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Scaffold Changelog

What's new in Scaffold 5.0.0

Mar 19, 2021
  • Added:
  • Implemented a new license key system
  • Implemented custom peptide thresholds for MSFragger scores
  • Bundled Percolator into the Scaffold installer
  • Created a new set of demo files
  • Incorporated new graphics and colors to update the look and feel of the program and installers
  • Added the ability to link already installed X! Tandem and MSFragger executables to Scaffold
  • Added support for MSFragger searches of raw data through Scaffold
  • Added support for using either MSFragger or X! Tandem for supplementary searches through Scaffold
  • Added a dialog to the Loading Wizard for specification of search parameters for MSFragger
  • Added the ability to run MSFragger or X! Tandem supplementary searches through Scaffold Batch
  • Added the option to use Percolator to assess peptide probabilities during data loading
  • Added a Properties dialog to allow adjustment of axes and other graph properties to Scatterplots and Volcano Plot
  • Added support for reading FragPipe results
  • 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
  • Changed the wording of the SFDB and mzIDentML to reflect move from perSPECtives to Scaffold LFQ
  • Changed the wording of the warning when loading large data sets
  • Changed the wording in the custom peptide threshold dropdown list
  • Updated the wording in the Memory Preferences dialog
  • Improved performance of the search box
  • Realigned the headers and columns in the Spectrum Report
  • Adjusted reading of modifications and peptide sequences from Comet to accommodate different coding in newer versions
  • Adjusted the Comet file reader to accommodate Comet's changes in naming of its scores
  • Allowed duplication of spectrum identifications in mzIdentML files loaded into Scaffold
  • Fixed:
  • Fixed an error that occurred with very long sample names
  • Fixed a problem with labeling modified peptides when a modification applies to more than one amino acid
  • Fixed a problem with adding multiple star colors through Scaffold Batch
  • Corrected calculation of PeptideProphet with High Mass Accuracy adjustment when delta masses are very large
  • Corrected an error in labeling modifications from MaxQuant
  • Corrected an error in computing the charge state of peptides
  • Corrected an error that sometimes prevented export of SFDB files
  • Corrected an error in counting protein clusters
  • Corrected a problem with incorrectly saved thresholds causing inconsistent values on file reopening
  • Corrected an error in counting the number of spectra loaded from mzIdentML files with LFDR as the probability model
  • Corrected an error that produced duplication of input file names when loading newer PEAKS files
  • Corrected the behavior of the Batch setup GUI for handling of prefiltered data
  • Removed:
  • Eliminated 32-bit installers
  • Deprecated the LFDR scoring system in the Loading Wizard
  • Removed the option to condense during loading
  • Stopped bundling X! Tandem into the Scaffold installer

New in Scaffold 4.11.1 (Sep 25, 2020)

  • Scaffold Bug Fixes:
  • Corrected an error in indexing modifications when condensing files during saving.
  • Scaffold Q+ Bug Fixes:
  • Corrected reading of MS3 TMT 16-plex data from Proteome Discov

New in Scaffold 4.11.0 (May 12, 2020)

  • Scaffold Q+ Features:
  • Added support for TMTpro 16plex quantification.
  • Revised and expanded the purity correction dialog.
  • Added the start and stop position in the protein sequence to the Peptides Table.
  • Scaffold Q+ Bug Fixes:
  • Removed normalization constants for unused samples from the Publish View.
  • Scaffold Features:
  • Added the ability to calculate peptide probabilities using Percolator scores from Proteome Discoverer.
  • Added a warning about use of the condense during loading option.
  • Added support for Byonic 3.8.13.
  • Added an Alternate ID column to reports.

