Scaffold 3.0.04 release notes

 

Bug fixes

-No longer saves condensed files as frozen.
-Will now properly use the downloaded GOA database. Users must redownload the database for changes to take effect.
-Will now load SEQUEST data without a specified enzyme.
-Can now merge condensed files.
-Can rename sqlite database on Linux machines.
-No longer shows the same spectra twice when loading data from multiple search engines.
-Will now allow user to filter on a searched modification even if that modification is absent from the data.
-Can now load certain X tandem files that would not load previously.
-Properly updates sequence coverage when applying a database after data loaded.
-T test P-values are now correct.
-PPM values consistent between Scaffold and its Excel reports.

 

New features

-Can now filter on negative OMSSA values.

Scaffold 3.0.03 release notes

 

Bug Fixes

-Fixed a bug where Scaffold would suddenly exit

-Fixed multiple errors in converting Scaffold 2 files to Scaffold 3 files

-Fixed an error in Scaffold's Venn diagram where it was reporting the wrong values

-Fixed an error where files were unable to be merged

-Fixed a problem were Scaffold would assign modifications to the N terminus even if they were actually present on a different amino acid

-Fixed problems with Scaffold saving sqlite files on Linux machines

-Scaffold Q+ samples report now includes sample names

-Fixed an bug where condensing IdentityE data would throw a nullpointer errors

-All modification are now seen on the publish page

-Opening older sfd files that contain quantitative tests now works

New Features

-Enabled scientific notation for IdentityE users

-Differentiation between decoy database FDRs and probability based FDRs

-Mac users are now able to select multiple files simultaneously

Scaffold 3.0.02 release notes

 

Scaffold bug fixes

-Fixed a bug in Scaffold's delta ppm calculations

Scaffold 3.0.01 release notes

 

Scaffold bug fixes/features

-Fixed a bug where Scaffold was not reading MSF file delta cN values properly.
-Fixed a bug where Scaffold was throwing an NPE on Spectrum Export.
-Fixed a bug where Scaffold was mis-reading modifications if the peptide had already been modified.
-Added updated help to Scaffold 3.

 

Scaffold 3.0.0 release notes - Major Release Notes

 

Scaffold 2.6.01 release notes

 

Scaffold Bug fixes

-Fixed a bug where deltaCN values where miscalculated when read from Discoverer MSF files.

-Fixed a bug where Scaffold was dropping some spectral information from Discoverer MSF files.

-If accession numbers or descriptions are corrupt Scaffold will now display a warning to notify the user that their data is corrupt.

-Fixed a bug in the Mascot parser that was mis-reading modifications and then feeding them to X! Tandem. Scaffold now properly reads in Mascot modifications and feeds them to X tandem.

-Fixed a bug where Scaffold was improperly assigning peptides that differed in one "I" versus "L" assignment. This bug fix also corrected numerous grouping errors associated with peptide selection.

-Fixed a bug where Scaffold was not remembering when the automated peptide checkbox setter was used after a file was closed. Formerly Scaffold was reverting the changes back to 50%, but now Scaffold keeps the setting that the user selected.

-Fixed a bug where Scaffold had been incorrectly picking the second peptide in closely related OMSSA search results.

 

Scaffold 2.6.00 release notes

 

Scaffold Features:
-Condensing data is now switched on by default. Condensing improves the speed and memory consumption of Scaffold without changing any scoring.
-New option to toggle the sample wide normalization for spectrum counting statistical tests.
-Sample Export of "Quantitative Value"s will now contain two significant digits past the decimal point for more accurate post-processing calculations.
-New option in custom peptide filters to filter on both search engine scores and prophet probabilities simultaneously.

 

Additional Scaffold Q+ Features:
-Spectrum Report now exports additional columns containing raw intensity values.
-New Quantitative Settings options for both "Minimum Dynamic Range" and "Minimum Intensity", which extend and replace the original "Minimum Value" setting.
-New graphical charts in Quantitative Settings showing dynamic range and intensity values across experiments.
-New reporter ion bar graph in Spectrum Pane showing raw and normalized intensity values for each spectrum.

 

Scaffold Bug Fixes:
-Fixed Discoverer .MSF reader error reading new Discover version 1.0.43.2 (and later) files.
-Fixed Discoverer .MSF reader error identifying variable modifications in certain files.
-Fixed rare Statistics View error when viewing Spectrum Mill results.
-Fixed database exporter for reverse/random concatenated databases where the last reversed/random protein was left off.
-Standardized saving of Scaffold analysis options from session to session.
-Fixed error when downloading GOA databases on Linux computers.
-Fixed error when using GOA databases in ScaffoldBatch.
-Fixed error exporting "Total Number of Spectra" column in Excel reports with "Condensing" option turned on.
-Fixed error calculating Number of Enzymatic Termini (NTT) in Proteins View.

 

Additional Scaffold Q+ Bug Fixes:
-Fixed error labeling reporter ions in data sets with high mass accuracy daughter ions.
-Fixed error displaying Proteins View in certain poor quality data sets.

 

Scaffold 2.5.00 release notes

 

Bug Fixes:

* Fixed a bug where Scaffold Q+ was unable to unlock via e-mail.

* Fixed a bug where Phenylalanine was interfering with iTRAQ reporter ion 121.

* Fixed a minor error were Scaffold would not recognize number formats from international locations (1,000.00 versus    1.000,00).

* Scaffold's spectrum counting report now correctly reports the unweighted spectral count.

* ScaffoldBatch can now turn NCBI annotations off.

* Fixed a bug where Scaffold Q+ was mislabeling TMT modifications.

New Features:

* Warning introduced when data searched against multiple databases is loaded into Scaffold.

