Scaffold, Q+, and Q+S Release Notes

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Version 4.8.1 Scaffold Release Notes (2017-06-02)

Scaffold Features

Added support for managing multiple Scaffold jobs with ease.

Added support for additional search engine thresholds when defining a custom peptide threshold.

Added support for custom thresholds to use notions like, 'at least', 'exactly', 'less than', 'between' etc.

Added support for specifying Any/All when a search engine threshold evaluates

Added support for loading multiple samples for Proteome Discoverer 2.1

Point to the FAQs in the new Help Center from the Help menu

Added support for specifying project directory so that supplementary ROV files for input XMLs can be associated during load.

Added support for saving QuantificationSetup from Q+ to SCAFML.

Support Spectrum Mill versions 5 and 6 (B.05 and B.06).

Allow Scaffold to load Spectrum Mill data with protein terminal modifications.

Add ability to read MGF files with decimal points in charges.

Add 'Prefiltered Mode,' allowing users to load data already filtered by a search-engine. We do not create a probability model, and hence do not report peptide or protein probabilities in this mode.

Added support for pre-filtered mode in Scaffold Batch

LFDR will exclude scores for which the target and decoy distributions are too similar (as measured by the Mann-Whitney U Test rho-statistic).

Add a warning message and ability to cancel when it is judged that a Fisher's Exact Test will be long-running.

Add a dialog to configure the Samples Report. Allow user to select export of a single Display Option, or all Display Options. Allow user to configure display of clusters and isoforms.

Allow the user to specify any probability in the Reset Peptide Validation Dialog.

Allowed Viewer users to create and edit custom peptide thresholds from the Edit menu.

Add an option to the Load Data Wizard allowing the user to forgo computation of FDR thresholds during loading.

Automatically exclude some scores, such as modsite localization and homology threshold, from use in LFDR.

Detect and throw an informative error on malformed Spectrum Mill files that contain lines without a forward or reverse sequence.

Make sure all relevant GO Terms are listed in tooltip and Samples View exports.

Updated the taxonomy.list, gene_ontology.obo and unimod.xml files included in the installer.

Scaffold Bug Fixes

Fixed issue with duplicate MultiFastaDatabase elements reported in SCAFML.

Fixed issue with not handling some encoded variable modifications for Mascot files which caused some missing peptides.

Fixed issue with SCAFML not properly encoding as UTF-8

Fixed issue with newly indexed fasta file reporting as "Untitled Database" instead of filename.

Fixed issue with where Scaffold crashed when loading msf files created by Proteome Discoverer 1.4.

Fixed a bug where some SF3 files would throw an NPE when opened in Batch.

Fix a bug which would cause some enzyme names to not be recognized when reading mzIdentML data.

Fix a bug where in some cases decoy peptides were not being linked to their decoy protein in MaxQuant.

Fixed a bug where some Mascot scores might not being reported in the Peptide Report.

Properly parse Mascot dat headers to read all FASTA databases searched.

Fix a bug where no purity correction would be applied to iTRAQ/TMT experiments despite being specified in the Load Data Wizard.

Fix a bug which could cause precursor intensity data to be lost.

Fix a bug in which could cause scores to not appear in the Peptides Table in the Protein view when loading mzIdentML data.

Fix a bug which could cause SILAC or MS3 data to be lost when attempting to reanalyze SF3s a different version of Scaffold Q+ or Scaffold Q+S than the one they were created in.

Fixed an error where some fixed or variable modifications might not be listed in the Load Data View or available in the Req Mods Filter when loading Spectrum Mill data.

Fixed a bug in Load Data Wizard in which files could be added to an already existing Biosample when trying to create a new Biosample.

Fix a bug in which precursor intensity from multiply modified peptides could be incorrectly rolled together with that from singly modified peptides for analysis in Scaffold Q+.

Version 4.7.5 Scaffold Release Notes (2017-01-26)

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.

Version 4.7.3 Scaffold Release Notes (2016-12-02)

Scaffold 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.

Version 4.7.2 Scaffold Release Notes (2016-10-14)

Scaffold Bug Fixes

Ensured that GO annotations previously applied and saved appear upon file opening.

Version 4.7.1 Scaffold Release Notes (2016-10-06)

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.

Version 4.6.2 Scaffold Release Notes (2016-08-26)

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.

Version 4.6.1 Scaffold Release Notes (2016-06-06)

Scaffold Bug Fixes

Fixed in-program Q+ user's guide.

Fixed bug wherein number of decoys not showing up in Samples View, above protein list.

Version 4.6.0 Scaffold/Q+/Batch Release Notes (2016-06-03)

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.

Version 4.5.3 Scaffold Release Notes (2016-04-18)

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.

Version 4.5.1 Scaffold Release Notes (2016-03-15)

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.

