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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 24, 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 Discoverer.

New in Scaffold 4.11.0 (May 11, 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)

  • Corrected reading of Iodo TMT 6-Plex data from MaxQuant.
  • Stopped reading iTRAQ or TMT intensity values from spectra in MS3 data.

New in Scaffold 4.8.9 (Dec 4, 2018)

  • 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 4.8.8 (Oct 17, 2018)

  • Scaffold Features:
  • Added the ability to look up proteins on websites based on alternate ID’s such as gene name.
  • Added a link to Wiki Pathways for looking up proteins by gene names.
  • Scaffold Bug Fixes:
  • Adjusted the Minimum Dynamic Range parameter for X! Tandem runs.
  • Ensured that the correct ion types are searched in X! Tandem analyses.
  • Corrected reading of custom modification names in Proteome Discoverer 2.2 files containing Mascot results.
  • Corrected reading of modifications from MaxQuant 1.6.2 files.
  • Corrected alignment of headers in the Samples Report.
  • Corrected an error in exporting mzIdentML files containing titin.
  • Corrected a problem in rendering theQuantitative Scatterplot for TIC values.
  • Allowed loading of X! Tandem results with fragment mass error greater than one.

New in Scaffold 4.8.7 (Jun 2, 2018)

  • Scaffold Features:
  • Updated to a newer version of X! Tandem (Alanine).
  • Improved scoring for Comet files.
  • Added the ability to search for protein-terminal Acetyl modifications with X! Tandem.
  • Scaffold Bug Fixes:
  • Improved handling of unexpected characters in protein names when exportin mzIdentML files.
  • Prevented loading of mzIdentML files from unsupported search engines with more than five scores.
  • Prevented use of non-score metrics, such as drift time, as peptide scores in probability calculations when loading mzIdentML files.
  • Corrected a comparison error that occurred occasionally when loading mzIdentML files.
  • Updated the URL in an error message that can appear during loading of MSF files.

New in Scaffold 4.8.6 (May 4, 2018)

  • Scaffold Bug Fixes
  • Returned to zero-filling blank cells in the Samples Report.
  • Modified BLIB export to improve compatility with Skyline.
  • Corrected an error in writing to spectra to the BLIB export.
  • Converted retention times read from Mascot files to seconds.
  • Corrected an error in loading Byonic mzIdentML files.
  • Corrected a potential error in loading MS-GF+ mzIdentML files.
  • Updated the code-signing certificate.

New in Scaffold 4.8.5 (Apr 21, 2018)

  • Scaffold Q+ Features
  • Added a volcano plot
  • Support TMT 11-plex
  • Added ability to read SILAC values from Proteome Discoverer 2.2 files.

New in Scaffold 4.8.4 (Sep 12, 2017)

  • Scaffold Q+ Bug Fixes:
  • Modified MaxQuant results reader to support MS3 quantitation from MaxQuant 1.6.
  • Corrected an error in reading MS3 data from Proteome Discoverer 2.2.
  • Modified the Quantitative Spectrum Report to reflect the source of missing values when exporting fold-changes.
  • Scaffold Features:
  • Added the option to display proteins with infinite fold-changes or very small p-values on the volcano plot.
  • Scaffold Bug Fixes:
  • Corrected reading of accession numbers in Proteome Discoverer 2.2 files.
  • Corrected the calculation of the Mascot Identity Threshold from Proteome Discoverer 2.2 files.
  • Modified the scoring of Mascot results in the LFDR algorithm.
  • Corrected a problem that prevented some older Scaffold files from opening in the newer versions.

New in Scaffold 4.8.3 (Aug 3, 2017)

  • Scaffold Q+ Bug Fixes:
  • Restored the ability to quantitatate using dimethyl labeling in files from Proteome Discoverer.
  • Corrected an error in updating the Proteins View upon double-clicking in the Samples View.
  • Scaffold Bug Fixes:
  • Improved compatibility with Proteome Discoverer 2.2.
  • Restored the ability to merge Scaffold files.

New in Scaffold 4.8.2 (Jul 3, 2017)

  • Corrected an error in LFDR scoring when loading Mascot, Byonic or MS-GF+ files.
  • Added defined discriminant scores to the set of scores used in LFDR.
  • Ensured that all search engine scores are reported in mzIdentML exports.
  • Restored function of the "Add BioSample" button when opening previously saved Scaffold files.
  • Restored function of the Req Mods filter when FDR thresholds applied.
  • Allowed loading of mzIdentML files with Protein Detection Hypotheses containing no Peptide Identification Hypotheses by skipping the proteins with no peptides.
  • Ensured that all search engine scores are reported in the Peptides Report.
  • Corrected loading of MSF files with MuDPIT and Condense options on.
  • Corrected an error when loading MSF files with protein terminal modifications.
  • Clarified that the version numbers reported for search engines run as Proteome Discoverer nodes refer to the Proteome Discoverer version.
  • Provided a warning message when the X! Tandem option is selected during loading of mzIdentML files that do not specify searched modifications.
  • Improved automatic identification of the quantitative technique in MaxQuant files.

