0.0.316

Release Notes:

• Bug fix: Increased the size limit of calibrated files.
• Docker Update: MetaMorpheus docker releases are now compatible with Nextflow.

0.0.315

Release Notes:

• Fixed a bug where the experimental design was not utilized if normalization was not enabled.
• Fixed a bug where the Calibration Task did not alter the file paths in the Experimental Design file.
• Protein quant included via FlashLFQ was updated to follow the median polish approach.
• Protein quantification intensities for fractionated data are now summarized into Biorep-level intensities.
• ExperimentalDesign.tsv file is copied to output folder in the Search task.
• Enable copy and pasting of labels into Experimental Design Window
• Feature enabling the Calibration task to write indexed .mzML files (with a checkbox option to write non-indexed files) was added.

0.0.313

• In the command-line version, a directory containing spectra files can be specified for use instead of listing all spectra files separately.
• Cross-validation was incorporated for PEP calculation. All identifications are broken down into four groups and four models are generated. For each model, three groups are used for training and one for testing. The process is repeated until all identifications are scored by a separately trained model, and the quality metrics from each of the four models are averaged to provide a single value.
• Fixed a bug where files with periods in the name could not be loaded by MetaDraw.
• Fixed a bug where text in the output directory field of the GUI could not be deleted.
• Fixed a bug where extraneous messages warning about duplicate modifications were displayed upon MetaMorpheus startup.

0.0.312

• Fixed an issue where the Docker image could not be run properly in Singularity
• Added a new optional command-line flag, --mmsettings, which can be used to specify a directory to read/write MetaMorpheus settings from/to. This enables the use of MetaMorpheus in readonly filesystems
• Fixed crashes related to different regions formatting decimal numbers differently

0.0.311

Bugfixes/new additions for the GUI:

• Can select multiple DB/spectra files and delete them
• Delete key on the keyboard will delete tasks
• Plus or minus keys will move tasks up or down
• Double-clicking a file or task will open it
• If all spectra files are deleted, the output file path is cleared
• Can right click -> Delete All for spectra, protein DBs, tasks
• Can right click -> Move task up or Move task down
• Clicking the "Select" button in MetaDraw (to add a spectra file or results file) will correctly display .mgf and .tsv as options
• Fixed a crash loading XL Task results in MetaDraw
• Increased the font size of the tasks in the Run tab from 11 to 13
• Added ability to resize the DB/spectra/tasks areas in the Run tab
• Added "Use" checkboxes back to the GUI for protein DBs and spectra

0.0.310

• Reverted a change in 0.0.309, in which the calibration task wrote indexed .mzML files. This was causing OutOfMemoryException crashes with some spectra files

0.0.309

• MetaMorpheus has a new, redesigned GUI!
• MetaDraw can now open multiple spectra files at once
• Fixed a bug where if MetaMorpheus settings were opened and a program was not associated with the .toml file format, the settings .toml would not open. This file will now open with Notepad
• Replaced the default contaminants database with a new one that correctly shows protein accessions, etc. in the output
• The calibration task now writes indexed .mzML files (these files will open more quickly in MetaDraw)
• Lactylation has been added as a modification, under the "Less Common" category
• Moved the "Score Cutoff" setting in the search task from the "Scoring Options" area to "Output Options"

0.0.308

• The command-line version of MetaMorpheus now has verbosity options and returns non-zero exit codes when a MetaMorpheus run fails
• The machine-learning PEP algorithm now only trains on decoys as false positives, instead of decoys and low-scoring targets
• Moved the glycan databases to [MetaMorpheus App Data]\Glycan_Mods instead of [MetaMorpheus App Data]\Data\Glycan_Mods for the installed Windows version of MetaMorpheus
• Fixed a bug where the .mzID file was not written for searches with only one spectra file
• Fixed a rare crash that occurred when a non-existent protease was used in the file-specific settings
• The glyco search now correctly writes .psmtsv file format instead of .tsv for its glycopeptide search results, and these files correctly appear in the GUI when written
• The glyco search can now be run in the command-line version of MetaMorpheus

0.0.307

• Fixed a bug where the autoupdater in versions 0.0.305 and 0.0.306 was not functional. If you're running those versions of MetaMorpheus and you want to use the autoupdater, you may need to download the latest version and update manually instead

0.0.306

• Added a beta version of a glycopeptide search task
• New MetaMorpheus releases are automatically uploaded to Docker Hub
• Added q-value filtering to mzID output
• Added options in the search task for how to label contaminants and targets with the same accession
• Fixed a crash in the GPTMD task when searching low-resolution CID data
• Fixed a bug where selecting "Yes and don't ask me again" when being asked if MetaMorpheus should be closed did not save the preference to not ask again