MetaMorpheus v1.0.7
We are excited to announce the latest release of MetaMorpheus! This update includes numerous improvements, bug fixes, and feature enhancements to improve performance, usability, and accuracy. Below are the key changes in this release:
New Features
- Added Isodec as a new Deconvolution algorithm #2442
Calibration
- Alter the process for calibration. An initial search is performed using wide ppm tolerance. The distribution of ppm errors for precursor and fragments are determined and used moving forward. Calibration is performed and if the number of identifications increases, it is attempted for a second time. The final distribution of mass errors is determined and used to create a file specific toml. The tolerance written to that file now has a limited number of decimal places, to eliminate small variations in those numbers, which can complicate analysis reproduction.
G-PTM-D
- GPTMD has been promiscuous in the addition of potential modifications to the xml database. This PR reduces the number of candidate modifications added to those that produce the highest score for each possible PTM localization. Thread safety of GPTMD was also addressed.
False Discovery Rate
- The best PSM/PrSM used to represent a peptide/proteoform is now selected based on PEP, as opposed to MetaMorpheus score. This affects the AllPeptides.psmtsv result file #2431
- When training a model to compute PEPs for top-down search results, we are more permissive in what we accept as a positive training example. This change reduces overfitting #2427
- This PR changes the threshold used for using the more stringent and correct q-value calculation (D+1)/T to a total of 1000 PSMs. Below that level we use D/T. This will help with top-down files that contain fewer PTMs. #2426
Output Enhancement
- PEP now reports the number of positive and negative training examples used to train the model #2424
- Additional optional Search Task output to see all modified forms of each peptide/protein that was searched #2460
Quality of Life Improvements
- Ensured consistency in all task window text boxes for integer and double type inputs #2417 #2433
- Task windows now launch significantly faster #2461
- Re-fragmentation analysis in MetaDraw now allows a custom ppm tolerance for fragment matching #2420
- Added several hotkeys into the GUI #2470
Maintenance - Code only changes, user not impacted
- Update README.md with .Net8 links #2416
- Removed unused variables, improved access modifiers, marked relevant properties as readonly, and added many new terms to the solution dictionary #2421
- Improved performance when filtering which PSMs/Peptides that are written out #2430
- Eliminate NUnit legacy code #2438
- Switched AnalyteType (e.g. peptide vs proteoform) from string to enum to ensure consistency in naming conventions #2434
- Created an MVVM structure for deconvolution parameters in the GUI to enable seamless addition of new deconvolution engines #2429
- SpectralMatch.MatchingFragmentIons property is set differently in ResolveAllAmbiguities(). This change is intended to improve stability of calibration #2465
- Updated MzLib to version 1.0.559 #2451 #2456 #2457 #2464 #2441
Bug Fixes
- Non-specific search engine has a bug where a second modification is attempted to be added to a peptide with set mods where there is an existing modification at that position. This PR adds a check that prevents addition of the second mod. #2453
- MetaDraw no longer uses fallback options when an outdated config file is found, it instead creates a new config file and salvages as much of the old file as it can #2420
- Eliminated crash in MetaDraw that occurred when switching from chimeric scan view to fragmentation scan view on an ambiguously identified peptide #2420
Bug Fixes – Race Conditions
- Fixed race conditions and crashes that could occur due to improper use of locks. Changes affect
For a complete list of changes, please refer to the full changelog: [Full Changelog](1.0.6...1.0.7)
Thank you for using MetaMorpheus! We appreciate all feedback and contributions from our community.