MannLabs · GeorgWa · Sep 10, 2024 · Sep 10, 2024 · Sep 10, 2024 · Sep 10, 2024
diff --git a/alphadia/__init__.py b/alphadia/__init__.py
@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.7.2"
+__version__ = "1.8.0"
diff --git a/alphadia/constants/default.yaml b/alphadia/constants/default.yaml
@@ -89,9 +89,9 @@ search:
 
   target_num_candidates: 2
   # target ms1 tolerance in ppm
-  target_ms1_tolerance: 15
+  target_ms1_tolerance: 5
   # target ms2 tolerance in ppm
-  target_ms2_tolerance: 15
+  target_ms2_tolerance: 10
   # target ion mobility tolerance in 1/K_0
   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
@@ -143,10 +143,10 @@ search_initial:
   initial_ms2_tolerance: 30
 
   # initial ion mobility tolerance in 1/K_0
-  initial_mobility_tolerance: 0.08
+  initial_mobility_tolerance: 0.1
 
   # initial retention time tolerance in seconds if > 1, or a proportion of the total gradient length if < 1
-  initial_rt_tolerance: 240
+  initial_rt_tolerance: 0.5
 
 selection_config:
   peak_len_rt: 10.

diff --git a/alphadia/libtransform.py b/alphadia/libtransform.py
@@ -324,11 +324,11 @@ def forward(self, input: SpecLibBase) -> SpecLibBase:
         model_mgr = ModelManager(device=device)
 
         # will load other model than default generic
-        if self.peptdeep_model_type is not None:
+        if self.peptdeep_model_type:
             logging.info(f"Loading PeptDeep models of type {self.peptdeep_model_type}")
             model_mgr.load_installed_models(self.peptdeep_model_type)
 
-        if self.peptdeep_model_path is not None:
+        if self.peptdeep_model_path and self.peptdeep_model_path != "":
             if not os.path.exists(self.peptdeep_model_path):
                 raise ValueError(
                     f"PeptDeep model checkpoint folder {self.peptdeep_model_path} does not exist"

diff --git a/docs/index.md b/docs/index.md
@@ -1,6 +1,6 @@
 
 # AlphaDIA Documentation
-**Version:** 1.7.2 | [Github](https://github.com/MannLabs/alphadia)
+**Version:** 1.8.0 | [Github](https://github.com/MannLabs/alphadia)
 
 Open-source DIA search engine built with the alphaX ecosystem. Built with [alpharaw](https://github.com/MannLabs/alpharaw) and [alphatims](https://github.com/MannLabs/alphatims) for raw file acces. Spectral libraries are predicted with [peptdeep](https://github.com/MannLabs/alphapeptdeep) and managed by [alphabase](https://github.com/MannLabs/alphabase). Quantification is powered by [directLFQ](https://github.com/MannLabs/directLFQ).
 

diff --git a/gui/package.json b/gui/package.json
@@ -1,7 +1,7 @@
 {
   "name": "alphadia",
   "productName": "alphadia-gui",
-  "version": "1.7.2",
+  "version": "1.8.0",
   "description": "Graphical user interface for DIA data analysis",
   "main": "dist/electron.js",
   "homepage": "./",

diff --git a/gui/src/main/modules/engine.js b/gui/src/main/modules/engine.js
@@ -260,7 +260,7 @@ class CMDExecutionEngine extends BaseExecutionEngine {
                                         "--no-capture-output",
                                         "alphadia",
                                         "--config",
-                                        path.join(workflow.output_directory.path, "config.yaml")
+                                        `"${path.join(workflow.output_directory.path, "config.yaml")}"`
                                     ] , { env:{...process.env, PATH}, shell: true});
             run.pid = run.process.pid
 
@@ -420,7 +420,7 @@ class BundledExecutionEngine extends BaseExecutionEngine {
             // use binary location as cwd and binary name as command
             run.process = spawn(prefix + binaryName,
                 ["--config",
-                path.join(workflow.output_directory.path, "config.yaml")
+                `"${path.join(workflow.output_directory.path, "config.yaml")}"`
                 ],
                 {
                     env:{...process.env, PATH},

diff --git a/gui/src/main/modules/profile.js b/gui/src/main/modules/profile.js
@@ -3,7 +3,7 @@ const path = require("path")
 const { app, shell, BrowserWindow} = require("electron")
 const { dialog } = require('electron')
 
