From 4bbc022270cfc634134e01c67962421f3d52909c Mon Sep 17 00:00:00 2001 From: odespard Date: Fri, 30 Aug 2024 15:30:37 +0200 Subject: [PATCH 1/2] make automatic default --- alphadia/constants/default.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alphadia/constants/default.yaml b/alphadia/constants/default.yaml index 8fba4bab..12cdbd31 100644 --- a/alphadia/constants/default.yaml +++ b/alphadia/constants/default.yaml @@ -93,9 +93,9 @@ search: # target ms2 tolerance in ppm target_ms2_tolerance: 15 # target ion mobility tolerance in 1/K_0 - target_mobility_tolerance: 0.04 + target_mobility_tolerance: 0.0 # default is to optimize automatically # target retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1 - target_rt_tolerance: 60 + target_rt_tolerance: 0.0 # default is to optimize automatically quant_window: 3 quant_all: True From 45eb17b7a5d8d26d743b6729154390c2a676320d Mon Sep 17 00:00:00 2001 From: odespard Date: Fri, 30 Aug 2024 15:33:36 +0200 Subject: [PATCH 2/2] use try_narrower_parameters for ms2 by default with maximal_decrease=0.5 --- alphadia/constants/default.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/alphadia/constants/default.yaml b/alphadia/constants/default.yaml index 12cdbd31..9ca9c6fe 100644 --- a/alphadia/constants/default.yaml +++ b/alphadia/constants/default.yaml @@ -268,8 +268,8 @@ optimization: targeted_update_factor: 1.0 automatic_update_percentile_range: 0.99 automatic_update_factor: 1.1 - try_narrower_values: False - maximal_decrease: 0.2 + try_narrower_values: True + maximal_decrease: 0.5 favour_narrower_optimum: False maximum_decrease_from_maximum: 0.1 ms1_error: