tima 2.13.0

Breaking changes

  • sanitize_spectra(): cutoff parameter now defaults to NULL (dynamic) instead of 0
  • annotate_spectra() / create_edges_spectra(): the misspelled qutoff parameter is deprecated; use cutoff instead
  • install() is deprecated in favor of install_tima()
  • validate_install_inputs() no longer accepts a test parameter
  • show_system_messages() no longer accepts a test parameter
  • R.utils moved from Imports to Suggests

New features

  • Added full mzTab-M support across import, preparation, and export:

    • read_mztab() imports mzTab-M into TIMA feature/spectra/metadata files
    • prepare_annotations_mztab() maps mzTab structural annotations to TIMA schema
    • write_mztab() exports TIMA weighted annotations to mzTab-M (including merge mode)

  • Added mzTab-M validation hardening with schema-backed required columns and strict SME checks

  • annotate_spectra() now reports forward and reverse dot product scores (candidate_score_similarity_forward, candidate_score_similarity_reverse) alongside the main similarity score. Forward considers only query peaks (normalized by all query and matched library intensities); reverse considers only library peaks (normalized by matched query and all library intensities). Both are computed in C for consistency with the GNPS scoring engine.

  • Added support for additional NPClassifier and ClassyFire taxonomy caches in prepare_libraries_sop_merged(), allowing structures missing taxonomy in the merged libraries to be enriched from external cache files. Caches grow over time as library entries are written back.

  • Added a new validation helper, see https://taxonomicallyinformedannotation.github.io/tima/vignettes/articles/0-validating.html

  • Added BiGG as SOP library

  • Added basic isotopologues handling

  • Added external identifiers to the final results (#142)

  • Added NORMAN SUSPECT LIST DATA in silico spectral libraries

  • Added multiple new sub-libraries and a new tag column

  • Added mzmine annotation support

  • Added Sirius spectral results support

  • Added special “Biota” superdomain handling for shared core metabolism

  • annotate_masses() now enforces graph-level adduct consistency across connected edge hypotheses (removing globally impossible combinations while preserving consistent exotic states) and canonicalizes adduct states by parsed/net summed modifications so reordered loss/cluster text forms are treated as equivalent

  • Enhanced sanitize_spectra() with adaptive noise filtering:

    • Dynamic intensity thresholds (MAD-based, now default when cutoff = NULL)
    • Low noise removal targets repetitive instrumental artifacts

Internal / performance

  • Improved log and error messages
  • More in-depth molecular sanitization
  • Standardized error handling to use cli::cli_abort() in exported functions
  • Replaced nested ifelse() in format_bytes() with findInterval()
  • Fixed 1:n patterns to use seq_len() for safety
  • Updated the C implementation of the spectral similarity

Bug fixes

  • Fixed adduct annotation bug and harmonization
  • Fixed recognition of uncommon negative charges
  • Fixed split_tables_sop() collapsing numerically identical exact masses into "mass1 $ mass2" strings due to clean_collapse() treating them as different character values; now uses resolve_numeric_or_na() with floating-point tolerance
  • Removed xlogp from the structure metadata (str_met) table: xlogp is stereo-sensitive (Crippen atom-typing can differ between stereoisomers), so it is no longer collapsed by inchikey_no_stereo; the per-SMILES value computed by process_smiles() in the annotation pipeline is used instead

Documentation

  • Startup message now uses cli::cli_inform()

Data updates

  • Updated to Massbank version 2025.10
  • Updated to MSnLib v7

tima 2.12.0

Breaking changes

  • .RDS spectra are now stored more efficiently. To avoid errors, delete any .RDS files created before version 2.12.0
  • tima_full() has been deprecated in favor of run_tima()
  • Updated minimal R version to 4.4.0 (and related Bioconductor dependencies)

New features

  • Added automatic retention time conversion (in minutes)
  • Added a minimal output
  • Added a parameter to limit the numbers of neighbors used for chemical consistency calculation (#193)
  • Added MERLIN spectral libraries (#190)
  • Added optional compound name from RT libraries
  • Added RDKit-based structures processing through reticulate (#19)
  • Introduced similarity method argument (entropy and GNPS for now)

