Recent changes to Home

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:43:02 -0000

--- v6
+++ v7
@@ -39,13 +39,9 @@
 ### **Quick start**

  1.    Download the desktop executable:
 https://sourceforge.net/projects/sugarbase-x/files/SugarBase_v08032026.zip/download
-
-2. Open the desktop executable:
-![Screenshot_SugarBase.png](https://sourceforge.net/projects/sugarbase-x/files/Screenshot_SugarBase.png)
-
+2. Open the desktop executable
 3. Download the test data:
 https://sourceforge.net/projects/sugarbase-x/files/Test_data_SugarBase.zip/download
-
 4. Select your input folder. A maximum of three .mzXML files is allowed per analysis. 
 5. Select your output folder.
 6. Enter a sample name.
@@ -53,18 +49,9 @@
 8. 'Targeted' -> requires a Target.xlsx file which should include the chemical formulas of the sugars you want to target, e.g. C6H12O6.
 9. 'Discovery' -> no Target.xlsx file is required. 
 10.    To run the analysis with default parameters, click "Run Analysis":
-
- 
-
 11.    A tabular output will show up, presenting the identified nucleotide-sugar hits with their total score. 
 12.    The table can be exported as an Excel file, using the "Export" function. 
-
- 
-
 13.    Each nucleotide-sugar hit can be explored interactively by selecting one of the hits in the table:
-
- 
-
 14.    For a description of the input and output parameters, the reader is referred to the ReadMe file.

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:42:24 -0000

--- v5
+++ v6
@@ -41,7 +41,7 @@
 https://sourceforge.net/projects/sugarbase-x/files/SugarBase_v08032026.zip/download


 2. Open the desktop executable:
-![](https://sourceforge.net/projects/sugarbase-x/files/Screenshot_SugarBase.png)
+![Screenshot_SugarBase.png](https://sourceforge.net/projects/sugarbase-x/files/Screenshot_SugarBase.png)


 3. Download the test data:
 https://sourceforge.net/projects/sugarbase-x/files/Test_data_SugarBase.zip/download

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:41:11 -0000

--- v4
+++ v5
@@ -41,7 +41,7 @@
 https://sourceforge.net/projects/sugarbase-x/files/SugarBase_v08032026.zip/download


 2. Open the desktop executable:
- ![image](U:\PhDJvE\P1.0_NT_Sugars\Desktop_exe\Picture1.png)
+![](https://sourceforge.net/projects/sugarbase-x/files/Screenshot_SugarBase.png)


 3. Download the test data:
 https://sourceforge.net/projects/sugarbase-x/files/Test_data_SugarBase.zip/download

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:34:59 -0000

--- v3
+++ v4
@@ -7,23 +7,23 @@
 SugarBase can be used to discover the nucleotide-sugar profile in microbial extracts without requiring any prior knowledge. 

 ### **Workflow** 

-   1.  Parameter initialization.
-    2. Specify discovery or targeted mode analysis.
-    3. Generation of a theoretical chemical space of nucleotide-activated sugar compositions.
-    4. Peak lists are extracted from .mzXML files.
-    5. Odd/even scans are separated into pseudo-MS1 and fragmented MS2 datasets.
-    6. MS1 data pre-processing 
+1. Parameter initialization.
+2. Specify discovery or targeted mode analysis.
+3. Generation of a theoretical chemical space of nucleotide-activated sugar compositions.
+4. Peak lists are extracted from .mzXML files.
+5. Odd/even scans are separated into pseudo-MS1 and fragmented MS2 datasets.
+6. MS1 data pre-processing 
         •  Optional deisotoping
         •  Filter MS1 data by m/z window, retention time and minimum intensity thresholds.
-    7. Fragment extraction and MS1-MS2 alignment
+7. Fragment extraction and MS1-MS2 alignment
         •  Identify diagnostic nucleotide fragments in MS2 spectra.
         •  Align fragment signals with MS1 precursor peaks.
         •  Match precursor masses against the theoretical chemical space.
-    8. CDP-sugar detection
+8. CDP-sugar detection
         •  Detect CMP fragments to specifically identify CDP-activated sugars.
         •  Annotate candidates with a CDP-sugar flag.
-    9. Candidate precursors are retained only if detected in ≥3 consecutive scans with the corresponding nucleotide fragment in MS2.
-    10.    Candidate scoring; assign scores based on several criteria:
+9. Candidate precursors are retained only if detected in ≥3 consecutive scans with the corresponding nucleotide fragment in MS2.
+10.    Candidate scoring; assign scores based on several criteria:
         •  Occurrence across consecutive scans
         •  Pearson correlation 
         •  MS1 signal intensity
@@ -31,17 +31,17 @@
         •  Precursor (MS1) intensity/Fragment (MS2) intensity ratio (non-CMP-sugars)
         •  Precursor (MS2) intensity/Fragment (MS2) intensity ratio (CMP-sugars)
         •  nitrogen rule consistency (CMP-sugars)
-    11.    Interactive dashboard enables exploration or results.
-    12.    Tabular output with nucleotide-sugars hits and their likeliness score. 
-    13.    Extracted ion chromatograms and pseudo-MS1 and MS2 spectra are generated. 
-    14.    Results can be exported as Excel table. 
+11.    Interactive dashboard enables exploration or results.
+12.    Tabular output with nucleotide-sugars hits and their likeliness score. 
+13.    Extracted ion chromatograms and pseudo-MS1 and MS2 spectra are generated. 
+14.    Results can be exported as Excel table. 


