alphapept - Release v0.5.0

Summary:

Major

File reading changed to AlphaRaw

• This allows SciEx support. FF is not yet optimized for SciEX yet
• Adjusted memory limits for raw conversion, raw conversion for Bruker is now faster
• Bruker legacy files are supported with the one-click installer but not for the Python version anymore. Install python-lzf or install with the legacy requirements,
• Working docker files

Minor

• Option to change the top_n peptides
• Option to select the initial score for ML scoring
• Fixed a bug in peptide generation that would not consider the last AA
• Added a new protease protease_dict["trypsin/p"] = "[KR]"
• Small UI improvements

Performance:

• Overall, Bruker runs should be 25% faster. We will expect further speed increases once the FF is exchanged
• IDs dropped ~5%, but FDR estimates are well below 1% now

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.4.9...v0.5.0

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Published by github-actions[bot] almost 3 years ago

alphapept - Release v0.4.9

What's Changed

• Upgraded to NBDEV 2.0
• More documentation
• Better display of AlphaPept version number

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.4.8...v0.4.9

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Published by github-actions[bot] about 3 years ago

alphapept - Release v0.4.8

What's Changed

• Multiple small optimizations
• Plot for precursor calibration, general optimization of the calibration
• New generic score to replace the x_tandem
• Memory optimizations
• Changed the default prectol to 20, defaultmass_tol to 50
• #488: fix error when scoring on machines with more than 60 cpus by @mschwoer in https://github.com/MannLabs/alphapept/pull/489

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.4.7...v0.4.8

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Published by github-actions[bot] over 3 years ago

alphapept - Release v0.4.7

What's Changed

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 https://github.com/MannLabs/alphapept/pull/465
• FEAT: create headless option by @swillems in https://github.com/MannLabs/alphapept/pull/464 #449
• Develop by @straussmaximilian in https://github.com/MannLabs/alphapept/pull/478

New Contributors

• @k-Vartika made their first contribution in https://github.com/MannLabs/alphapept/pull/450
• @elena-krismer made their first contribution in https://github.com/MannLabs/alphapept/pull/454

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.4.6...v0.4.7

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Published by github-actions[bot] over 3 years ago

alphapept - Release v0.4.6

What's Changed

• Link to Renku @cmdoret https://github.com/MannLabs/alphapept/pull/433
• Optimized quantification (proper integration of signal on MS1 level), now uses apex of isotope envelope
• Caching of data frames for matching @mschwoer https://github.com/MannLabs/alphapept/pull/438
• 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, see constants-tab in GUI

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.4.5...v0.4.6

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Published by github-actions[bot] over 3 years ago

alphapept - Release v0.4.5

What's Changed

Revision of how fractions are handled

• This should improve performance on fractionated samples #424 #389
• Scoring was adapted. For fractionated samples each raw file is scored individually.
• In the GUI there are now two additional columns: Sample_group and Fraction: All files with the same Sample_group will be quanted together. Fraction is meant to be enumerated for fractionated samples and is used for the delayed normalization step.

Acceleration

• @hugokitano made their first contribution in https://github.com/MannLabs/alphapept/pull/412
• This is a speedup for the delayed normalization. Thanks!

Misc

• The version performance is updated and shows results from version 4.
• Automated test now include fractionated samples and matching.
• Pip installation on Windows should be more robust (fixed tables dependency)

Package Updates

Several Python packages have been updated:

