Update the 4.0 changelog according to Alexey's modifications.

CHANGELOG.md

@@ -3,15 +3,14 @@
 All notable changes to this project are documented in this file.
 
 ## 4.0 - 2023-12-XX
-- Add `DDA+` data type: `data_type=3`. It significantly boosts the number of IDs compared to the DDA data type.
-- Add support for the detailed mass-offset search. Mass-offsets can have their own modified sites, neutral losses, and diagnostic ions.
-- Overhaul the mass calibration and parameter optimization for DIA data type
+- Implement new MSFragger-DDA+ mode, triggered when DDA data is annotated as `DDA+` (MSFragger parameter `data_type=3`). MSFragger will perform full isolation window search, identifying multiple co-fragmented peptides from chimeric DDA spectra. This mode significantly boosts the number of IDs compared to conventional DDA search.
+- Implement detailed mass-offset search mode. Each specified mass offset can have their own modification sites, neutral losses, and diagnostic ions.
+- Overhaul the mass calibration and parameter optimization procedure for DIA data
 - Significantly improve the ddaPASEF .d loading speed
 - In the pin file, write all proteins in one column
 - Extract and print isolation window sizes when checking the LC-MS files
-- Add peptide length `< 8`, `8`, `[9, 30]`, and `> 30` Boolean scores to pin files
+- Replace ‘peptide_length’ score with Boolean peptide length scores (length `< 8`, `8`, `[9, 30]`, and `> 30`) in pin files
 - Remove `log10_kl_negative_1` and `log10_kl_negative_2` from the DDA pin file
-- Remove `peptide_length` score from pin files
 - Remove `add_topN_complementary` option
 - Various bug fixes and improvements