-const VERSION = "1.7.2"
+const VERSION = "1.8.0"
 
 const Profile = class {
 

diff --git a/gui/src/renderer/components/ParameterInput.js b/gui/src/renderer/components/ParameterInput.js
@@ -16,8 +16,7 @@ const SingleFolderSelection = ({parameter, onChange = () => {}}) => {
             console.log(err);
         })
     }
-
-    const folderName = parameter.replace(/^.*[\\\/]/, '')
+    const folderName = parameter ? parameter.replace(/^.*[\\\/]/, '') : ''
 
     return (
         <>

diff --git a/gui/workflows/PeptideCentric.v1.json b/gui/workflows/PeptideCentric.v1.json
@@ -35,13 +35,6 @@
                     "description": "Number of threads to use for parallel processing.",
                     "type": "integer"
                 },
-                {
-                    "id": "reuse_calibration",
-                    "name": "Reuse Calibration",
-                    "value": false,
-                    "description": "AlphaDIA will save the calibration parameters in the project file. If this option is enabled, the calibration parameters will be reused for subsequent searches of the same file.",
-                    "type": "boolean"
-                },
                 {
                     "id": "reuse_quant",
                     "name": "Reuse Ion Quantities",
@@ -153,7 +146,7 @@
                 {
                     "id": "max_var_mod_num",
                     "name": "Maximum variable modifications",
-                    "value": 1,
+                    "value": 2,
                     "description": "Variable modifications for in-silico digest. At the moment localisation is not supported. Semicolon separated list \n Example: Oxidation@M;Acetyl@ProteinN-term",
                     "type": "integer"
                 },
@@ -241,7 +234,7 @@
                 {
                     "id": "peptdeep_model_path",
                     "name": "PeptDeep Model Path",
-                    "value": "",
+                    "value": null,
                     "description": "Select a custom PeptDeep model for library prediction. This can be a DDA or DIA trained model. Please make sure that you use the same instrument type and NCE for prediction as the model was trained on.",
                     "type": "singleFolderSelection"
                 },
@@ -265,6 +258,34 @@
             "name": "Search",
             "hidden": false,
             "parameters": [
+                {
+                    "id": "target_ms1_tolerance",
+                    "name": "MS1 Tolerance",
+                    "value": 5,
+                    "description": "MS1 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
+                    "type": "float"
+                },
+                {
+                    "id": "target_ms2_tolerance",
+                    "name": "MS2 Tolerance",
+                    "value": 10,
+                    "description": "MS2 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
+                    "type": "float"
+                },
+                {
+                    "id": "target_mobility_tolerance",
+                    "name": "Mobility Tolerance",
+                    "value": 0.0,
+                    "description": "Mobility tolerance in 1/K_0. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached. Set to enable automatic optimization.",
+                    "type": "float"
+                },
+                {
+                    "id": "target_rt_tolerance",
+                    "name": "RT Tolerance",
+                    "value": 0.0,
+                    "description": "Retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached. Automatic optimization is enabled if set to 0.",
+                    "type": "float"
+                },
                 {
                     "id": "channel_filter",
                     "name": "Channel Filter",
@@ -293,34 +314,7 @@
                     "description": "For every precursor in the library a number of top scoring candidates will be extracted. This number is the maximum number of candidates that will be extracted per precursor.",
                     "type": "integer"
                 },
-                {
-                    "id": "target_ms1_tolerance",
-                    "name": "MS1 Tolerance",
-                    "value": 5,
-                    "description": "MS1 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
-                    "type": "float"
-                },
-                {
-                    "id": "target_ms2_tolerance",
-                    "name": "MS2 Tolerance",
-                    "value": 10,
-                    "description": "MS2 tolerance in ppm. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
-                    "type": "float"
-                },
-                {
-                    "id": "target_mobility_tolerance",
-                    "name": "Mobility Tolerance",
-                    "value": 0.04,
-                    "description": "Mobility tolerance in 1/K_0. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
-                    "type": "float"
-                },
-                {
-                    "id": "target_rt_tolerance",
-                    "name": "RT Tolerance",
-                    "value": 100,
-                    "description": "Retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1. Search windows are optimized and calibrated during processing. The window is reduced until this tolerance is reached.",
-                    "type": "float"
-                },
+
                 {
                     "id": "quant_window",
                     "name": "Quant window",
@@ -332,7 +326,7 @@
                 {
                     "id": "quant_all",
                     "name": "Use all MS2 observations",
-                    "value": false,
+                    "value": true,
                     "description": "Use all MS2 observations for quantification. If disabled only the best scoring observation is used for quantification. Recommended for synchro-PASEF data.",
                     "type": "boolean"
 