* Scaffold can now import Thermo Scientific's Discoverer *.msf file format (xscore)

* Scaffold cannot yet load ETD data searched with Z-core algorithm in Discoverer.

Other:

* Earlier versions of Scaffold may not be able to open files created in Scaffold 2.5. Please update to the latest release of Scaffold.

 

Scaffold 2.2.1 release notes

 

Scaffold 2.2.1 fixes an issue where indexing GOA database on 64 bit
windows and mac machines was very slow.  This is the only change in this
version and users on 32 bit machines need not upgrade.  (1714)

 

Scaffold: 2.2.0 release notes

 

* Scaffold now supports loading protein annotations from the Gene Ontology Annotations (GOA) database. In addition to retrieving annotations from the NCBI, Scaffold can now annotate against a local database that is more extensive (particularly for the UniProt database) and includes information about the provenance of the annotation (for example, whether it was made by a human or a computer program). Scaffold also now allows you to choose exactly which GO terms are displayed.
(1593-1595 and others)

* Re-written "Queue files from Mascot Server" feature allows filtering and sorting, and improves performance and reliability. (1577)

* ScaffoldBatch 2.2 supports platform independent paths in scafml (batch
driver) files. In other words:

<Scaffold pathsep="/">
<!-- ... -->
<InputFile>../foo/bar/baz.dat</InputFile>
<!-- ... -->
</Scaffold>

should work on Windows. (1473)

* A bug where Scaffold could, in some rare cases, loose protein isoforms has been fixed. In order to restore these isoforms, Scaffold will automatically re-perform protein grouping on file open. (1691)

* Improved collation of spectra across multiple search engines, especially for non-mudpit searches. (1588)

* A bug where certain Mascot files could cause Scaffold to erroneously register very large numbers of modifications has been fixed. (1616)

* Scaffold now attempts to recover data files after a crash. (1673)

* Fixed a bug where Scaffold 2.x incorrectly detected ETD/ECD data in Mascot files. (1692)

* Performance improvements made to looking up proteins in large FASTA databases. (1693)

* Restored output of modified amino acids in spectrum report. (1615)

* Updated the set of gene ontology terms that Scaffold uses. (1634)

* Fixed a problem with Spectrum Mill modifications. (1644)

* Added "End of File" to all Scaffold exports. (1664)

* Converting version 1.x files is now faster. (1395)

Scaffold 2.1.2 release notes

 

- Uncheck visible checkbox in Scaffold's Samples view now correctly unchecks one protein, not two.

- SRF file parent error tolerance is now properly read by Scaffold.

- Percent coverage display in Scaffold's Samples view now works.

- Reset peptide validation option has been replaced after being removed. It is located under the "Experiment" option on

the task bar.

 

Version 2.1.1

 

-File merging now works.

-Thinning no longer lowers protein probabilities.

-Venn Diagram numbers now correctly represent the number of protein identifications.

-Correctly read error tolerance from *.srf files.

-Fixed bug in View drop down menu so that Show lower scoring matches filter works
-Canceling a Scaffold analysis during the collation step will no longer cause errors in the resulting Scaffold file.
-When loading mascot data from the server, we now save the data in the SFD file until it has been analyzed.
-Various fixes for Spectrum Mill (collation, load times, etc.

 

Version 2.1.0

 

Protein probability updated
Adding NCBI annotations now turns on Save option
Wait icon in Samples view now gives correction indication of busy system
In Edit > Preferences > Processors, Scaffold is now able to choose the number of
available processors.
Condense Data On Load capability is now operational
Collation now operational
Load from Directory with Unicode/MCBS now functional
Relative paths in scafml now functional
Updated Converter
ProtXML now exports correct calc_neutral_pep_mass for peptides.

 

Version 2.0.5

 

-Mascot file loading no longer stops if a single file has an error -- unless that is the only file we are loading.
-Able to unlock scaffold via E-Mail.
-Changed command line arguments to deal with garbage collection better.
-Eliminated spurious Out of Memory errors.
-Fixed C and N term modifications are applied only to the end termini and not throughout the peptide for SEQUEST files.
C and N termini are given as deltas for SEQUEST.
-SEQUEST out files now have lines ignored they are not parse-able.
-Improved error handling of broken files. We now skip only the files that we can not parse rather then halting on a bad file.
-We now properly parse the decoy_peptide section of the Mascot file and add in the reverse hits under different protein names.
-Properly identify variable modifications in Mascot data.
-SRF Files now have their accession numbers parsed correctly.
-Tar files for SEQUEST now have all their content read.
-Memory is now able to be set at 4x the physical memory in cases where Java doesn't see all the memory.
-Load cache objects sooner, this increases performance and helps with batch processing.

 

Version 2.0.3

 

-Fixed bug where SEQUEST files in tar.gz format would not be read properly.
-Fixed bug in Scaffold reader where some scientific notation could cause the parser to crash.
-Fixed bug in Mascot reader where new contentTypes could in certain cases confuse the parser.
-Fixed bug with multiple Amino Acid issue in SEQUEST parser.
-Fixed bug where converted files would lose the name of their database.
-Fixed bug where database parsing was broken. Could not load valid databases, only invalid databases.

 

Version 2.0.2

 

-General: added new 64 bit linux JRE for proper 64 bit execution.
-General: fixed execution bug when running batch mode.
-Fixed null pointer error when rendering with Statistics progress bars.
-Fixed bug with Quantitation pane where the linear regression divides by zero.
-Fixed reported errors with FASTA parsing.
-Changed "Thinning" text to "Condensing."
-Fixed bug when passing average fragment mass information to X! Tandem.
-Fixed bug locking Scaffold to computer.
-Fixed bug with extracting modifications due to Mascot parsing order rearrangement.