alphapept

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As written in the changelog for some 0.4.x versions, some changes in namings are included:

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.

For backward compatibility, I am sharing some changes which might help also others:

• Sample names are not ending on .ms_data.hdf anymore. This suffix seems removed.
• In the peptide table, these columns seem to be changed:
  • 'mobility_calib' -> "mobility" (or removed?)
  • 'int_sum' -> "ms1_int_sum"
  • 'naked_sequence' -> 'sequence_naked'
  • 'int_sum_dn' -> 'ms1_int_sum_dn'
  • removed trailing space in "prec_offset_raw ", "prec_offset_raw_ppm "

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To the alphapept developers: could we include these (for me as a user) breaking changes in the future in the changelog? This can be supported by the community, of course 💪😊

Hi, thanks for reporting. This is indeed unfortunate, and we can try to be transparent about this in the changelog. The current aim is to freeze the variable names once we reach 1.0.0.

Thanks! Since alphapept is an pre-alpha version, these kinds of changes are totally expected 👍

Just for the documentation: column names of the peptide table seem to have changed in AlphaPept 0.4.6:

• Removed "ms1_int_sum_dn"
• Changed "ms1_int_sum" to "ms1_int_sum_apex"

Note that "_dn" will always be added when there is delayed normalization.

Closing this, for now; feel free to comment in case there is more in the future.