New in Scaffold 4.10.0 (Oct 3, 2019)

  • Q+/Q+S Bug Fixes:
  • Corrected reading of Iodo TMT 6-Plex data from MaxQuant.
  • Stopped reading iTRAQ or TMT intensity values from spectra in MS3 data.
  • Scaffold Features:
  • Added a header to the PSEA Quant report.
  • Changed the default parsing for UniProt/Swiss-Prot accession numbers.
  • Added the ability to populate the alternate ID field by parsing the Accession Number or Protein Name fields.
  • Allowed use of Alternate IDs for fetching annotations from NCBI.
  • Added the ability to select whether to use Accession Number or Alternate ID when adding annotations.
  • Added a warning to the Add or Edit Annotations dialog to indicate the type of alternate IDs required for selected searches.
  • Scaffold Bug Fixes:
  • Included GO terms in SFDB export for Scaffold perSPECtives.
  • Corrected the default sort order of proteins in the Samples View.
  • Allowed loading of very large files directly from the Mascot server.
  • Modified the parameters passed to X! Tandem when run during loading of MaxQUant data.
  • Added an error message indicating the presence of multiple parameter files during loading of Proteome Discoverer data.
  • Corrected an error in loading multifile projects from Mascot Distiller.
  • Corrected an error in applying Spectrum Mill score-based peptide thresholds.
  • Included all modifications in Load Data View from Spectrum Mill searches.
  • Prevented loading Spectrum Mill data with multiple unrelated enzymes.
  • Clarified the warning message displayed when X! Tandem produces no results.
  • Corrected a problem in parsing N-terminal modifications from Byonic.
  • Removed Decoys from the legend in the Peptide Prophet charts in the Statistics View.
  • Improved error handling in PSEA Quant analysis.
  • Replaced publication-sized chart image exports with fully scalable SVG exports.
  • Annotated iTRAQ/TMT peaks in spectra in the BioSample viewing mode.
  • Ensured that all temp files are properly closed.

New in Scaffold 4.9.0 (Jun 3, 2019)

  • Q+/Q+S Features:
  • Added support for iodoTMT 6-plex quantification.
  • Q+/Q+S Bug Fixes:
  • Corrected the purity correction matrix for TMT 11-plex.
  • Scaffold Features:
  • Added a BLIB export.
  • Added an SFDB export to write Scaffold perSPECtives fies.
  • Added the ability to fetch and display WikiPathway information for proteins.
  • Added the ability to fetch and display Reactome pathway information for proteins.
  • Added the ability to select which GO terms or pathways should be displayed using the PSEA-Quant algorithm.
  • Added a Pathways Bar Chart.

New in Scaffold 4.8.9 (May 2, 2019)

  • Bug Fixes:
  • Adjusted the parent tolerance parameter value for X! Tandem runs when loading MaxQuant data.
  • Added an informative message when an attempt is made to load very large data files directly from the Mascot server.
  • Allowed processing to continue but with a warning message displayed when an mzIdentML file containing no spectra is loaded.
  • Scaffold Batch:
  • Corrected error handling when a file error is encountered.

New in Scaffold 4.7.5 (Jan 31, 2017)

  • Scaffold Features:
  • Added the ability to directly download GO Annotation files for individual taxonomies from the Gene Ontology Consortium web site.
  • Scaffold Bug Fixes:
  • Corrected an error that occurred when downloading very large GOA files.
  • Corrected an error in creating exports for PRIDE.

New in Scaffold 4.7.3 (Dec 20, 2016)

  • Bug Fixes:
  • Updated NCBI access protocol to accommodate changes in the API.
  • Modified the method of downloading and parsing GOA databases.
  • Corrected a concurrent modification error.
  • Corrected an error that could cause failure to launch.
  • Added scores to Spectrum Report for search engine results read from mzIdentML files.
  • Modified parsing of modifications from PLGS files.

New in Scaffold 4.7.2 (Oct 17, 2016)

  • Scaffold Bug Fixes:
  • Ensured that GO annotations previously applied and saved appear upon file opening.