• Bump addressable from 2.7.0 to 2.8.0 in /docs by @dependabot in https://github.com/MannLabs/alphapept/pull/269
• Bump matplotlib from 3.3.3 to 3.5.1 by @dependabot in https://github.com/MannLabs/alphapept/pull/376
• Bump scikit-learn from 0.24.2 to 1.0.2 by @dependabot in https://github.com/MannLabs/alphapept/pull/380
• Bump h5py from 3.4.0 to 3.6.0 by @dependabot in https://github.com/MannLabs/alphapept/pull/384
• Bump pyinstaller from 4.2 to 4.10 by @dependabot in https://github.com/MannLabs/alphapept/pull/415
• Bump pyteomics from 4.4.2 to 4.5.3 by @dependabot in https://github.com/MannLabs/alphapept/pull/416
• Bump pandas from 1.3.4 to 1.4.2 by @dependabot in https://github.com/MannLabs/alphapept/pull/411
• Bump sqlalchemy from 1.4.23 to 1.4.35 by @dependabot in https://github.com/MannLabs/alphapept/pull/413
• Bump streamlit-aggrid from 0.2.2.post4 to 0.2.3.post2 by @dependabot in https://github.com/MannLabs/alphapept/pull/417
• Bump pyyaml from 5.4.1 to 6.0 by @dependabot in https://github.com/MannLabs/alphapept/pull/418
• Bump tqdm from 4.56.0 to 4.64.0 by @dependabot in https://github.com/MannLabs/alphapept/pull/419
• Bump scipy from 1.7.1 to 1.8.0 by @dependabot in https://github.com/MannLabs/alphapept/pull/421
• Bump networkx from 2.6.3 to 2.8 by @dependabot in https://github.com/MannLabs/alphapept/pull/422
• Bump pyinstaller from 4.10 to 5.0 by @dependabot in https://github.com/MannLabs/alphapept/pull/420

Full Changelog: https://github.com/MannLabs/alphapept/compare/0.4.4...v0.4.5

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Published by github-actions[bot] almost 4 years ago

alphapept - Release 0.4.4

This summary includes the changes from the previous .4.xx:

0.4.4

• New maximum iterations for LFQ: This should avoid the "not converged"-messages when doing LFQ
• Auto-adjustment of settings for non-specific search: This should avoid memory errors when using non-specific as protease

0.4.3 * Bugfix for LFQ

0.4.2

FEAT: Better logging for LFQ. This will now log if a solver does not converge. FIX: Correct setting of cores when searching w/o saving database. DOCUMENT: Updated DOCS

0.4.1

FIX: Fixed a bug in LFQ that made LFQ take very long. 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

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Published by github-actions[bot] almost 4 years ago

alphapept - Release v0.4.2

This also includes the changes from the previous .4.xx:

0.4.2

• FEAT: Better logging for LFQ. This will now log if a solver does not converge.
• FIX: Correct setting of cores when searching w/o saving database.
• DOCUMENT: Updated DOCS

0.4.1

• FIX: Fixed a bug in LFQ that made LFQ take very long.

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

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Published by github-actions[bot] almost 4 years ago

alphapept - Release v0.4.1

Description will follow shortly

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Published by github-actions[bot] almost 4 years ago

alphapept - Release v0.4.0

Description and Update will follow shortly

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Published by github-actions[bot] almost 4 years ago

alphapept - Release v0.3.33

What's Changed

Bugs

• Fixed a bug that lead to duplicate hills for Thermo #386
• Fixed a bug where the number of processes being used was not set correctly
• Fixed a bug in the Align step where progress was not reported correctly
• Fixed a bug where Match-between-Runs wouldn't work
• Fixed a bug when the number of found ions was smaller than needed for fragment calibration

GitHub

• Reorganization of GitHub Actions so that they run sequentially and not in parallel when testing environments

User notes:

For large number of files when you don't use MBR deactivate the align step as this could take a very long time.

Full Changelog: https://github.com/MannLabs/alphapept/compare/v0.3.31...v0.3.33

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Published by github-actions[bot] about 4 years ago

alphapept - Release v0.3.31

• Improved fragment calibration. AlphaPept will now save a figure with the fragment calibration for each raw file. Results for files with bad fragment calibration should be drastically improved. Example Plot below.
• Reorganization of requirements
• Fix #374
• Scaffold for TMT support
• Scaffold for Fractions: Note that fractions are still experimental, and results are not as good as we want them to be. We expect to have a very conservative FDR.

New Contributors: Thanks to @romanzenka for fixing a Typo.

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Published by github-actions[bot] about 4 years ago

alphapept - Release v0.3.29

• Stability improvements
• support of running multiple mzML-files #316
• Auto-refresh of Status page #203
• Moved custom plots to home directory
• Coverage map added by mgleeming #320

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Published by github-actions[bot] over 4 years ago

alphapept - Release v0.3.28

• 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 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.