Bug fixes

  • Fixed memory crashes in case of large number of ties, limiting to 7 with note (#216)

Internal / performance

  • Externalized spectral libraries preparation to SpectRalLibRaRies
  • Implemented GNPS similarity method in C
  • Improved high confidence filtering
  • Improved logs using logger (#189)
  • Keep (only) the best molecular formula and canopus annotations from SIRIUS
  • Reduced dependencies and moved some to Suggests
  • Refactored adducts parsing to read adducts like [M+H]+/[M]+
  • Refactored MS1 annotation step to work per sample (#194)
  • Refactored tests
  • Renamed some functions/utils for consistency
  • Replaced logger with lgr for covr compatibility

Documentation

  • Switched documentation from pkgdown to altdoc

Data updates

tima 2.11.1 (unreleased)

  • Added SIRIUS feature tables support (#185)
  • Added .rar compression support for SIRIUS workspaces (#186)

tima 2.11.0

  • Added convenience function to change small parameters (#177)
  • Added demo files download to the app
  • Better packaging
  • Improved documentation
  • Fixed all CRAN warnings
  • Fixed some edge cases in spectra import
  • Reduced dependencies
  • Reduced exports
  • Removed CompoundDb dependency as it was causing too many issues
  • Removed pak install and switched to r-universe
  • Replaced internal functions by Spectra equivalents (#166)
  • Shinylive version available at https://taxonomicallyinformedannotation.github.io/tima-shinylive
  • Simplified install and vignettes
  • Switched from base::lapply to purrr::map

tima 2.10.0

  • Added alt text to vignettes
  • Added the possibility to add internal libraries through the GUI (#159)
  • Added the possibility to filter confident annotations only (#140)
  • Added number of peaks in spectrum
  • Brought back some older dependencies to be compatible with oldrel
  • Changed package name, usethis update
  • Clearer handling of SIRIUS scores (#146, #147)
  • Exposed more parameters to the GUI (#159)
  • Facilitated install, no need to clone the directory anymore
  • Finally made it to the r-universe
  • Fixed adducts and removed nitrogen rule
  • Fixed number of matched peaks
  • Improved imports
  • Reduced warnings
  • Updated benchmarking steps

tima 2.9.6

  • Added light-switch thanks to pkgdown 2.1.0.
  • Attempt to simplify installation
  • Fixed library/adducts confusion (#123)
  • Fixed some incorrect adduct differences annotations
  • Refactored adducts / neutral losses / dimers annotation to allow for more flexibility (#141, #144)

tima 2.9.5

  • Do not re-package if already the latest version
  • SIRIUS 6 default and compatible (keeping SIRIUS 5 backward compatibility)
  • Updated to Massbank version 2024.06

tima 2.9.4

  • Automated update
  • Added an option to remove ties (#134)
  • Added some details for SIRIUS, added manual workspace addition (#132)
  • Additional preprocessing (reduction) of noisy spectra
  • Dependencies update
  • Docker updates (#131)
  • Handle cases when same (feature_id, mslevel) pairs are present within an MGF (#133)
  • Improved documentation
  • New working directory at $HOME/.tima
  • Updated R and Bioconductor versions

tima 2.9.3

  • Allowed for SIRIUS jobs containing only summaries
  • Allowed for underscores in job pattern
  • Changed some default values (less stringent)
  • Dependencies update
  • Migrated app testing to shinytest2
  • Removed further some inconsistent MS1 annotations
  • Removed tests dependencies by default

tima 2.9.2

  • Added Nitrogen rule to filter out some annotations
  • Better handling of partial downloads (#118)
  • Dependencies update (mainly targets 1.5.1, will invalidate previous targets)
  • Fixed some port issues in Shiny (#122)
  • Removed completely empty columns from final output to avoid confusion (#120)