@@ -374,13 +368,6 @@
                         "heuristic"
                     ]
                 },
-                {
-                    "id": "competetive_scoring",
-                    "name": "Competetive Scoring",
-                    "value": true,
-                    "description": "If enabled, only the best scoring candidate per target decoy pair is retained.",
-                    "type": "boolean"
-                },
                 {
                     "id": "channel_wise_fdr",
                     "name": "Channel wise FDR",
@@ -405,7 +392,7 @@
                 {
                     "id": "initial_num_candidates",
                     "name": "Number of Candidates",
-                    "value": 2,
+                    "value": 1,
                     "description": "Initial number of candidates to extract per precursor.",
                     "type": "integer"
                 },
@@ -426,14 +413,14 @@
                 {
                     "id": "initial_mobility_tolerance",
                     "name": "Mobility Tolerance",
-                    "value": 0.08,
+                    "value": 0.1,
                     "description": "Initial mobility tolerance in 1/K_0.",
                     "type": "float"
                 },
                 {
                     "id": "initial_rt_tolerance",
                     "name": "RT Tolerance",
-                    "value": 240,
+                    "value": 0.5,
                     "description": "Initial retention time tolerance in seconds if greater than 1 or as a proportion of the gradient length if less than 1.",
                     "type": "float"
                 }
@@ -445,7 +432,7 @@
             "hidden": true,
             "parameters": [
                 {
-                    "id": "multiplexed_quant",
+                    "id": "enabled",
                     "name": "Enable Multiplexing",
                     "value": false,
                     "description": "Quantify and score identification across non-isobaric labled channels.",

diff --git a/misc/.bumpversion.cfg b/misc/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.7.2
+current_version = 1.8.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

diff --git a/release/macos/build_backend_macos.sh b/release/macos/build_backend_macos.sh
@@ -2,7 +2,7 @@
 
 pip install build
 python -m build
-pip install "dist/alphadia-1.7.2-py3-none-any.whl[stable]"
+pip install "dist/alphadia-1.8.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

diff --git a/release/macos/build_pkg_macos.sh b/release/macos/build_pkg_macos.sh
@@ -2,7 +2,7 @@
 
 # Set up package name and version
 PACKAGE_NAME="alphadia"
-PACKAGE_VERSION="1.7.2"
+PACKAGE_VERSION="1.8.0"
 
 ARCH=$(uname -m)
 if [ "$ARCH" == "x86_64" ]; then

diff --git a/release/macos/build_zip_macos.sh b/release/macos/build_zip_macos.sh
@@ -2,7 +2,7 @@
 
 # Set up package name and version
 PACKAGE_NAME="alphadia"
-PACKAGE_VERSION="1.7.2"
+PACKAGE_VERSION="1.8.0"
 
 ARCH=$(uname -m)
 if [ "$ARCH" == "x86_64" ]; then

diff --git a/release/macos/distribution.xml b/release/macos/distribution.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>alphaDIA 1.7.2</title>
+    <title>alphaDIA 1.8.0</title>
     <background mime-type="image/png" file="alphadia.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

diff --git a/release/macos/info.plist b/release/macos/info.plist
@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alphadia.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphadia.1.7.2</string>
+	<string>alphadia.1.8.0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.7.2</string>
+	<string>1.8.0</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

diff --git a/release/windows/alphadia_innoinstaller.iss b/release/windows/alphadia_innoinstaller.iss
@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaDIA"
-#define MyAppVersion "1.7.2"
+#define MyAppVersion "1.8.0"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphadia"
 #define MyAppExeName "alphadia-gui.exe"
@@ -25,7 +25,7 @@ LicenseFile=..\..\LICENSE.txt
 PrivilegesRequired=lowest
 PrivilegesRequiredOverridesAllowed=dialog
 OutputDir=..\..\dist
-OutputBaseFilename=alphadia-1.7.2-win-x64
+OutputBaseFilename=alphadia-1.8.0-win-x64
 SetupIconFile=..\logos\alphadia.ico
 Compression=lzma
 SolidCompression=yes

diff --git a/release/windows/build_backend.ps1 b/release/windows/build_backend.ps1
@@ -3,7 +3,7 @@ Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
 
 pip install build
 python -m build
-pip install "dist/alphadia-1.7.2-py3-none-any.whl[stable]"
+pip install "dist/alphadia-1.8.0-py3-none-any.whl[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller tbb