Update CHANGELOG.md

CHANGELOG.md

@@ -4,28 +4,28 @@ All notable changes to this project are documented in this file.
 
 ## 4.1 - 2024-05-29
 - Require Java 11+
-- Calculate and report more modification-related scores for the open and mass-offset searches
+- DDA+ mode supports ddaPASEF data
+- Significantly faster loading of Thermo raw files
+- Calculate and report more modification-related scores for PSMs identified in open and mass-offset search workflows (especially useful for chemoproteomics workflows). The following columns added to PSM.tsv files: 
  - `ptm_mass`: mass of the modification
  - `localization_peptide`: a peptide string with lowercase amino acids to indicate the sites with the best score
  - `best_positions`: a list of sites with the best score in the format `<amino acid 1><site index 1>:<amino acid 1><site index 1>:...`. For example `T(4)I(5)`.
  - `number_best_positions`: number of the sites with the best score
- - `score_all_unshifted`: the score when matching only unmodified fragments
- - `score_best_position`: the score when putting the modification on the best site
+ - `score_all_unshifted`: the score when matching only unshifted fragments (unshifted fragment is a fragment not containing any modification mass)
+ - `score_best_position`: the score when putting the modification on the best (i.e. higest scoring) site
  - `score_second_best_position`: the score when putting the modification on the second best site
- - `score_shifted_all_positions`: the score when putting the modification on all sites and matching only the modified fragments
+ - `score_shifted_all_positions`: the score computed based on all possible shifted fragments (useful for identifying PSMs labeled with probes that can bind to multiple sites on the peptide, such as in some PAL data)
  - `position_scores`: a string with peptide sequence and scores when putting the modification on the specific site. For example `P(2.32)E(2.41)P(2.57)T(5.36)I(5.36)D(3.87)E(2.56)K(1.34)`.
- - `ions_all_unshifted`: the number of matched fragments when matching only unmodified fragments
+ - `ions_all_unshifted`: the number of matched fragments when matching only unshifted (unmodified) fragments
  - `ions_best_position`: the number of matched fragments when putting the modification on the best site
  - `ions_second_best_position`: the number of matched fragments when putting the modification on the second best site
- - `ions_shifted_all_positions`: the number of matched fragments when putting the modification on all sites and matching the modified fragments
- - `score_shifted_best_position`: the score when putting the modification on the best site and matching only the modified fragments
- - `ions_shifted_best_position`: the number of fragments when putting the modification on the best site and matching only the modified fragments
- - `shifted_only_position_scores`: similar to `position_scores` but only matching modified fragments
- - `shifted_only_position_ions`: similar to `shifted_only_position_scores` but showing the number of matched fragments
-- DDA+ mode supports ddaPASEF data
+ - `ions_shifted_all_positions`: the number of matched fragments when putting the modification on all sites and matching all possible shifted (modification-containing) fragments
+ - `score_shifted_best_position`: the score when putting the modification on the best site and matching only the shifted fragments
+ - `ions_shifted_best_position`: the number of fragments when putting the modification on the best site and matching only the shifted fragments
+ - `shifted_only_position_scores`: similar to `position_scores` but only matching shifted fragments
+ - `shifted_only_position_ions`: similar to `shifted_only_position_scores` but showing the number of matched shifted fragments
 - Add `analyzer_types` parameter
 - Add a new mass calibration and parameter optimization mode, 4, for calibrating the mass and adjusting only the fragment mass tolerance
-- Significantly improved the Thermo raw file loading speed
 - Propagate instrument info to calibrated and uncalibrated mzML files
 - Various bug fixes and improvements