0.0.304

• Upon selecting certain proteases in the calibration/GPTMD/search tasks, a popup appears which recommends settings and asks if they should be applied
• The classic search is a bit faster and more memory-efficient
• Modern search is now considerably faster for open-mass searches
• The crosslink search is faster and more accurate
• Fixed several bugs in the command-line version of MetaMorpheus for Linux/OSX (file paths were not passed in properly, making the program difficult to run)
• Fixed a bug in low-resolution CID/HCD searches that caused high memory usage

0.0.303

• The Percolator output has been updated to include more features to train on. This set of features is identical to the set of features that MetaMorpheus's machine-learning PEP calculation trains on
• You can now edit the default settings for MetaMorpheus's tasks. To save a task as default, create a new task, edit the settings you want, and then click the "Save As Default" button. You can access saved default .tomls by going to Data -> Open folder with mods/data files -> DefaultParameters. Be aware that updates to MetaMorpheus may add new settings; these new settings will not exist in old default .toml files. Any new setting that is not specified in a .toml will take the default value for that setting

0.0.302

• MetaMorpheus has a new icon!
• A machine-learning algorithm similar to Percolator is used to estimate PSM-level error probabilities (the posterior error probability, "PEP"). This replaces the e-value calculation
• MSFileReader is no longer needed to read Thermo .raw files. Just drag your files in and accept the Thermo licence! Reading .raw files is faster now too
• Added protein ambiguity to the crosslink search
• In the crosslink search, if a single peptide outscores the alpha peptide, the single peptide is preferred. This helps correctly assign spectra with loop-linked missed cleavages
• Added many UniMod accession numbers to MetaMorpheus's modifications, which are reported in the .mzID file
• Fixed a bug where the nativeID for each PSM in the .mzID file was not correctly formatted
• Fixed a bug where sometimes parsimony was very slow when many PTM-containing peptides were present and "Treat modified peptides as different peptides" was unchecked
• Fixed a bug where the text boxes to search for a modification in the GUI would stop working

0.0.301

• The Search task settings have been grouped into "basic" and "advanced" settings
• SILAC quantification has been added!
• Custom amino acids are now supported. Go to "Data -> Create new amino acid". Protein databases containing the specified letter will be read as the defined custom amino acid
• G-PTM-D now does not annotate a mod in the database if an existing UniProt mod with the same mass already exists on that residue
• Crosslinkers are now stored in a file so that custom crosslinkers can be stored without needing to re-make them every time
• Proteins removed by the "top-picked" FDR method are now re-added with a conservative estimate of their FDR
• Additional peak-filtering options have been added to the advanced settings menu in the Search task
• Fixed a bug in the "PSM Count (unambiguous, <0.01 q-value)" output column
• Fixed a few bugs in the fast Non-Specific search mode
• Fixed a crash if a spectra file has no MS2 scans

0.0.300

• Fixed a somewhat rare bug where proteins with ">" in the protein name had truncated names when read from a .fasta database. This also caused a crash in modern search. This bug was present in v0.0.298/299
• Fixed a bug where the peptides listed in AllPeptides.psmtsv did not have the correct value under "PSM Count". The header for this column has been changed/clarified to "PSM Count (unambiguous, <0.01 q-value)"

0.0.299

• Fixed a crash in MetaDraw's PDF exporting function
• Fixed a somewhat rare crash when some scans in some files do not have a well-defined precursor ion

0.0.298

• MS3 and mixed-mode MS2 (e.g., HCD/ETD) searches are possible in the crosslink search now. This is a preliminary implementation, and these extra scans are not used for scoring yet, but you can search them and then view them with MetaDraw
• Added some MetaDraw features (font size, bold font, etc.). MetaDraw also has a more minimalistic look
• The warning for not having C++ redistributable installed is shown immediately on startup now instead of when adding a .raw file
• Fixed a bug where peptide-level q-values were not calculated if "write decoys" was unchecked in the search task
• Fixed a bug in naming protein isoforms

0.0.297

• Low-resolution HCD/CID data is now searchable with better results, using XCorr instead of the Morpheus score. To use it, change dissociation type to "LowCID"
• Fixed a crash in calibration if modifications without chemical formulas were used
• Fixed crashes related to different regions formatting decimal numbers differently
• Fixed a match-between-runs crash

0.0.296

• Peptide-level q-values are re-calculated instead of using the PSM's q-value
• MetaDraw can now export PDFs
• A custom dissociation type has been re-added (select your own ion types to search for)
• Each PSM now includes how many PSMs of that same peptide sequence were observed <0.01 q-value (i.e., a spectral count)
• Fixed a bug in the Percolator-formatted output in the XL search (the sequences did not include modifications properly)

0.0.295

• MetaDraw can annotate XL search results (no base sequence annotation yet)
• Matching-between-runs (quantification) is more accurate and much more RAM-efficient
• Fixed a bug in reporting XL search progress