MannLabs / alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.

https://mannlabs.github.io/alphapept/

Apache License 2.0

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Develop 0.5.0 #548

Closed straussmaximilian closed 1 year ago

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straussmaximilian commented 1 year ago

Summary (for release notes later):

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