Alphapept Versions Save

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

• 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.

• 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

• 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.

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 XX_file_formats notebook

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)

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)

• 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)

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)