

Scaffold Batch Bug Fixes

Fixed an error that was causing Scaffold Batch to reindex FASTA files on each run.

Delete the old parser before reindexing a FASTA file to correct some parsing problems in Scaffold Batch.

Fixed a Null Pointer error in Scaffold Batch that occurred when exporting reports.

Scaffold Q+ and Q+S Features

Load MaxQuant files with multiple experiments in a single file, or with a single experiment created with an Experimental Design Template into Q+S.

Scaffold Q+ and Q+S Bug Fixes

Eliminated a spurious error message about a missing DAT file when loading SILAC data from Mascot Distiller.

Corrected an error that sometimes caused the program to hang when going into Q+.

Scaffold Features

Display original value in ToolTip in cases where the delta ppm value has been adjusted by the mass of one or more neutrons.

Sort database names in Edit Databases window when column header is clicked.

Place Add Database option in the Experiment>Apply New Database dialogue.

Default to the Experimental Methods tab in the Publish View.

Disable Similarity View when Independent Sample Protein Grouping is used.

Scaffold Bug Fixes

Corrected the high mass accuracy adjustment.

Changed the calculation of Precursor Intensity values when the Top 3 or Average options are selected. Now all measurements for the same peptide are combined across charge states and MS-Samples.

Eliminate unnecessary reindexing of fasta databases.

Allow more flexible matching of GO annotations from the GOA database to accession numbers.

Respect all filter options in mzIdentML exports.

Fixed the ToolTip in the Configure Database Parser dialogue.

Fixed the right-click option Show Fixed Modifications in the Protein Sequence display.

Correctly write multi-byte characters. This corrects an error that prevented certain saved Scaffold files from opening. These files will need to be reloaded and saved again.

Changed MS2/SQT reader to handle an alternate file format encountered in some MS2 files.

Corrected an error in reading Phenyx files.

Warn if directory containing Spectrum Mill data is zipped in an incompatible format.

Corrected an error in reading certain Spectrum Mill files.

Corrected an error that prevented certain files from loading.

Restored compatibility with Mac OS 2.5.

Added decimal places to the displayed mass figures in the spectrum report.

Changed the default name of the Samples Report with Isoforms.

Scaffold Batch Features

Load and organize SILAC data through Scaffold Batch if registered with a Q+S license.

Scaffold Batch Bug Fixes

Correctly retrieve protein sequences from fasta databases in Scaffold Batch.

Correct display of precursor mass tolerance options when SQT files loaded through Scaffold Batch.