v0.5.1

Change Log for v0.5.1

General

• Moved from setup.py to pyproject.toml
• Updated package to the current glycowork version (~=1.50)
• Updated dependencies for Python 3.12 / numpy 2 compatibility

Model

• Switched to monosaccharide vector input instead of precursor mass for better specificity
• Enhanced compositional model with improved prediction accuracy
• Updated model weights and reference glycans

Prediction

• Added CandyCrumbs scoring for improved glycan annotation quality
• Optimized batch inference and results consolidation
• Added better support for uncertainty in glycan structure predictions
• Added ppm cutoff for better mass error handling
• Added CSV import/export capabilities for MS spectral data

Analysis

• Improved support for positive mode fragmentation
• Upgraded charge state handling for more flexible analysis
• Added support for glycoproteomics MS2 annotation

Tests

• Expanded test suite with multiple experimental setups in test cases

v0.4.1

Change Log

general

updated package to the current glycowork version (~=1.30)

analysis

• Added further sulphation fragment support to Neu5Ac, Neu5Gc, HexNAc, and HexA
• Added HCO3 adduct fragment support

v0.4.0

Change Log

general

• updated package to the current glycowork version (~=1.20)

analysis

• Generalised monosaccharide mass retrieval
• Added '02X', '02A' dHex cross ring fragments
• Added phosphorylated fragments
• Added '02A', '24X' HexNAc cross ring fragments
• Added '15X', '24X', '25X', '02A', '04A', '14A', '15A', '24A' sialic acid cross ring fragments
• Added '04X', '24X', '35X', '15A', '03A' Hex cross ring fragments

v0.3.0

Change Log

general

• updated package to the current glycowork version (~=1.1.0)

analysis

• Added '03X', '15X', and '24X' cross ring fragments

cli

• Added candycrunch_predict and command line functionality

prediction

• Added glytoucan_map to harmonize predicted glycans and display GlyTouCan IDs in outputs
• Added to generation of possible structures by generalising Neu5Ac/Neu5Gc sequence substitutions
• Added to generation of possible structures by generalising GlcNAc/GlcNAc6S sequence substitutions
• Added Neu5Ac isomer deduplication based on Neu5Gc isomers
• Added user defined RT cutoffs rt_min, rt_max, rt_diff to narrow downs spectra of interest
• Added functionality to filter out duplicates based on RT
• Added plot_glycans_excel support for output excel spreadsheets
• Added wrap_inference_batch to run inference on multiple inputs at once and group structures across files

model

• Updated model checkpoint

v0.2.2

• updated package to the current glycowork version (1.0.1)
• added required dependencies

v0.2.1

• fixed indentation in process_mzML_stack

v0.2.0

• refactored spectral grouping and averaging
• general code refactoring for readability and efficiency
• filter out very low and very high RT spectra if possible
• added some ancillary functionality, such as combining relative abundances across multiple charge states
• some preparations for eventually accepting glycowork v0.9, including supporting more adducts etc.

v0.1.3

• updated model weights (better performance)
• agglomerative clustering for RT grouping
• generalized handling of tag masses in wrap_inference
• calculate ppm error

v0.1.2

• updated package to the current glycowork version (0.8.1)
• updated model checkpoint with internal (better) model

v0.1.1

• made torch compatibility more flexible