New in Scaffold 4.7.5 (Feb 7, 2017)

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

New in Scaffold 4.6.1 (Jun 8, 2016)

  • 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 8, 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.

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 (Apr 19, 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 5, 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 2, 2015)

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

New in Scaffold 4.4.7 (Nov 6, 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 (Sep 25, 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 (Jun 18, 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 (Jun 1, 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 (Apr 18, 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.
  • Scaffold Q+ Bug Fixes:
  • Corrected an error in the calculation of the purity correction factors for iTRAQ.

New in Scaffold 4.4.1 (Nov 20, 2014)

  • 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 (Nov 20, 2014)

  • 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.
  • Scaffold Q+ Bug Fixes:
  • Added "Log 2" to the name of the intensity option in the Display Option dropdown to accurately describe the value shown when the option is selected.
  • Ensured that the setting for the Quant Uniqueness Model is respected in all cases.
  • Ensured that the Display Settings option selected in the Samples View is correctly reflected when moving to the Proteins View via the Proteins button.
  • Corrected a null pointer error that could occur when generating the Quantitative Spectrum report and the Quantitative Peptide Report.

New in Scaffold 4.3.3 (Jun 20, 2014)

  • Scaffold Q+ Bug fixes:
  • Corrected an error that caused Q+ to stall when opening in certain files.
  • Corrected an error that prevented loading of multiple Mascot Distiller files together.
  • Corrected an error that caused incorrect naming of Q+ quantitative samples when precursor intensity Biosamples were renamed through the Scaffold file loading wizard.
  • Label SILAC samples "Light", "Medium" and "Heavy" in Q+ sample organization dialog.
  • 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.
  • 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 (May 2, 2014)

  • Scaffold Q+ Bug fixes
  • Corrected an error that interfered with opening the quantitative module of Scaffold Q+ in files created in earlier versions with TMT data.
  • Corrected the export of statistical test results from Scaffold Q+/Q+S.
  • 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 (May 2, 2014)

  • Scaffold Q+ Features
  • Added the ability to display a fold change ratio comparing two categories. This is done by choosing samples belonging to two distinct categories in the Quantitative Analysis Setup, and then selecting the Fold Change option in that screen. It displays as a column similar to the display of statistical tests.
  • Adjusted the masses of TMT six-plex labels to correspond to the reagents currently distributed by Thermo.
  • Added explanatory text about blocking levels to the Q+ Quantification Setup screen.
  • Added an option to select fold change of 1.2 to the fold change filter dropdown.
  • Scaffold Q+ Bug Fixes
  • Fixed an error in opening the Q+ Proteins View when selecting a protein that has no values to display.
  • Filter out values more than four standard deviations below the mean to avoid very large coefficients of variation.
  • 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 (May 2, 2014)

  • Scaffold Q+ Bug Fixes
  • Increased the precision of values in the Samples View export.
  • 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.

New in Scaffold 4.2.1 (Oct 31, 2013)

  • Recompiled the linux versions of X! Tandem to ensure compatibility with Red Hat (RHEL) and CentOS.
  • Restored the ability to apply a new database.
  • Corrected a problem in picking up sequence data during loading when database has been parsed differently.
  • Corrected an error in spectrum counts when X! Tandem is run using a different parsing of the database.
  • Adjusted the delta mass calculations for iTRAQ and TMT data from MaxQuant.
  • Fixed the interface for entering decoy parse rules for use with Auto Parse.
  • Fixed the Scaffold complete export.
  • Corrected a collation problem when loading Myrimatch mzIdentML files with other files.
  • Corrected a null pointer error that occurred while loading Spectrum Mill data.
  • Changed the link for the Scaffold forum to point instead to Scaffold FAQ in the Help Menu.

New in Scaffold 4.2.0 (Oct 12, 2013)

  • Scaffold Bug Fixes:
  • Corrected a spectrum collation error between Mascot and X! Tandem.
  • Corrected a scrolling issue in the Peptides Table.
  • Corrected a null pointer error in loading Mascot files with no data.
  • Ensured that all clustering is rolled back if the clustering operation is canceled.
  • Made setting of the decoy status consistent when different parsers are used in the same experiment.
  • Made decoy proteins with no visible peptides disappear when Hide Decoy is selected.
  • Corrected sizing of publication sized JPEG images.
  • Disabled the Tranche upload button.

