Zeng, Wen-Feng

MacOS gets different results with Windows for the same raw file.

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I used ```alphapept import``` to extract ms1 and ms2 on Windows, and then run ```alphapept workflow``` to identified the extracted ms_data. I could get extractly the same identifications comparing with...

plot_elution_profile()

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plotting.plot_elution_profile() is hard to viz for the details of each fragments when there are many ion matched. I suggest to use hovermodel="closest" instead of "x unified"

Tuning MS2 by low-quality fragment matches on all DIA PSMs at apex_rt resulted in low-quality MS2 prediction

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1. Using DIA PSMs identified by DIA search engine to refine MS2 model may result in low-quality MS2 prediction due to low-quality precursor matches; 2. Using spectral library tsv to...

FIX noqa by using register_reader(), address many side effects

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Review this PR after #171 Changes: - Remove `alphabase.io.psm_reader` as all functionalities are already in `alphabase.psm_reader` module. - register_reader() for all reader modules - register_decoy() for protein_level_decoy

Remove noqa

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- Fix noqa: modify imports of `alphabase.constants.element` to `alphabase.constants.atom`; add FutureWarning. - Fix noqa: modify imports of `alphabase.peptide.precursor.is_precursor_sorted()` to `alphabase.peptide.precursor.is_precursor_refined()`; add FutureWarning. - Fix noqa: modify imports of `alphabase.peptide.precursor.calc_precursor_mz()` to...

https://github.com/MannLabs/alphabase/blob/development/alphabase/psm_reader/sage_reader.py#L81 The modification site in alphabase (`mod_sites`) is `1

We should do the same as https://github.com/MannLabs/alphabase/pull/163.

Move peptdeep_hla back to peptdeep 1. non-specific digestion and peptdeep-hla prediction 2. deduce proteins from peptides 3. put pseudo-proteins in hla lib, and search by alphadia

As huggingface upgrades time to time, making the import very unstable. And peptdeep only requires the model code, without other dependencies such as tokenizer and others, so we should copy...