Scaffold
Scaffold
5.0.0

0.0

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Scaffold free download for Mac

Scaffold for Mac5.0.0

19 March 2021

MS/MS proteomics experiments visualization.

What is Scaffold for Mac

Scaffold helps you visualize and validate complex MS/MS proteomics experiments

  • Compare samples to identify biological relevance
  • Identify regulated isoforms and protein PTMs
  • Drill down into spectrum details and counts
  • Identify proteins intuitively and confidently
  • Create comprehensive lists of target proteins
  • Classify proteins by molecular function or organelle
  • Harness high through-put batch processing

What's new in Scaffold

Version 5.0.0: Added:
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

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App requirements: 
  • Intel 64
  • Mac OS X 10.7.3 or later
License: 
PaidOne-Time Purchase

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