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@trishorts trishorts released this 08 Sep 15:24
· 67 commits to master since this release
1.0.3
7dfe22b
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What's Changed

New UniProt

  • Fixed bug that arose when downloading protein databases from the current version of UniProt

Visualization Update

  • "Show Decoy" and "Display Internal Ions" settings are now recorded when MetaDrawSettings are saved
  • Sequence Coverage will no longer display internal ions if "Display Internal Ions" is not checked
  • Eliminated xaml binding error in MetaDrawSettingsWindow
  • Fixed glyco child scan display where child fragment ions were not being displayed properly

Spectral recovery

  • Renamed the "MBR Analysis" option in Quantification to "Spectral Recovery" to avoid confusion. This change affects the Search Task window as well as function names/namespace. Addresses issue #2268

Glyco write individual file results

  • Glyco search now writes individual result files for each file searched.

Updated MzLib from 1.0.538 -> 1.0.541

mzLib 1.0.539

  • There was a bug wherein adding two chemical formulas with negative isotopes gave the wrong answer. The example was deamidation (H-1N-1O) plus deamidation. The expected answer is H-2N-2O2 but the original gave O2. Added by @trishorts in #697
  • Averaging Updates by @nbollis in #683
  • MsDataFile is now an abstract type defining methods to read data from files, both statically and dynamically.
  • Previously supported data types (.raw, .mzml. .mgf) are still supported with previous syntax, but can also now be constructed with the unified syntax below:

mzLib 1.0.541

  • Rectifies a significant slowdown caused by Readers refactor #698
  • Fixed chemical formula bug
  • Update to uniprot ptmlist.txt loader
  • Fixed xml.gz compression bug so we load complete xml
  • Added support for FlashDecon and TopFD file parsing
  • Improved ability of FlashLFQ to handle unusual characters in file input
  • Added support for negative deconvolution

Added additional support for TMT

  • Reporter ions for multiplex tags now have their own columns in AllPSMs and AllPeptides .psmtsv files.

Filtering refactor

  • Users are now able to specify PEP or PEP Q-Value thresholds that are used to filter results before quantification, spectral library generation, and output.
  • Protein parsimony is not affected. Filtering for parsimony is still hard-coded in PostSearchAnalysisTask.ProteinAnalysis.

Added null checks to enable display of XL results

  • Previously, attempting to view crosslink search results in MetaDraw would cause a crash.

Eliminate PEP from FDR analysis during calibration

Write spectrum library from PsmTsv in MetaDraw

  • MetaDraw now includes a button that allows users to export selected PSMs as a spectral library
  • Added a new method to PsmFromTsv called ToLibrarySpectrum() that produces the library spectrum objectI copied the pdf/png export code in MetaDraw
  • The output was tested both in metadraw and in search. The written libraries load into metadraw and produce spectral angles in search.

Database download Test

  • Expanded test coverage

Changed the main MetaMorpheus window to own Task windows

  • New task windows will always appear on top of the main window when first launched.

Ethcd complementary ions

  • Enabled the generation of complimentary ions with the EThcD activation type.

Fix string split in glyco protein parsimony

  • Some protein accessions contain hyphens. Previously, this caused a crash during the glyco search task. This release replaces the hyphen with the hashtag eliminating the crash.

Averaging code added but not implemented

  • Added code for the Spectral Averaging Task to refine the isotopic envelopes of top-down data prior to a database search.
  • Currently, Averaging can't be performed by users due to multiple known issues
  • Known Issue: On some devices, the averaging task window will crash upon launch when MetaMorpheus is installed via the .msi installer
  • Known Issue: On some devices, averaging task will begin and crash half way through

Full List of PRs

New uniprot by @Jevs242 in
#2264

Glyco write individual file results by @trishorts in
#2252

Visualization Update Rebase by @nbollis and @trishorts in
#2266

Spectral recovery by @Alexander-Sol in
#2269

Update to MzLib 1.0.539 by @nbollis and @Alexander-Sol in
#2276

Added additionally support for tmt labeling by @Alexander-Sol and @nbollis in
#2278

Averaging task in MetaMorpheus by @nbollis, @avcarr and @elaboy in
#2281

Filtering refactor by @Alexander-Sol in
#2285

Added null checks to enable display of XL results by @Alexander-Sol in
#2290

Eliminate PEP from FDR analysis during calibration by @trishorts in
#2294

Write spectrum library from PsmTsv in MetaDraw by @trishorts in
#2295

Database download Test by @elaboy in
#2282

Changed the main window to own the subsequent windows by @nbollis in
#2297

Ethcd complementary ions by @trishorts in
#2274

Updated to MzLib 1.0.541 and updated one unit test by @nbollis in
#2304

Fix string split in glyco protein parsimony by @trishorts in
#2305

Full Changelog: 1.0.2...1.0.4

Note The version number for this release and the GitHub tag are both 1.0.3, but this release is actually tagged 1.0.4. This will be fixed in the next release

Contributors

avcarr, trishorts, and 4 other contributors
Assets 4
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