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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[2.9.2] - 2024-06-03

Updated

  • baseline_correction() function:
    • Fixed an issue where the Random=False part was yielding an error.

[2.9.1] - 2024-03-08

Updated

  • filter_PSMs() and filter_peptides() functions:
    • Changed the order of filtering; removal of any TMT channels with at least one NA value is now performed at the end.

[2.9.0] - 2024-03-06

Updated

  • filter_PSMs() and filter_peptides() functions with several enhancements:
    • Updates in filter_PSMs:
      • Removed filtering for TMT channels with at least one NA value.
      • Other filtering criteria remain unchanged.
    • Updates in filter_peptides:
      • Removed filtering for TMT channels with at least one NA value.

[2.8.5] - 2024-02-06

Added

  • PSMs_to_Peptide() function:
    • Separates the functionality from baseline_correction for merging PSMs into peptides using specified columns.
    • Auto-detects 'Theo. MH+ [Da]' column using regular expressions even if the name does not fully match.

[2.8.4] - 2024-01-18

Updated

  • The script now supports PSMs and Peptide file processing for both MS2 and MS3 measurements across both PD_input and plain_text_input classes.
  • filter_peptides() function now specifically works for peptide files.
  • Added filter_PSMs() function for PSM files, removing isolation interference > 50%.
  • Updated extract_heavy() and extract_light() functions to support a broader range of labels.
  • Major updates to baseline_correction() function:
    • New usage parameters and functionality adjustments.
    • Improved baseline correction process and integration with PSM and Peptides file identification.

[2.7.0] - 2023-12-05

Updated

  • filter_peptides() function:
    • Enhanced to remove sum of intensities equal to 0.
    • Now converts NaN values to 0 for cleaner data handling.