v2.0.0-dev

Development release of version 2.0.0 for public testing

• Code is fully migrated to .NET 8, thus, Mono dependency is obsolete
• Added an action for automatic building and testing on all code changes
• Added an action to produce self-contained and framework-based binaries for all major platforms on release
• Parquet format is updated to version 0.2
• Charge state array can be included in mzML and MGF output
• Precursor ion intensity in MGF output
• Support for precursor ion and neutral/loss gain scans
• Cleaner error messaging and improved error handling
• Introduce the latest instrument CV terms (PSI-MS 4.1.204)

v1.4.5

• Fixing CV annotations in PROXI format

v1.4.4

• Speedup the processing of files when only some MS levels are written to the output (closes #176)
• Handling of raw files missing the supplementary activation flag (closes #175)
• Using CVTerm "Orbitap" instead of "FTICR" for Orbitrap-based instruments (closes #177)
• Unification of command line arguments (#179)
• Fixing metadata output for files missing MS part (partial #178)
• Minor fixes to mzML output and cleaning unused code

v1.4.3

• Update Thermo .NET assemblies to 5.0.0.93
• Added support for Thermo Astral
• Added support for PRM files without MS1 (shout-out to @lazear, fixes #163 #164)
• Fix for negative values in isolation window (fixes #162)
• Complete support for raw files without MS data (only for MzML and metadata output) (shout-out to @wolfgangcolsman, fixes #157)
• Added expected runtime to metadata output (shout-out to @wolfgangcolsman, fixes #166)

v1.4.2

• Proper handling of precursors in decision tree methods from tribrids
• Output file extension always follows the file format and (if employed) gzip compression
• Support for input files provided as symlinks
• Support for single file output for xic subcommand
• Allowing optional field comment in XIC input json file
• Thermo .NET assemblies were updated to version 5.0.0.88

v1.4.1

• Files with missing trailer information can be processed
• Using dedicated CV term for mzML output
• Support for all possible MS levels in MGF output
• Proper processing of empty RAW files
• Fixed a bug in handling isolation offset in mzML output
• Refining OS exit codes reporting and "warning as error" key
• More logging levels
• Exit codes and logging work in the same way for subcommands

v1.4.0

• Precursor intensity was added to mzML files
• Support for all possible MS levels
• -x switch has reversed its meaning
• Plain mzML (non-indexed) is forced when using -s and mzML format
• Updated Ontology terms for ionization methods (HUPO PSI-MS version 4.1.79)
• Switch to include noise and baseline data (-N)
• Spectral points are sorted by mass
• Metadata, format, and logging switches recognize both numeric and string values of parameters

(See release notes for details)

v1.3.4

comment fix

v1.3.3

• removed BOM prefix in indexed mzML output
• addition of MS:1000576 (no compression) CV term when no compression is used
• Same metadata output for both TEXT and JSON formats
• FAIMS compensation voltage output
• Thermo libraries upgrade to 5.0.0.71

v1.3.2

• Flag -x include reference and exception peaks
• SPS masses are included as precursors in mzML
• Ignore all not .raw files when processing folder
• Updates in instrument and detector mapping to PSI-MS CV terms