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Published by github-actions[bot] over 4 years ago

alphapept - Release 0.3.26

0.3.26

General

• Included changelog to track what changed and what not

Stability

• Reduced memory usage for search by capping to top 5 search results #249
• CMD interface is now wrapped in a try and except statement to better track error messages #251
• Included SSL libraries #251

GUI

• Refresh folder button for new experiment #240

Features

Documentation

• added more documentation to XXfileformats notebook

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Published by github-actions[bot] over 4 years ago

alphapept - Release 0.3.25

Major changes

• TBA

Installation Notes

If you have a previous AlphaPept installation, please deinstall. If possible, also remove files in the AlphaPept user folder (on Windows C:\Users\Username\.alphapept\

Windows 7

When testing on a Windows 7 machine, AlphaPept would not start (flashing terminal and close). When launching AlphaPept.exe via the command line, the following error message could be retrieved: ImportError: DLL load failed while importing _ssl: The specified module could not be found. A fix was to install OpenSSL. When installing, one was additionally asked to install some Visual Studio components. After installation, a test run did run through successfully.

Windows 10

There is a known bug for outdated Windows 10 versions that don't have KB4598291. In this case, AlphaPept will not start. Updating Windows should solve the problem (see: https://tinyurl.com/y3dm3h86)

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Published by github-actions[bot] over 4 years ago

alphapept - Release 0.3.23-dev0

Major changes

• Start page
• Revised calibration
• Applying protein_fdr on all files
• Option to change the plots via a settings file

Installation Notes

If you have a previous AlphaPept installation, please deinstall. If possible, also remove files in the AlphaPept user folder (on Windows C:\Users\Username\.alphapept\

Windows 7

When testing on a Windows 7 machine, AlphaPept would not start (flashing terminal and close). When launching AlphaPept.exe via the command line, the following error message could be retrieved: ImportError: DLL load failed while importing _ssl: The specified module could not be found. A fix was to install OpenSSL. When installing, one was additionally asked to install some Visual Studio components. After installation, a test run did run through successfully.

Windows 10

There is a known bug for outdated Windows 10 versions that don't have KB4598291. In this case, AlphaPept will not start. Updating Windows should solve the problem (see: https://tinyurl.com/y3dm3h86)

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Published by github-actions[bot] over 4 years ago

alphapept - Release 0.3.22-dev0

• FASTA Download
• Terminate Processes
• Some basic plots (protein numbers, ions, protein rank)
• default settings changed (mtol, offset to 30 ppm, acetylation of protein)
• changed user path to .alphapept

Known Bugs: There is a known bug for outdated Windows versions which don't have KB4598291. In this case, alphapept will not start. Updating Windows should solve the problem (see: https://tinyurl.com/y3dm3h86)

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Published by github-actions[bot] almost 5 years ago

alphapept - Release 0.3.20-dev0

Streamlit Release

Known Bugs: There is a known bug for outdated Windows versions which don't have KB4598291. In this case, alphapept will not start. Updating Windows should solve the problem (see: https://tinyurl.com/y3dm3h86)

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Published by github-actions[bot] almost 5 years ago

alphapept - Release 0.3.13-dev0

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Published by github-actions[bot] almost 5 years ago

alphapept - Release 0.3.11-dev0

0.3.11-dev0

• pyinstaller tests running
• systems check indicate quantification is working
• thermo FF is not memory optimized

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Published by github-actions[bot] about 5 years ago

alphapept - Release 0.3.9-dev0

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Published by github-actions[bot] about 5 years ago

alphapept - Release 0.3.6-dev0

This is the 0.3.6. Release that should enable the Windows Installation and GUI.

Known Bugs: * The progress bar might not be very accurate. For runs with single files, the first steps will be much slower than the last ones as they will be skipped (e.g., LFQ / matching) * Feature Finding is slower in GUI than in CMD (some 30%) * Fasta paths are shown in the GUI although to be set in the Experiment tab * recalibration_min option present in search allthough not used * feature finding option present also for not-broker files

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Published by github-actions[bot] about 5 years ago