Scaffold PTM Release Notes

The following document contains release notes for Scaffold PTM

Scaffold PTM 4.0.1 Release Notes (2021-04-02)

Fixed a bug where a new installation of the program required Java on the system. All users should update to ensure that the correct version of Java is used

Scaffold PTM 4.0.0 Release Notes (2021-03-18)

Updated colors, icons, and GUI look-and-feel for Scaffold PTM 4.0

Updated to using new licensing system

Fixed an incorrect warning about saved scores for multiply-modified peptides

Fixed a bug that could result in using the wrong summarization level when switching tabs in the Quant view

Fixed a bug where display type controls would sometimes not appear in the Quant view

Disabled analysis of PTM sites without a known location in the protein sequence to prevent incorrect results and errors when viewing such sites in the Proteins and Quant views

Removed 32-bit installers

Removed support for PTM Batch/Console

Scaffold PTM 3.3.0 Release Notes (2019-07-16)

Scaffold PTM Features

Added peptide-level tables to the Quantify View.

Added TIC options for quantitation.

Added multi-protein quantitative reports with selectable display options.

Added a validation message to the memory allocation setting in the installer.

Updated to a newer SQLite version.

Added a demo file to display protein-normalized quantitation.

Updated the installer file names.

Scaffold PTM Bug Fixes

Corrected an error in reading modifications with specified neutral losses.

Removed preceding spaces when the peptide sequence cell is copied.

Ensured that sort order is retained in the Quantify View when summarization is changed.

Corrected an error in the motif search code that could prevent files from loading.

Ensured that the preference setting for default view is respected.

Added an index to the QuantData table to improve performance.

Scaffold PTM 3.2.0 Release Notes (2017-06-08)

Scaffold PTM Features

Added the option to include neutral loss peaks in the Ascore calculation.

Updated the code-signing certificate.

Scaffold PTM Bug Fixes

Corrected rendering errors in the spectrum display.

Corrected the display of the spectrum ladder in the spectrum display.

Ensured that all caches are cleared when a file is closed.

Corrected an error in the Edit > Modification Colors option in the context menu in the protein sequence tab.

Ensured that export menu items are disabled when no file is open.

Scaffold PTM 3.1.0 Release Notes (2017-06-02)

Scaffold PTM Features

Update to Java 1.8.

Added coverage view for multiple samples in proteins view.

Added visual improvements to protein sequence panel.

Switch from using the Wilcoxon Sign-Rank Test to the Mann-Whitney U Test to compute p-values in the Quantitation Table.

Introduce a new normalization of log-ratios at each modsite based on the reference sample(s).

Add ability to view just Ratio in addition to Log2 Ratio in PTM Quantitation Table.

Add the ability to export data from the volcano plot and scatterplot in the Quantify View.

Reorganizing and add options to Preferences Dialog.

Add selector to PTM Spectrum Counts Table to specifiy viewing of Modified Count or Modified Count / Total.

Display an informative message instead of a blank panel when data aren't available for the Ascore/Spectrum tabs in the Proteins View.

Scaffold PTM Bug Fixes

Fixed issue where a query could have too many variables and cause SQL error.

Improved performance when querying data for the Spectrum Count Table in the Quantify View.

Fix a bug in Spectrum Counting that occurred if multiple MS Samples had the same name.

Fix a bug which would cause some peptides to not appear in the Proteins View.

Improved performance and optimized queries to avoid out-of-memory errors with large files.

Link to Scaffold PTM FAQ in the new Help Center through the Help menu.

Fix an error that could occur when removing columns that were sorted on in the Modlist View.

Fix a bug which would cause only modified peptides to appear in the Peptide Table in the Proteins View.

Increase precision of computation of localization probabilities to avoid problems with rounding in extremities of distributions.

Skip spectra with new peak data in Ascore calculation instead of throwing an error.

Fix bug that would sometimes lead to a DomainStoppedException.

Fix inconsistent behavior in when automatic motif search would be run during loading.

Fix a bug which would cause 'Copy EMF' to fail for charts.

Scaffold PTM 3.0.0 Release Notes (2015-11-13)

Scaffold PTM Features

Support precursor intensity quantitation when ratios are exported from Scaffold Q+/Q+S.

Support annotation of proteins with GO terms.

Added the ability to select which modifications should be displayed.

Added a report that exports only the visible modifications and proteins.

Added a column for each sample in the Site Quantitation table indicating a p-value to assess the significance of the fold-change.

Added a Volcano Plot.

Added the ability to hide columns through the right-click context menu.