Version 4.5.0 Scaffold Release Notes (2016-03-04)

Scaffold General

Dropped support for Mac OS X 10.6.x and below.

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.

Version 4.4.8 Scaffold Release Notes (2015-12-02)

Scaffold Bug Fixes

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

Version 4.4.7 Scaffold Release Notes (2015-11-06)

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.

Version 4.4.6 Scaffold Release Notes (2015-09-24)

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

Version 4.4.5 Scaffold Release Notes (2015-06-17)

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.

Version 4.4.4 Scaffold Release Notes (2015-05-29)

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.

Version 4.4.3 Scaffold Release Notes (2015-04-17)

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.

Version 4.4.1 Scaffold Release Notes (2014-11-18)

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.

Version 4.4.0 Scaffold Release Notes (2014-11-03)

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.

Version 4.3.3 Scaffold Release Notes (2014-06-09)

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.

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.

Version 4.3.2 Scaffold Release Notes (2014-02-25)

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.

Version 4.3.0 Scaffold Release Notes (2014-02-03: includes fixes/features from 4.2.2 below)

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.

Version 4.2.2 Scaffold Release Notes (2014-01-09: internal release, download unavailable)

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.

Version 4.2.1 Scaffold Release Notes (2013-10-30)

Scaffold Bug Fixes

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.

Scaffold Q+ Bug Fixes

Corrected an error that prevented Q+ from opening if there was no quantitative data in the first sample.

Forced the Samples View to rebuild after changing the Req Mods filters in Q+.

Ensured update of the req mods filter when returning to Scaffold after it has been adjusted in Q+.

Added TMT 10-plex support for MaxQuant.

Changed Q+ Samples View to display 'No Values' rather than blank when a protein is not found in a sample in label-free quantitation.

Version 4.2.0 Scaffold Release Notes (2013-10-11)

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.

Scaffold Q+ Features

Implemented Protein Clustering in Q+.

Added support for iTRAQ and TMT data from MaxQuant.

Added support for TMT 10-plex and 8-plex.

Added support for Dimethyl quantitation from MaxQuant and Proteome Discoverer.

Implement bulk operations through right-click context menu in Q+.

Added standard deviation to the Samples report when reporting Normalized Intensity values.

Allow MaxQuant data to be loaded from zipped directories.

Read the spectra from MaxQuant 1.4 searches from their original locations.

Added the option to export chart information for the Average CVs and Pre/Post Normalization tabs in the Statistics View.

Specify that minimum fold changes are plus or minus.

Scaffold Q+ Bug Fixes

Made the Req Mods filter in Q+ consistent with Scaffold's.

Fixed the zoom function in the Intensity Weighting graph.

Customize the Q+ Publish page to reflect the selected normalization model.

Corrected a null pointer error when exporting the Raw Data report.

Corrected an error in transitioning to Q+.

Made changes in Quant Sample organization take effect immediately.

Version 4.1.1 Scaffold Release Notes (2013-09-04)

Scaffold Q+ Bug fixes

Adjusted the intensity values for the iTRAQ 121 ion in cases where phenylalanine isotopes distorted them.

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.

Version 4.0.7 Scaffold Release Notes (2013-07-24)

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.

Version 4.0.6 Scaffold Release Notes (2013-07-11)

Scaffold Q+ Bug fixes

Improved performance when launching Q+.

Corrected a null pointer triggered by recalculating clusters before moving to Scaffold Q+.

Sped up the calculation of the Median Density Chart.

Modified the permutation test for small numbers of data points.

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.

Version 4.0.5 Scaffold Release Notes (2013-04-25)

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"'.

Version 4.0.4 Scaffold Release Notes (2013-03-29)

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.

Version 4.0.3 Scaffold Release Notes (2013-03-04)

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.

Version 4.0.1 Scaffold Release Notes (2013-03-04)

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.

Version 4.0.0 Scaffold Release Notes (2013-03-04)

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.



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.

Version 4.0.0 Scaffold Q+/Q+S Release Notes (2013-03-04)

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.

Version 3.6.5 Scaffold Q+/Q+S Bug Fixes (2012-12-05)

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.

Version 3.6.5 Scaffold/Scaffold Batch Features (2012-12-05)

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.

Version 3.6.5 Scaffold Bug Fixes (2012-12-05)

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.

Version 3.6.4 Scaffold Features/Bug Fixes (2012-10-18)


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.

Version 3.6.3 Scaffold Features/Bug Fixes (2012-10-08)

Scaffold Features

Support loading of MaxQuant files from versions through

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.

Version 3.6.2 Scaffold Features/Bug Fixes (2012-08-20)

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.

Version 3.6.0 Scaffold Features/Bug Fixes (2012-07-06)

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.