Scaffold for Mac5.0.0

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