New in Scaffold 4.7.1 (Oct 11, 2016)

  • Scaffold Q+ features:
  • Changed the default experimental design to "Between-subjects (Independent Groups)".
  • Scaffold features:
  • Updated java version to Java 8 for better compatibility with Windows 8 and 10 and with the NCBI database.
  • Scaffold bug fixes:
  • Allowed loading of MSF files from folders containing multiple Proteome Discoverer experiments.
  • Corrected an error in loading MSF files created by the Proteome Discoverer Daemon.
  • Corrected an error that created duplicate spectra from certain MSF files.
  • Corrected an error that prevented performing the MuDPIT operation on multiple samples from a single MSF file.
  • Corrected an error in restoration of backup files that could prevent saving of files after loading.
  • Made parsing of the PDStudy file name case-insensitive.
  • Corrected an error in the mzIdentML export of files with NCBI annotations that prevented uploading to PRIDE.
  • Corrected an error that caused the Samples View table to appear as empty after Peptide Validation reset.

New in Scaffold 4.6.2 (Aug 29, 2016)

  • Scaffold Q+ Features:
  • Added the ability to use Scaffold's protein filters through the Q+ Samples View.
  • Display the current thresholds in the Q+ interface. Thresholds must be adjusted through Scaffold.
  • Added the standard deviation to the tooltip for log2 fold changes in the Q+ Samples View.
  • Added the standard deviation for log2 fold changes or the geometric standard deviation to the Q+ Samples Report and the Q+ Samples View Report.
  • Scaffold Q+ Bug Fixes:
  • Modified the method of recognizing quantitative data from Proteome Discoverer 2.1.
  • Corrected an error in rendering the Signal to Noise chart in Q+.
  • Corrected an error in creation of Q+ category and protein level charts in ratio-based quantitation.
  • Scaffold Features:
  • Modified the MaxQuant file reader to read precursor intensity values even if another quantitative method is specified.
  • Scaffold Bug Fixes:
  • Improved performance in applying FDR Thresholds.
  • Reinstated interactivity in the FDR Browser.
  • Corrected an error in the mzIdentML export that resulted in certain proteins being incorrectly marked as not meeting thresholds.
  • Improved the speed of the mzIdentML export.
  • Corrected an error in mzIdentML exports from very large Scaffold files.
  • Updated the link for download of GOA databases.
  • Corrected a problem in selection of the correct database when running X! Tandem.
  • Corrected updating of the Samples View when adding or deleting BioSamples.
  • Corrected an error that occurred when attempting to MuDPIT a large number of samples.
  • When loading mzIdentML files with no enzyme information specified, set enzyme to "NON_SPECIFIC".
  • Ensured that the Load Data button becomes active when a new database has been added through the data loading wizard.
  • Corrected the behavior on double-clicking of the protein ambiguity stars in the Samples View to correctly open the Similarity View.
  • Corrected an error that occurred under Mac OS X when loading very large FASTA files.
  • Scaffold Batch Features:
  • Added the ability to specify Q+ Quantitation setup parameters in Batch XML driver file (SCAFML).
  • Scaffold Batch Bug Fixes:
  • Ensured that the proper quantitative technique setting is applied to MaxQuant samples loaded through Batch.

New in Scaffold 4.6.1 (Jun 7, 2016)

  • Bug fixes:
  • Fixed in-program Q+ user's guide.
  • Fixed bug wherein number of decoys not showing up in Samples View, above protein list.

New in Scaffold 4.6.0 (Jun 3, 2016)

