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Changelog

Last change: 20-JUL-2022, MTS

0.4.7

  • Updated multiple packages & documentation
  • Print traceback when there is an error running AlphaPept
  • Updated modifications.tsv, Button to reload modifications via GUI
  • Changed slider input widget to a number input
  • Fixed links in GUI when downloading FASTA
  • Fixed GUI Errors #460
  • Fixed bug when launching file watcher
  • Option to use relative file paths for the size check @hugokitano
  • New functionality to filter fragments by local rank. This should improve performance for noisy datasets.
  • Cleaned up print output/deprecation & performance warnings
  • Macbook crash fix by @swillems in #465
  • FEAT: create headless option by @swillems in #464 #449
  • Develop by @straussmaximilian in #478

0.4.6

  • Link to Renku @cmdoret
  • Optimized quantification (proper integration of signal on MS1 level), now uses apex of isotope envelope
  • Caching of dataframes for matching @mschwoer
  • Minor code reorganization
  • Bugfixes in interface @hugokitano
  • Initial estimates for delayed normalization
  • Bugfix for Threadripper Systems #434, #264
  • Updated docs
  • More flexibility for custom modifications

0.4.5

  • Revision of how fractions are handled
  • LFQ Acceleration @hugokitano
  • Update of various packages

0.4.4

  • New maximum iterations for LFQ
  • Auto-adjustment of settings for non-specific search

0.4.3

  • LFQ Fix @hugokitano

0.4.2

  • Better logging for LFQ
  • Correct setting of cores when searching w/o saving database
  • Fixed Docs

0.4.1

  • Fixed a bug in LFQ

0.4.0

This version contains a lot of variable renaming to be more consistent with other Alpha*-packages. This will probably lead to incompatibility with previous history modes.

  • Optimized recalibration to be more memory efficient
  • Fixed a bug where peptide_fdr was not accurately saved. This should affect reported protein / peptide ids.
  • Included additional export of identifications, e.g. the best sequence for each recorded MS2-spectrum
  • Usability improvements when starting AlphaPept multiple times
  • Revised History Mode

0.3.33

  • Versionbump for requirements

0.3.32

  • Bugfixes for fragment calibration
  • Bugfixes for matching
  • Bugfix for duplicate hills in Thermo #386
  • Bugfix calling LFQ on MaxQuant files w/o calling delayed normalization

0.3.30

  • Improved fragment calibration, this increases performance
  • Support for fractionated data (Note the performance is not yet satisfactory)
  • Basic scaffold for TMT quantification
  • Community contributions by @mgleeming (Coverage Map) and @romanzenka (Typo)
  • Multiple small bugs and improvements

0.3.29

  • Stability improvements
  • support of running multiple mzML-files #316
  • Auto-refresh of Status page #203
  • Moved custom plots to home directory

0.3.28

  • Automatic fragment tolerance estimation for better support of MS2=Iontrap Thermo runs #305
  • Updated error message handling
  • consistent renaming of o_mass to prec_offset
  • Fixed a bug in how fragments_int_ratio is calculated in first_search
  • Enabled handling of mzML-files in GUI / Core
  • Improved Documentation
  • Ion export for search parallel
  • Moved loss_dict to constants.