Added multiprocessing option for LFQ.

Updated Enzyme, KO, and Pathway databases.
Updated MetaX_Cookbook.

Docs/ChangeLog.md

@@ -1,9 +1,14 @@
+# Version: 1.115.1
+## Date: 2024-10-03
+### Changes:
+- New: added multiprocessing option for LFQ.
+
+
 # Version: 1.115.0
 ## Date: 2024-10-02
 ### Changes:
 - New: added DriectLFQ algorithm option for quantification.
 
-
 # Version: 1.114.5
 ## Date: 2024-09-23
 ### Changes:

Docs/MetaX_Cookbook.md

@@ -275,6 +275,16 @@ Click **Create Proteins Intensity Table** to sum peptides to proteins if the Pro
 
 ### Data preprocessing
 
+- **Quantitative Method：**
+
+  - **<u>Sum</u>**: Sum the peptides intensity directly to Taxa, Functions or OTFs intensity.
+
+  - **<u>DirecteLFQ</u>**: Using DirecteLFQ to normalize the peptides and then estimate the intensity by using  *intensity traces*.
+
+
+
+- **Outlier handling:**
+
 There are several methods for detecting and handling outliers.
 
 - Two steps will be applied:

metax/data/pathway.tsv

@@ -9,6 +9,7 @@ map01232	Nucleotide metabolism
 map01250	Biosynthesis of nucleotide sugars
 map01240	Biosynthesis of cofactors
 map01220	Degradation of aromatic compounds
+map01310	Nitrogen cycle
 map00010	Glycolysis / Gluconeogenesis
 map00020	Citrate cycle (TCA cycle)
 map00030	Pentose phosphate pathway
@@ -27,15 +28,16 @@ map00562	Inositol phosphate metabolism
 map00190	Oxidative phosphorylation
 map00195	Photosynthesis
 map00196	Photosynthesis - antenna proteins
-map00710	Carbon fixation in photosynthetic organisms
-map00720	Carbon fixation pathways in prokaryotes
+map00710	Carbon fixation by Calvin cycle
+map00720	Other carbon fixation pathways
 map00680	Methane metabolism
 map00910	Nitrogen metabolism
 map00920	Sulfur metabolism
 map00061	Fatty acid biosynthesis
 map00062	Fatty acid elongation
 map00071	Fatty acid degradation
 map00073	Cutin, suberine and wax biosynthesis
+map00074	Mycolic acid biosynthesis
 map00100	Steroid biosynthesis
 map00120	Primary bile acid biosynthesis
 map00121	Secondary bile acid biosynthesis
@@ -220,7 +222,8 @@ map03262	Virion - Coronavirus
 map03261	Virion - Influenza virus
 map03263	Virion - Enterovirus
 map03264	Virion - Flavivirus
-map03265	Virion - Ebolavirus and Lyssavirus
+map03265	Virion - Ebolavirus, Lyssavirus and Morbillivirus
+map03272	Virion - Hepatitis viruses
 map03266	Virion - Herpesvirus
 map03268	Virion - Orthopoxvirus
 map03267	Virion - Adenovirus
@@ -581,6 +584,7 @@ ko01232	Nucleotide metabolism
 ko01250	Biosynthesis of nucleotide sugars
 ko01240	Biosynthesis of cofactors
 ko01220	Degradation of aromatic compounds
+ko01310	Nitrogen cycle
 ko00010	Glycolysis / Gluconeogenesis
 ko00020	Citrate cycle (TCA cycle)
 ko00030	Pentose phosphate pathway
@@ -599,15 +603,16 @@ ko00562	Inositol phosphate metabolism
 ko00190	Oxidative phosphorylation
 ko00195	Photosynthesis
 ko00196	Photosynthesis - antenna proteins
-ko00710	Carbon fixation in photosynthetic organisms
-ko00720	Carbon fixation pathways in prokaryotes
+ko00710	Carbon fixation by Calvin cycle
+ko00720	Other carbon fixation pathways
 ko00680	Methane metabolism
 ko00910	Nitrogen metabolism
 ko00920	Sulfur metabolism
 ko00061	Fatty acid biosynthesis
 ko00062	Fatty acid elongation
 ko00071	Fatty acid degradation
 ko00073	Cutin, suberine and wax biosynthesis
+ko00074	Mycolic acid biosynthesis
 ko00100	Steroid biosynthesis
 ko00120	Primary bile acid biosynthesis
 ko00121	Secondary bile acid biosynthesis
@@ -783,7 +788,8 @@ ko03262	Virion - Coronavirus
 ko03261	Virion - Influenza virus
 ko03263	Virion - Enterovirus
 ko03264	Virion - Flavivirus
-ko03265	Virion - Ebolavirus and Lyssavirus
+ko03265	Virion - Ebolavirus, Lyssavirus and Morbillivirus
+ko03272	Virion - Hepatitis viruses
 ko03266	Virion - Herpesvirus
 ko03268	Virion - Orthopoxvirus
 ko03267	Virion - Adenovirus