From aec54a17e33c4f97ab813b8162fd34d47e83cd0a Mon Sep 17 00:00:00 2001 From: Fengchao Date: Sat, 16 Dec 2023 17:48:11 -0500 Subject: [PATCH] Update the 4.0 changelog according to Alexey's modifications. --- CHANGELOG.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 21b997e..6b60dd5 100644 --- a/CHANGELOG.md +++ b/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