  • SCAFFOLD Q+ FEATURES:
  • Added support for MS3 quantitation from Proteome Discoverer and MaxQuant. Mascot Distiller places MS3 intensities into the MS2 spectra and is supported as if it were MS2 quantitation.
  • Added a spectral quality filter requiring that all quantitative values are present in a spectrum in order for it to be used in quantitation.
  • SCAFFOLD Q+ BUG FIXES:
  • Improved recognition of TMT 10-plex reporter peaks in MS2 spectra.
  • Corrected behavior of Raw Quantifiable Intensity Chart when one or more of the quant samples contains no data.
  • Corrected a minor error in the Mann-Whitney Test calculation.
  • Corrected an error that prevented changing the quantitative method of a SILAC file and restoring it.
  • SCAFFOLD FEATURES:
  • Clean up user interface for peptide thresholds dropdown for clarity -- matches protein thresholds.
  • Allowed specification of multiple fasta databases when loading data.
  • Added the option to filter the database used in X!Tandem searches to provide the ability to limit the search based on, eg taxonomy.
  • Added an optional column to the Samples View to display a gene ID or other alternate identifier.
  • Added the ability to specify an additional parse rule when indexing a fasta database to populate the alternate ID column. The default parse rules for IPI and Uniprot databases were updated to include rules to parse the Gene Name field as the alternate ID.
  • Added an option to the NCBI GO Annotation option to allow retrieval of Gene IDs and various other alternate ID forms from the NCBI database.
  • Added the ability to edit alternate ID’s individually and an option to clear all alternate IDs through the right-click menu.
  • Provided support for Proteome Discoverer 2.1.
  • Added a dialog to allow selection of files for inclusion in a specific BioSample when loading multiple samples from a single MSF file.
  • Modified Samples View to allow simultaneous display of statistical test results and fold-changes.
  • Added the ability to read precursor intensities from mzIdentML/MGF files generated by PLGS.
  • Improved performance during file loading and responsiveness of the GUI.
  • Added reading of retention times when loading MaxQuant data.
  • Added an option to the right-click menu in the Edit > FASTA Databases dialog to locate a FASTA file.
  • Modified the default parsing rules for NCBI databases to comply with their new format.
  • Scaled the NSAF quantitative display type to conform to the generally accepted definition.
  • Provided a dialog to allow selection of the folder containing ROV files for individual samples when loading multi-sample Mascot Distiller experiments.
  • SCAFFOLD BUG FIXES:
  • Corrected reading of the number of proteins in the searched database for MSF files.
  • Changed the reporting of databases when exporting mzIdentML files for PRIDE.
  • Made the Peptides Table retain column order set by user when changing proteins.
  • Changed the sort order of Categories to natural sort.
  • Corrected the Volcano Plot to correctly recognize significant differential expression when a multiple test correction is applied.
  • Corrected display of MaxQuant custom modifications when the modifications.xml file is placed in Scaffold’s parameters folder.
  • Prevented inappropriate display of the warning message for incorrect MaxQuant parameters.
  • Added automatic selection of newly added fasta databases.
  • Corrected a grammatical error in the support contract expiration dialog.
  • Modified NCBI annotation lookup for IPI accession numbers to eliminate calls to a defunct database.
  • Adjusted interaction of thresholding and filtering to improve performance. This results in slight changes in behavior of the Show Entire Protein Clusters option.
  • SCAFFOLD BATCH BUG FIXES:
  • Fixed possible divide by zero bug.
  • Fixed issue where mzid could not be created when writePeaklists="false".
  • Removed support for Tranche SCAFMLs
  • Fixed issue in MZID with generating spectrum identification result element without spectrum identification items.
  • Fixed issue with newly added attribute saveCondensed interfering with discardBelowThresholds attribute.
  • Fixed issue with duplicate peptide thresholds appearing in dropdown when loading and SF3 created from Batch.
  • Fixed crucial issues with identity and uniqueness for peptide thresholds.
  • Fixed issue with data not being recomputed for subsequent export element declarations.
  • Fixed minor issue with log message using SI prefix units for max memory where it should have been binary.
  • Fixed issue with using incorrect attribute for BioSample element name
  • Fixed issue with exported SCAFML not finding sequences for proteins even though UI does.
  • SCAFFOLD BATCH FEATURES:
  • Generated improved annotated SCAFML document.
  • Separated the annotated SCAFML driver from the user guide, and cleaned up user's guide.
  • Multi-FASTA database support in SCAFML for Batch.
  • Added functionality to specify protein grouping type for experiment.
  • Q+ and Q+S exports now available in batch.
  • Added functionality to specify FDR thresholds via attributes: maxProteinFDR and maxPeptideFDR.
  • Automatically generate BioSamples for individual files from MaxQuant (options for experiment and fractions).
  • Added support for annotation star states for Batch.
  • Added functionality to specify the display type for generated SF3s and protein family as collapsed or expanded.
  • Add ability to specify GO source in Scaffold Batch
  • Added numberOfProcessors attribute which is used for X! Tandem threads.
  • Added databaseVersion attribute for FastaDatabase element.
  • Added functionality to encode multiplex experimental design in SCAFML.
  • Display type defaults to Protein Identification Probability when no quantitative display type is present.