Implemented a Publish View providing information about the data loaded and the analyses performed.

Added the ability to select a subset of peptides to be used as the foreground in Motif Analysis, as well as the option to use the remaining peptides as the background.

Linked protein selection and highlighting in quantitative charts, PTM List View and Protein View.

Added the ability to move to the correct Modification Site in the Proteins View upon double-clicking in the Motifs or Quantitative View.

Added a tooltip to the Proteins View to indicate the existence of any peptides with unknown positions in the protein sequence.

Changed format of reports from Tab-delimited to CSV files.

Improved the SQL custom export dialog.

Implemented time-based keys based which allow upgrades only with a valid support contract.

Added notification of available upgrades.

Allow launch of a second instance of Scaffold PTM in Viewer mode.

Standardized the installation directories used by Scaffold PTM for configuration and licensing information to be consistent with other Proteome Software products.

Added the ability to specify the memory allocation setting during installation.

Bundled the JRE with the installer for Mac OS X systems.

Updated and renamed the demo files.

Changed the default experiment name.

Scaffold PTM Bug Fixes

Improved GUI responsiveness.

Corrected highlighting of peaks in ETD spectra.

Fixed an error that caused intermittent failure in starting Scaffold PTM.

Retain View selection when color preferences are modified.

Retain column order in Quantify View when changing summarization level.

Correctly highlight the selected protein when moving between Views.

Corrected the behavior of the Next Tab menu option in the Proteins View.

Refresh the Motif list upon "undo" and "redo" operations.

Ensured that the Help dialog opens in front of the current window when Help is selected from the Add Motif dialog.

Removed the "Add File" button from the PTM Viewer.

Ensured that the program terminates properly under Windows 8.

Scaffold PTM 2.2.0 Release Notes (2015-07-09)

Scaffold PTM Features

Tables style upgrade - All tables in Scaffold PTM are now improved for usability and customization.

All tables have column control buttons to conveniently show or hide columns.

Columns can be easily moved around by simply dragging them to the desired location.

Columns can be sorted in three different ways.

Hierarchical headings now have clear borders.

Rows can be group selected.

Organize View enhancements:

  • Multiple samples loaded in the organize view can now be group selected then checked or unchecked using the right click menu option Deselect # samples.

PTM List View enhancements:

  • Added a star column to the PTM table with 4 different types of selectable stars.
  • Added star filters.
  • Added global search functionality for protein names and accession numbers.
  • Columns in the PTM table only refer to modifications present in loaded samples.
  • Proteins and protein groups are formatted in red characters when they do not have proper peptide localization.

Proteins View enhancements:

  • Find function in the Proteins View now scans along the proteins sequence.
  • Copy protein sequence with Upper and Lower cases to distinguish location of identified peptide sequences.
  • Added WMF/EMF image exports.

Motifs View enhancements:

  • Added column with proteins name to Sequences table.
  • Entries in the Citation column of the Motif table are now click-able links that open the current browser to the indicated web page.

Help menu enhancements:

  • Upgraded About Scaffold PTM.
  • Added Show Log Files command.
  • Added Upgrade License Key.
  • Added Scaffold PTM FAQ/Resource Center command.


  • Implemented Windows Code signing.
  • From a viewer it is now possible to upgrade to a licensed version.

Scaffold PTM Bug Fixes

Improved header rendering in PTM List view.

The version of Scaffold that produced the loaded MZID is now recorded in the SPTM file in the table "AnalysisSoftware".

Improved Find command functionality

Un-checking of MS samples in Organize view now being reflected in other views.

Adjusting MS samples names in Organize view now is reflected in Proteins view.

Fixed errors in loading MZIDs created by Mascot.

Fixed anomalous behavior when loading QuantML exported from Scaffold Q+S.

Fixed various bugs related to exporting or copying images.

Scaffold PTM 2.1.3 Release Notes (2013-10-10)

Scaffold PTM Bug Fixes

Increased the maximum character string lengths for peptide sequence, peptide reference, modification ID and protein name.

Corrected an error in correlating related peptides across samples loaded from different mzIdentML 1.1.0 files.

Corrected a problem in parsing accession numbers containing spaces.

Scaffold PTM 2.1.2 Release Notes (2013-07-11)

Scaffold PTM Bug Fixes

Read the Spectrum ID from the Spectrum Title field for mzIdentML 1.1.0 format to give meaningful spectrum names.

Distinguish modifications with similar masses on the same residue.

Scaffold 4.0.6 is required for MZID compatibility in Scaffold PTM 2.1.2.

