From 90eb864f23bcdca00e2c6e3cab4cbd6774e71fcc Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 29 Jan 2026 19:56:57 +0000
Subject: [PATCH 1/3] Add Comet resolution parameter presets

Add High-Res and Low-Res presets for CometAdapter:
- High-Res (< 50 ppm): instrument=high_res, fragment_mass_tolerance=0.015 Da, fragment_bin_offset=0.0
- Low-Res (>= 50 ppm): instrument=low_res, fragment_mass_tolerance=0.50025 Da, fragment_bin_offset=0.4

https://claude.ai/code/session_01B8uy8fQnZ9q2tRsCiLuTev
---
 presets.json | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/presets.json b/presets.json
index 1099493..4a1a826 100644
--- a/presets.json
+++ b/presets.json
@@ -40,6 +40,22 @@
                 "algorithm:link:rt_tol": 30.0,
                 "algorithm:link:mz_tol": 10.0
             }
+        },
+        "Comet High-Res": {
+            "_description": "Optimized for high-resolution MS2 (Orbitrap, TOF) when using ppm fragment tolerance",
+            "CometAdapter": {
+                "instrument": "high_res",
+                "fragment_mass_tolerance": 0.015,
+                "fragment_bin_offset": 0.0
+            }
+        },
+        "Comet Low-Res": {
+            "_description": "Optimized for low-resolution MS2 (Ion trap) when using ppm fragment tolerance",
+            "CometAdapter": {
+                "instrument": "low_res",
+                "fragment_mass_tolerance": 0.50025,
+                "fragment_bin_offset": 0.4
+            }
         }
     }
 }

From 02dc15018a87033635975b983e03a09eb905b6d3 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 29 Jan 2026 20:06:51 +0000
Subject: [PATCH 2/3] Rename Comet presets to High Res MS and Low Res MS

https://claude.ai/code/session_01B8uy8fQnZ9q2tRsCiLuTev
---
 presets.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/presets.json b/presets.json
index 4a1a826..808bbe0 100644
--- a/presets.json
+++ b/presets.json
@@ -41,7 +41,7 @@
                 "algorithm:link:mz_tol": 10.0
             }
         },
-        "Comet High-Res": {
+        "High Res MS": {
             "_description": "Optimized for high-resolution MS2 (Orbitrap, TOF) when using ppm fragment tolerance",
             "CometAdapter": {
                 "instrument": "high_res",
@@ -49,7 +49,7 @@
                 "fragment_bin_offset": 0.0
             }
         },
-        "Comet Low-Res": {
+        "Low Res MS": {
             "_description": "Optimized for low-resolution MS2 (Ion trap) when using ppm fragment tolerance",
             "CometAdapter": {
                 "instrument": "low_res",

From 92e3e7251fb8ae2b4b0cf09fbd6ce18423a01073 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 29 Jan 2026 20:26:23 +0000
Subject: [PATCH 3/3] Remove other presets, keep only Comet resolution presets

https://claude.ai/code/session_01B8uy8fQnZ9q2tRsCiLuTev
---
 presets.json | 41 -----------------------------------------
 1 file changed, 41 deletions(-)

diff --git a/presets.json b/presets.json
index 808bbe0..d1878af 100644
--- a/presets.json
+++ b/presets.json
@@ -1,46 +1,5 @@
 {
     "topp-workflow": {
-        "High Sensitivity": {
-            "_description": "Optimized for detecting low-abundance features with higher noise tolerance",
-            "FeatureFinderMetabo": {
-                "algorithm:common:noise_threshold_int": 500.0,
-                "algorithm:common:chrom_peak_snr": 2.0,
-                "algorithm:mtd:mass_error_ppm": 15.0
-            }
-        },
-        "High Specificity": {
-            "_description": "Strict parameters for high-confidence feature detection",
-            "FeatureFinderMetabo": {
-                "algorithm:common:noise_threshold_int": 5000.0,
-                "algorithm:common:chrom_peak_snr": 5.0,
-                "algorithm:mtd:mass_error_ppm": 5.0
-            }
-        },
-        "Fast Analysis": {
-            "_description": "Faster processing with relaxed parameters for quick exploration",
-            "FeatureFinderMetabo": {
-                "algorithm:common:noise_threshold_int": 2000.0,
-                "algorithm:ffm:isotope_filtering_model": "none"
-            },
-            "FeatureLinkerUnlabeledKD": {
-                "algorithm:link:rt_tol": 60.0,
-                "algorithm:link:mz_tol": 15.0
-            }
-        },
-        "Metabolomics Default": {
-            "_description": "Balanced parameters for general metabolomics analysis",
-            "FeatureFinderMetabo": {
-                "algorithm:common:noise_threshold_int": 1000.0,
-                "algorithm:common:chrom_peak_snr": 3.0,
-                "algorithm:mtd:mass_error_ppm": 10.0,
-                "algorithm:ffm:charge_lower_bound": 1,
-                "algorithm:ffm:charge_upper_bound": 3
-            },
-            "FeatureLinkerUnlabeledKD": {
-                "algorithm:link:rt_tol": 30.0,
-                "algorithm:link:mz_tol": 10.0
-            }
-        },
         "High Res MS": {
             "_description": "Optimized for high-resolution MS2 (Orbitrap, TOF) when using ppm fragment tolerance",
             "CometAdapter": {