New in Scaffold 4.5.3 (Apr 19, 2016)

  • Scaffold Q+ Bug Fixes:
  • Allowed retention of quantitative sample names when reorganizing quant samples in files created in previous versions of Scaffold.
  • Restored the functionality of the Select All option in the right-click context menu of the Q+ Samples View.
  • Scaffold Bug Fixes:
  • Corrected an error in reading ratio values from MaxQuant SILAC data.
  • Corrected listing of fixed modifications in the spectrum export.
  • Corrected an error in Scaffold Batch that prevented running with older XML files.
  • Corrected a display error in the Venn Diagram pane.
  • Ensured that the lower pane of the Similarity View retains its size when a peptide is unchecked in the upper pane.

New in Scaffold 4.5.1 (Mar 15, 2016)

  • Scaffold Q+ Bug Fixes:
  • Corrected an error that caused Samples View-related exports to display incorrectly in Excel.
  • Corrected an error that occurred when quant sample names were edited after a statistical test had been applied.
  • Improved handling of quantitative data by the MaxQuant results reader.
  • Corrected a problem in handling missing references in Individual Spectrum Reference mode.
  • Insured that all quantitative analysis settings are properly recorded when saving a file.
  • Corrected an error in parsing modifications when reading Byonic search results from Proteome Discoverer 2.0 and earlier.

New in Scaffold 4.5.0 (Mar 4, 2016)

  • Scaffold Q+ Features:
  • Improved support for a variety of experimental designs in Q+, including correct reference alignment, blocking, statistical testing and multiple test correction.
  • Completely redesigned the interface for sample organization in Q+, providing a new Experimental Design Wizard.
  • Implemented the rANOVA and Friedman tests for repeated measures.
  • Added various techniques for multiple test correction of statistical tests, including Benjamini-Hochberg, Holm Step-down and Hochberg Step-up.
  • Added testing of the assumptions of applied statistical tests, with coloring of p-values to indicate potential problems.
  • Changed the treatment of multiple MS Samples loaded into a single Scaffold BioSample to treat each as an individual quant sample unless the MuDPIT option has been selected.
  • Added the ability to treat specified quant samples as technical replicates in the statistical analyses.
  • Replaced the previous ratio-based normalization model with a new version that performs normalization and statistical analysis of quantitative ratios in one or more samples.
  • Added the ability to display both Fold Change by Category and results of a statistical test simultaneously.
  • Provided the option to display only the analyzed samples when a quantitative test has been applied.
  • Added the ability to filter spectra with missing reference values from the set of spectra used for quantitation.
  • Added an export to provide details of the computations performed when applying a statistical test.
  • Improved the reporting in the Q+ Publish View.
  • Added a button to the toolbar to launch the Quantitative Testing dialog.
  • Added Scaffold Batch support for the new experimental designs in Q+.
  • Updated the demo files.
  • Scaffold Q+ Bug Fixes:
  • Modified the calculation of Coefficient of Variation so that it only applies when the experiment contains technical replicates and it assesses variation among the replicates.
  • Renamed "Quant Uniqueness Model" to "Blocking Level" in the Quantitative Settings dialog.
  • Repaired functionality of the Edit>Find option in Q+.
  • Refined the selection of spectra to be used in quantitation and changed the Exclusive Spectrum display type to Quantitated Spectrum Count.
  • Corrected an error in that inconsistently applied blocking depending on the display option selected.
  • Changed the name of the Quantitation Browser to the Quantitation Module.
  • Improved performance in the creation of the Q+ scatterplots.
  • Capped the displayed coefficient of variation at 1000%.
  • Standardized the annotation of missing values.
  • Modified the methods of calculation of mean and standard deviation in kernel density estimation.
  • Corrected an error in the display of the Pre/Post Normalization Box Plot in the presence of many missing values.
  • Corrected the Coefficient of Variation Box Plot to use all thresholded proteins, rather than the filtered set of proteins.
  • Modified the calculation of the Mean/Density Distribution Graph.
  • Scaffold Bug Fixes:
  • Modified the FASTA parser to handle cases where the EOL character between the protein header and protein sequence is missing.

New in Scaffold 4.4.8 (Dec 3, 2015)

  • Scaffold Bug Fixes:
  • Properly close resources while loading Proteome Discoverer files to prevent unexpected termination of the program.

New in Scaffold 4.4.7 (Nov 7, 2015)

  • Scaffold Features:
  • Added the ability to load individual files from MaxQuant experiments.
  • Added an informative message about preparation of data using Proteome Discoverer 2.0 to an error dialog.
  • Scaffold Bug Fixes:
  • Improved the efficiency of the mzIdentML export.
  • Corrected the calculation of Multiple Test Correction factors to include all proteins rather than the filtered set.
  • Corrected an error that appeared when checking MaxQuant parameters prior to running X! Tandem.
  • Corrected reading of FASTA database name and number of entries from Proteome Discoverer 1.4 files.
  • Changed the default tab selection behavior in the Proteins View.
  • Corrected an error that could cause an out-of-bounds exception when calculating iBAQ.
  • Scaffold Q+ Features:
  • Added the “Protein Quantition XML Report” to export ratios of protein levels for subsequent analysis in Scaffold PTM.
  • Write the SQML file to the same folder as the mzIdentML and MGF files in a ScaffoldQuantML export.
  • Scaffold Q+ Bug Fixes:
  • Removed the error information from the log2 intensity values reported in the Q+ Samples Report.
  • Corrected an error in writing BioSample ID's to the ScaffoldQuantML report.
  • Changed reporting of Intra-Sample Normalization factors in the Publish View when one MS-Sample in a BioSample has no quantitative data.

New in Scaffold 4.4.6 (Oct 12, 2015)

  • Scaffold Features:
  • Added an option to obtain protein information from the FASTA database during loading of mzIdentML files even if the mzIdentML contains the protein sequence information. This will allow parsing of protein names and accession numbers for PEAKS and other MZID files that contain sequences. By default, the FASTA will be preferred, but a setting in Edit > Preferences > MZID allows the user to switch to using only the information in the mzIdentML.
  • Scaffold Bug Fixes:
  • Corrected MZID export for PRIDE to work properly with multiple BioSamples.
  • Pick up modification information from Byonic searches done with Proteome Discoverer 1.4. The user needs to have saved the modification file through Byonic and to have placed it into the same directory as the MSF for loading.
  • Corrected an error in loading large data sets in MS2/SQT format.
  • Retain tab selection in lower pane of Proteins View when peptide selection is changed.
  • Properly report modifications on multiple residue sites in the Load Data View when loading Mascot data from Proteome Discoverer 2.0.
  • Report the FASTA database used in Mascot and MS Amanda searches through Proteome Discoverer 2.0.
  • Corrected an error in reporting modifications from MaxQuant 1.5.3.8.

New in Scaffold 4.4.5 (Oct 12, 2015)

  • Scaffold Features:
  • Support files produced by Proteome Discoverer 2.0 through the Daemon. Requires export of parameter file.
  • Scaffold Bug Fixes:
  • Corrected spectral counts in the Load Data View when loading MSF files from Proteome Discoverer 2.0 studies containing multiple analyses.
  • Corrected reading of modifications for Proteome Discoverer 2.0 files containing Mascot or Amanda results.
  • Changed sort order of peptides in the Proteins View for very large proteins.