New in Scaffold 4.1.1 (Oct 9, 2013)

  • Scaffold Features:
  • Added an option to export mzIdentML files formatted for loading into Scaffold perSPECtives.
  • Scaffold Bug fixes:
  • Better support loading of MaxQuant 1.4 results. Now Scaffold is able to read the spectrum files from their new default location, read decoy results (at the peptide level) allowing use of the LFDR algorithm, and perform precursor intensity quantitation whether the raw files are analyzed together or separately in MaxQuant 1.4. For more information click here.
  • Changed the algorithm for quantitation with IdentityE data to better match changes in the PLGS algorithms.
  • Display precursor intensity and retention time in the Peptides Table for IdentityE data.
  • Read and display the iaDBs software version that was used for quantitation by PLGS from IdentityE files.
  • Choose whether to read accession numbers from the Entry or Accession field of PLGS files based on their contents.
  • Correctly read Mascot unimod.xml files containing custom modifications.
  • Modified the LFDR algorithm to prevent overfitting by ignoring scoring factors that would uniquely discriminate between decoys and non-decoys.
  • Modified the LFDR algorithm to rely more on the primary score in several search engines, including MG-GF+, Byonic, Myrimatch and MaxQuant.
  • Corrected an error in loading MS-GF+ files.
  • Record whether or not peptides pass thresholds when writing unfiltered mzIdentML reports.
  • Display the decoy parse rule currently in effect when a database is selected for editing.
  • Fixed the interface for changing decoy parse rules through the regular expression editing interface.
  • Changed the displayed value for % coverage from "0" to "?" when the protein sequence has not been read.
  • Corrected a null pointer error that sometimes occurred when adjusting protein probabilities after loading data.
  • Scaffold Batch Features:
  • Added support for all mzIdentML export options in Batch.
  • Scaffold Batch Bug Fixes:
  • Remove prompt for key when -f flag used.
  • Allow export of mzIdentML files in Batch even if no spectra meet thresholds.

New in Scaffold 4.0.7 (Oct 9, 2013)

  • Scaffold Bug fixes:
  • Improved performance in opening Scaffold files on Mac systems.
  • Fixed an issue in mzIdentML export where spectrum identifications could inconsistently reference equivalent peptide sequences within a single protein.
  • Corrected reading of Byonic scores in mzIdentML files.

New in Scaffold 4.0.6 (Oct 9, 2013)

  • Scaffold Features:
  • Added the ability to choose the reference sample or category for fold-change.
  • Added an option not to write peaklists to the Advanced Options dialog for mzIdentML export.
  • Allow Scaffold Viewer users to add GO annotations.
  • Scaffold Bug Fixes:
  • Read all peptides from Proteome Discoverer 1.4 files, even if they do not have an associated protein. This corrects the behavior of LFDR for Sequest HT data.
  • Corrected reading of variable modifications from Proteome Discoverer 1.4 files.
  • Included a 64-bit version of X! Tandem with 64-bit installers.
  • Corrected ordering of BioSamples to respect order in the Load Data View. Samples can again be reordered by dragging and dropping in Load Data.
  • Adjusted LFDR algorithm to minimize the effects of extreme outliers in any individual scoring element. This may change LFDR results.
  • Changed the high mass accuracy adjustment algorithm. The changes are most obvious when the input files contain only a few decoy proteins.
  • Disabled Independent Sample Grouping when using protein cluster analysis. Modified the Protein Grouping section of the Load and Analyze Data dialog.
  • Fixed Mac file browser problem that prevented changing destination for GOA database.
  • Disabled export of a multiple samples as a single mzIdentML file when Independent Sample Grouping is selected.
  • Corrected weighting function when the same spectrum is assigned to different peptides.
  • Corrected an error that could result in loss of peptide identifications when the same peptide was identified by multiple spectra.
  • Report mono masses rather than average masses for searched modifications in mzIdentML export.
  • Corrected an error that prevented application of GO terms with gi| accession numbers.
  • Removed "-R" from the list of default decoy search terms.
  • Return to selected protein when returning to the Samples View.
  • Corrected coloring of search engine histograms in Statistics View when combining search engine results.
  • Corrected linking of files when loading Mascot Distiller multi-file projects. Note that Scaffold does not currently support loading Distiller projects created by the Mascot Daemon.
  • Changed the spectrum ID format in mzIdentML 1.1.0 exports to match Scaffold's spectrum IDs.
  • Adjusted lookup values of "trypsin(kr) and "kr/-" enzyme strings.
  • Corrected an out of bounds error when attempting to load a file using a database with a very low decoy percentage.
  • Retain ordering of Samples View when hiding proteins.
  • Repaired the NTT filter.
  • Mark decoy proteins in mzIdentML exports.
  • Show all quantitative value options and gray out those which are unavailable.
  • Improved progress listener for mzIdentML exports.
  • Added dialog to warn if there is insufficient disk space before beginning download of a GO database.
  • Changed the Disk Space requirements in the Add GO Annotation Database dialog for the full GOA database.
  • Updated the web link for the GOA site.
  • Check the support contract expiration date before beginning installation to avoid overwriting the old version if the user is not eligible for upgrades.
  • Updated the End User License Agreement (EULA).
  • Scaffold Batch Bug fixes:
  • Updated mzIdentML exports in Scaffold Batch.
  • Enabled setting of the unimod file path from Scaffold Batch.

New in Scaffold 4.0.5 (Oct 9, 2013)

  • 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"'.

New in Scaffold 4.0.4 (Oct 9, 2013)

  • 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.

New in Scaffold 4.0.3 (Oct 9, 2013)

  • 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.

New in Scaffold 4.0.1 (Oct 9, 2013)

  • 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.

New in Scaffold 4.0.0 (Oct 9, 2013)

  • 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.