1.0.6

MetaMorpheus v1.0.6 - Changes to FDR calculation

Update to .NET 8

• Updated from .NET 6 --> 8. .NET 8 install required in order to run MetaMorpheus v1.0.6. Download available here.

Overhauled PEP, Q-Value, and PEP Q-Value calculations

• Adjusted Q-value calculations to represent a true positive false discovery rate calculation. The overall number of results at Q <= 0.01 will differ for this release
• The ML classifier used for calculating PEP and PEP Q-Values was overhauled to eliminate contamination issues that could lead to anti-conservative estimates of FDR.
• New features for top-down data were added to the PEP model
• In Results.txt and AllResults.txt, text formatting has been changed

Visualization

• Can now match all fragment types to an experimental spectrum and visualize matched fragments in MetaDraw
• Can now export cross-link spectrum match plots

Bug Fixes and QOL

• Spectra file loading time has been reduced
• Search progress bar no longer scrolls infinitely after a spectral library search
• Spectral Libraries can now be used as databases from Command Line
• Added a significant amount of comments to Glyco Proteomics code

What's Changed

• Hydroxy proline diagnostic ion error by @trishorts in #2325
• Invert qvalue calculation by @trishorts in #2327
• Eliminate delta score option by @trishorts in #2338
• Add leucine to chymotrypsin cleavage motifs by @trishorts in #2336
• N-glyco search improvements by @trishorts in #2322
• Update Mzlib to 1.0.547 (Omics Update) by @nbollis in #2334
• Pass dissociation type not autodetect to diss type collection by @trishorts in #2343
• Added console output before and after uniprot tests by @Alexander-Sol in #2342
• Add XLMS paper to citations by @acesnik in #2345
• use mzlib LibrarySpectrum class by @trishorts in #2349
• Update .NET version in readme by @acesnik in #2350
• Deconvolution Generalization by @nbollis in #2339
• Shared pep box by @Alexander-Sol in #2354
• Glyco spectrum library search updates by @trishorts in #2351
• Spectral Match Generalization by @nbollis in #2340
• Eliminate PsmCount from PEP calculation by @trishorts in #2347
• Invert q-value by @trishorts in #2355
• Update to MzLib 1.0.549 by @nbollis in #2369
• Spectral Averaging Command Line by @nbollis in #2370
• Cross Link Spectrum Match Plot Export Bug Fix by @nbollis in #2371
• Stop scrolling of progress bar after calculating spectral angle by @nbollis in #2372
• Added precursor intensity to PSM, peptide proteoform output file by @zhuoxinshi in #2365
• Pep on peptides first by @trishorts in #2373
• MetaDraw Fragmentation Reanalysis by @nbollis in #2361
• Added some tooltips for the cross link search task view. by @avcarr2 in #2378
• Asynchronous file loading for search task by @nbollis in #2381
• Meta Draw Quality of Life Updates by @nbollis in #2379
• Spectral Library from Command Line by @nbollis in #2386
• Added new features to Top-Down PEP by @nbollis in #2377
• Kdn adding and diagnostic filtering by @RayMSMS in #2383
• Increased QValue cutoff for calibrating PSMs to 0.01 by @Alexander-Sol in #2392
• Changes to PEP Calculation and Filtering by @Alexander-Sol in #2387
• Net eight by @trishorts in #2391
• Updated to mzLib 1.0.550 by @Alexander-Sol in #2395
• Result Text and Individual File Result Cleanup by @nbollis in #2397
• Add the comment on glyco-searching and the search summary on the result file by @RayMSMS in #2367
• Github Actions 1: Cross Platform Build by @nbollis in #2398
• Polishing prose by @acesnik in #2403
• update mzlib nuget package to 551 by @trishorts in #2404
• Reworking PEP to prevent cross-contamination by @Alexander-Sol in #2394
• Explanation of the FdrCategory Enum in the Engine Layer which has always baffled me. by @trishorts in #2402
• Updated PEP to use set seed (42) by @Alexander-Sol in #2408

New Contributors

• @zhuoxinshi made their first contribution in #2365
• @avcarr2 made their first contribution in #2378
• @RayMSMS made their first contribution in #2383

Full Changelog: 1.0.5...1.0.6