New in Scaffold 4.4.4 (Oct 12, 2015)

  • Scaffold Features:
  • Support files produced by Proteome Discoverer 2.0
  • Scaffold Bug Fixes:
  • Highlight all identified peptides in sequence coverage map even for very large proteins.

New in Scaffold 4.4.3 (Oct 12, 2015)

  • Scaffold Features:
  • Support Byonic searches run through Proteome Discoverer. Note that filtering by modification is not yet supported.
  • Scaffold Bug Fixes:
  • Corrected an error that sometimes caused misalignment of columns upon filtering.
  • Updated the version of the sqlite driver to correct memory management issues in newer Mac OSX versions.
  • Adjusted precision of start and stop indices to handle very large proteins.
  • Changed default settings to exclude decoys from the PTM mzIdentML export.
  • Improved the tooltip for the header of the Actual Mass column in the Proteins View.

New in Scaffold 4.4.1 (Oct 12, 2015)

  • Scaffold Features:
  • Upgraded the installer for Mac OS X
  • Scaffold Bug Fixes:
  • Corrected an error in the Samples Report.
  • Corrected the alignment of column headers in the Samples View export.
  • Changed the wording of the Samples View context menu option to create a Peptide Report containing only starred proteins.

New in Scaffold 4.4.0 (Oct 12, 2015)

  • Scaffold Features:
  • Support loading of mzIdentML and MGF files generated by Protein Pilot 5.0.
  • Support precursor intensity quantitation from searches conducted on MGF files exported from Progenesis.
  • Improved the Quantify View
  • Added a Volcano Plot to the Quantitative Scatterplots, available only when a quantitative test that compares exactly two categories is applied.
  • Added a number of options to the Venn Diagram feature including: The option to display counts of protein clusters; and, the option to display counts and do filtering based on relative quantitative values in two or more categories.
  • Modified some behavior in the Venn Diagrams upon double-clicking: Double-clicking in a region with a value of "0" now has no effect. Double-clicking outside the Venn Diagram still clears the filter but no longer switches the View to Samples.
  • Improved the Quantitative Scatterplot displayed in the Quantify View.
  • Coordinated protein selection among panes in the Quantify View.
  • Added several options to the Quantitative Testing dialog. These include: The ability to specify a desired significance threshold; and, several options for applying multiple comparison corrections.
  • Added a "Quantitative Profile" column to the Samples View that displays relative levels of protein in compared categories. This column appears only when a test for statistical significance has been applied. Sorting and filtering on this column are supported.
  • Added iBAQ as a Quantitative Method option.
  • Added the ability to selectively display only certain panes in a View.
  • Changed the behavior of the "Show Entire Protein Clusters" option.
  • Removed the MCP Submission tab from the Publish View.
  • Added the Protein Name to the JPG export of the Spectrum Counts Histogram in the Quantify View.
  • Added accession numbers to the export generated by the "copy scatterplot data" option in the context menu of the Scatterplot in the Quantify View.
  • Scaffold Bug Fixes:
  • Dramatically improved performance when loading mzIdentML files.
  • Corrected an issue that caused the false display of an O+18 modification when Mascot 2.5 files were loaded.
  • Corrected a null pointer error that occurred when exporting mzIdentML files from Scaffold files created in older versions.
  • Corrected a problem that left a process running when the program closed on Windows 8 systems.
  • Corrected some behavior of the Venn Diagram feature when one category was set to "No Category Specified."
  • Retain category selections in Venn Diagram when moving between Views.
  • Improved pane resizing behavior in the Quantify View.
  • Renamed the Scatterplot in the Quantify View.
  • Improved the visibility of the warning message displaying the settings of "Show Lower Scoring Matches" and "Show Entire Protein Clusters" in the Quantify View.
  • In the Quantify View Scatterplot, when more than one protein maps to the same point, display all matching proteins in the tooltip.
  • Modified the tool tip for the column header of the #Spec column in the Proteins Table in the Proteins View to more accurately reflect its meaning under different grouping methods.
  • Corrected an error in the rendering of the "Assigned" column in the Proteins View after changing the protein grouping method.
  • Modified the appearance of some existing options in the Advanced Filters dialog.
  • Improved performance in the Edit Fasta Database dialog.
  • Restored missing tool tips to column headers in the MS/MS Samples Table in the Statistics View.
  • Corrected an error that could cause failure when loading data using PeptideProphet.