tima 2.9.1

  • Added Waystation action
  • Added structures from spectral libraries to SOP library (#113)
  • Exposed all parameters (#107, #108)
  • Fixed for Zenodo API
  • HMDB structures support
  • Optimized grep/gsub by adding perl=TRUE or fixed=TRUE
  • Updated to Massbank version 2023.11
  • Updated SIRIUS preparation (#74, #115)

tima 2.9.0

  • Added compounds names as parameter
  • Added MassBank spectral library (#77)
  • Allowed files outside data/source (#89)
  • Added RT library as annotation library (#86)
  • Better handling of download errors
  • Fixed Docker mount path
  • Improved naming (#91)
  • Internal variables refactoring
  • Multiple Shiny fixes and tests addition (#60)
  • Multiple fixes (#71, #81, #82)
  • New adducts (#79, #80)
  • Refactored adducts, clusters and neutral losses
  • Refactored biological and chemical score
  • Refactored RT matching (#76)
  • Refactored Sirius scores (#92)
  • Removed GNPS dependency by default

tima 2.8.2

  • Added spectral entropy
  • Added MS1 only possibility
  • Added Fluorine adduct
  • Changed from pbmclapply to pblapply
  • Documentation improvement
  • Fixed empty chemical classes
  • Fixed not classified taxa
  • GitHub Actions improvement
  • renv removal
  • Performance improvement by replacing the tidyverse by the fastverse (in progress)
  • Reduced warnings (CRAN and jscpd)

tima 2.8.1

tima 2.8.0

  • Added GUI prototype
  • Started using renv

tima 2.7.4

  • Clearer vocabulary
  • ECMDB support
  • Edges (mass and spectra-based) and components are generated if not present.
  • Fixed case when no GNPS job ID
  • Further Targets improvements
  • Lot of fixes
  • Parameters refactoring
  • Re-introduced Classyfire support.
  • Retention time matching additionally to MS2 if RT present in library
  • Steps refactoring

tima 2.7.3

tima 2.7.2

  • Benchmark update (including negative mode)
  • Improved parameters documentation
  • Minor fixes
  • Spectral comparison + intensity filtering update
  • Switched r-base Docker image to bioconductor with ARM support

tima 2.7.1

  • Added MONA helpers
  • Added parallelization on process_spectra
  • Added sqlite storing for spectra
  • Improved code documentation
  • Improved testing time
  • Minor fixes

tima 2.7.0

  • Added HMDB helpers for both taxo and ISDB
  • Added MS2 annotation capability (kudos @jorainer for the awesome Spectra suite)
  • Minor fixes

tima 2.6.0

  • Added Docker container
  • Changed data architecture
  • Minor fixes

tima 2.5.6

  • Dependencies removal (e.g. metabo-store)
  • Minor fixes
  • Partial functions cleanup

tima 2.5.5

  • Automation and parameters improvement
  • Minor fixes

tima 2.5.4

  • Minor fixes
  • Metadata completion improvement
  • Molecular formula and adducts formalism improvement

tima 2.5.3

  • Imports improvements
  • LOTUS update

tima 2.5.2

  • Packaging improvements

tima 2.5.1

  • Improved support for SIRIUS (with new summaries)

tima 2.5.0

  • LOTUS update
  • Minor fixes

tima 2.4.0

  • Added chemical names and xlogp to output (#33)
  • Added support for case when no consensus is found (#30)
  • Improved output (#34)
  • Minor fixes

tima 2.3.0

  • Added support for annotation without MN (#28)
  • Added support for multi tool annotations (#27)
  • Added support for classical MN GNPS jobs (#25)
  • Added support for new version of LOTUS
  • General improvements for manual inputs
  • Improved tests code coverage
  • Minor fixes
  • Updated adducts

tima 2.2.2

tima 2.2.1

  • Minor version name fixes

tima 2.2.0

  • Added benchmark (here)
  • Various fixes

tima 2.1.0

  • Fixes, deletion of binary dependencies.

tima 2.0.0

  • Initial version.