Scaffold PTM 2.1.1 Release Notes (2013-03-08)

Scaffold PTM Bug Fixes

Released Scaffold PTM version 2.1.1 for compatibility with Scaffold 4.0.

Updated Scaffold PTM to correctly read mzIdentML files generated by Scaffold 4.

Corrected a null pointer error encountered when changing to the Motif View.

Corrected an error in linking counts for the same protein from different mzIdentML files.

Scaffold PTM 2.1.0 Release Notes (2012-12-07)

Scaffold PTM Bug Fixes

Corrected protein grouping between files when loading PEAKS or Mascot mzIdentML files. Files produced by different programs should not be mixed because each program groups proteins differently and combining the different formats may result in incorrect grouping or loss of data.

Corrected an error in matching peptides when loading Mascot MZID files.

Correctly annotate ETD spectra.

Better align spectrum annotation between Scaffold and Scaffold PTM.

Label all modifications in iTRAQ spectra.

Correctly display N-terminal modifications.

Changed names of display options in PTM List view.

Look for MGF files with the same name as the MZID file in the same directory before prompting for file locations.

Corrected a bug in saving files.

Fixed the Current View export from the PTM Quantitation tab.

Update the top view box when a different spectrum is selected, even if there is no topview to display.

Update the PTM Sites table when a new protein is selected even if the protein has no PTM sites.

Adjusted size of Menu buttons in Linux.

No longer include the unused unimod.xml file in installer.

Scaffold PTM Features

Support loading of mzIdentML 1.1.0 as well as 1.0.0.

Added an export which reports the proteins and their associated motifs.

Implement the Print and Print Preview functions.

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

Display a warning when loading Mascot generated mzIdentML files exported without "Bold Red" option.

Display message when no PTM data is available for a protein because the protein sequence is missing.

Provide information during loading about number of proteins missing sequences.

Scaffold PTM 2.0.0 Release Notes (2012-05-18)

Scaffold PTM Bug Fixes

Corrected behavior when unable to find a missing MGF file.

Corrected an error that sometimes caused double counting of spectra when loading multiple files.

Unchecking a sample in the Organize View now removes the sample in all views.

Changed behavior when a file is deleted. Now deletes MS Samples, spectra, scores, etc. but not proteins, in order to prevent deletion of shared proteins.

Scaffold PTM Features

Added a Quantify View, moved the PTM Spectrum Counts table to this view, and added a new tab, PTM Quantitation, which displays when iTRAQ, TMT or SILAC data is loaded into Scaffold PTM. This tab displays the log2 ratios as calculated in Scaffold Q+ or Scaffold Q+S.

Added a Motif View, which allows the user to scan the data for over-represented patterns in the amino acid sequences surrounding modification sites, and by comparing the frequency of these patterns to background levels, to calculate a score indicating the likelihood that the pattern is meaningful. If the motif has been previously identified with a specific enzyme in a publication, the enzyme name and citation are provided.

The sequence logo of each identified motif is provided, allowing the user to visually inspect for additional motifs. Patterns may be added to the Motif pane and will be automatically scored and annotated.

Motif Background tab added to the Edit > Preferences screen to allow selection of the data set to be used for frequency comparisons.

Added a Minimum Localization Score filter.

Added a Summary Level dropdown, which allows data in the Quantify View to be summarized at either the MS Sample, Biosample or Category level.

Added a Find function, available through the Edit menu or by right-clicking in any table. Find does a string search, and can be used to locate a specific protein, modification, sequence or other string in any view.

Support ETD data.

Support loading of mzIdentML files exported from PEAKS 6.

Provide an interface to allow export of custom tables through SQL.

Scaffold PTM 1.1.0 Release Notes (2011-04-29)

Scaffold PTM Bug Fixes

Improved performance in loading files.

Corrected an inconsistency in displayed Ascores.

Corrected display errors associated with data sorting.

Added the MS-Sample name to the PTM Sites Table.

Scaffold PTM Features

For mzIdentML files exported from Scaffold versions 3.00.09 or later, the biological sample and category names specified in Scaffold will be retained.

User may select colors for display of PTMs.

Added paste button for installing license key. Also enabled pasting by right-click of mouse.

This allows selection of different colors for the same type of modification but on different amino acids.

Scaffold PTM 1.0.2 Release Notes (2011-03-01)

Scaffold PTM Bug fixes

The java heap space allocation has been modified in the installer for 32-bit Windows.

Files exported directly from Mascot with semi-enzymatic searches now load successfully.

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