New in Scaffold 4.3.3 (Oct 12, 2015)

  • Scaffold Bug fixes:
  • Corrected coloring of values in Samples View table.
  • Restored direct download of All Proteomes GO Database file.
  • Adjusted the axis label in the Quantitative Value Histogram to correctly reflect the type of displayed values.
  • Corrected a null pointer error that occurred when reading DAT files containing only decoy matches.
  • Allow loading of Spectrum Mill data containing empty *.pkl.spo files.
  • Corrected a problem in reading spectra from MaxQuant data when file names contained spaces.
  • Restored function of the context menu for Mac OS X 10.9
  • Fixed file chooser for Mac OS X 10.9.
  • Scaffold Features:
  • Added support for Protein Pilot 5.0 mzIdentML files.
  • Added support for Agilent Spectrum Mill version B.04.01. Spectra may be loaded from either mzXML or PKL files.
  • Parse spectrum title lines of DAT files to read retention times and/or intensities if they are specified there. Retention times must be specified in the form "rt=XXXXX" and retention times are assumed to be in seconds. Intensities must be in the form "intensity=XXXXX".
  • Write retention times and intensity values to spectrum title lines when exporting mzIdentML and MGF files.

New in Scaffold 4.3.2 (Oct 12, 2015)

  • Scaffold Bug fixes:
  • Modified the mzIdentML reader to prevent a possible infinite loop when storing spectra from mzIdentML files.
  • Corrected an error that prevented loading of some MSGF+ files.

New in Scaffold 4.3.0 (Oct 12, 2015)

  • Scaffold Features:
  • Added an option to hide the legend in the GO Terms Pie Chart.
  • Scaffold Bug Fixes:
  • Changed the input parameter specifications for X!Tandem to handle multiple modifications on the same residue.
  • Improved loading of Mascot Distiller files, including those created by Mascot Daemon.
  • Improved collation of spectra from different types of mzIdentML files.
  • Filter spectra from mzIdentML files so each spectrum will count only once in each protein.
  • Annotate spectra from mzIdentML/mgf files correctly regardless of fragmentation type.
  • Modified the mzIdentML reader to avoid using userParams as scores.
  • Adjusted the parameters for PeptideProphet analysis of MSGF+ files.
  • Prohibited overwriting of an older licensed copy of Scaffold with an expired support contract.
  • Restored sorting ability to all Scaffold tables.
  • Allowed panes in the Quantify View to adjust to smaller sizes.
  • Truncate the protein name in the dropdown in the Proteins View.
  • Corrected sorting of columns in the Similarity View.
  • Increased the allowable number of modifications per peptide.
  • Made minor changes to the wording in the Loading Wizard.
  • Scaffold Batch Features:
  • Added new Batch tags for exporting Quantitative Values. Details are provided in the Scaffold Batch User's Guide.
  • Scaffold Batch Bug Fixes:
  • Fixed the keypath command in Scaffold Batch.

New in Scaffold 4.2.2 (Oct 12, 2015)

  • Scaffold Bug Fixes:
  • Corrected non-deterministic behavior in loading mzIdentML files.
  • Corrected non-deterministic behavior in protein grouping.
  • Made ordering of modifications in X! Tandem parameters deterministic.
  • Improved the composition of subset databases created for X! Tandem search.
  • Corrected an error in the mzIdentML export that prevented proper loading in Skyline.
  • Fixed a null pointer error in loading certain mzIdentML files.
  • Fixed a problem in downloading NCBI annotations.
  • Changed the MaxQuant file reader to better handle files created on non-English systems.
  • Allow loading of files with slight corruption in their peaklists.