- ### **Quick Start**
+### **Quick start**
  1.    Download the desktop executable:
 https://sourceforge.net/projects/sugarbase-x/files/SugarBase_v08032026.zip/download


 2. Open the desktop executable:
- 
+ ![image](U:\PhDJvE\P1.0_NT_Sugars\Desktop_exe\Picture1.png)


 3. Download the test data:
 https://sourceforge.net/projects/sugarbase-x/files/Test_data_SugarBase.zip/download

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:29:29 -0000

--- v2
+++ v3
@@ -7,7 +7,7 @@
 SugarBase can be used to discover the nucleotide-sugar profile in microbial extracts without requiring any prior knowledge. 

 ### **Workflow** 

-    1. Parameter initialization.
+   1.  Parameter initialization.
     2. Specify discovery or targeted mode analysis.
     3. Generation of a theoretical chemical space of nucleotide-activated sugar compositions.
     4. Peak lists are extracted from .mzXML files.

Home modified by Jitske van Ede

Jitske van Ede — Thu, 19 Mar 2026 15:28:29 -0000

--- v1
+++ v2
@@ -1,8 +1,76 @@
-Welcome to your wiki!
+# **SugarBase: mapping glycomolecule precursors in microbes**

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+###  **Overview** ###
+SugarBase is designed to process LC–MS/MS data (in .mzXML format) to identify nucleotide-activated sugars (NT-sugars) based on diagnostic nucleotide fragments and a predefined chemical composition space. The workflow combines pseudo-MS1 precursor information with MS2 fragment evidence, filters candidate masses using theoretical chemical compositions, and assigns a confidence score to each detected hit.
+The pipeline supports both a discovery mode (screening a broad chemical space of possible nucleotide-sugars) and a targeted mode (searching only predefined compositions from an input list). The desktop executable allows to explore the results interactively, by providing the extracted ion chromatograms as well as the pseudo-MS1 and MS2 scans in which the potential NT-sugar was detected for each nucleotide-sugar hit. In addition, results can be exported as an Excel table.
+Key analytical steps include MS1 preprocessing (deisotoping and filtering), MS2 fragment extraction, MS1–MS2 alignment, precursor matching against a theoretical chemical sugar space, detection of consistent signals across consecutive scans, and multi-parameter scoring to rank candidate nucleotide-sugar hits.
+SugarBase can be used to discover the nucleotide-sugar profile in microbial extracts without requiring any prior knowledge. 

-The wiki uses [Markdown](/nf/markdown_syntax) syntax.
+### **Workflow** 

+    1. Parameter initialization.
+    2. Specify discovery or targeted mode analysis.
+    3. Generation of a theoretical chemical space of nucleotide-activated sugar compositions.
+    4. Peak lists are extracted from .mzXML files.
+    5. Odd/even scans are separated into pseudo-MS1 and fragmented MS2 datasets.
+    6. MS1 data pre-processing 
+        •  Optional deisotoping
+        •  Filter MS1 data by m/z window, retention time and minimum intensity thresholds.
+    7. Fragment extraction and MS1-MS2 alignment
+        •  Identify diagnostic nucleotide fragments in MS2 spectra.
+        •  Align fragment signals with MS1 precursor peaks.
+        •  Match precursor masses against the theoretical chemical space.
+    8. CDP-sugar detection
+        •  Detect CMP fragments to specifically identify CDP-activated sugars.
+        •  Annotate candidates with a CDP-sugar flag.
+    9. Candidate precursors are retained only if detected in ≥3 consecutive scans with the corresponding nucleotide fragment in MS2.
+    10.    Candidate scoring; assign scores based on several criteria:
+        •  Occurrence across consecutive scans
+        •  Pearson correlation 
+        •  MS1 signal intensity
+        •  CO₂ neutral loss
+        •  Precursor (MS1) intensity/Fragment (MS2) intensity ratio (non-CMP-sugars)
+        •  Precursor (MS2) intensity/Fragment (MS2) intensity ratio (CMP-sugars)
+        •  nitrogen rule consistency (CMP-sugars)
+    11.    Interactive dashboard enables exploration or results.
+    12.    Tabular output with nucleotide-sugars hits and their likeliness score. 
+    13.    Extracted ion chromatograms and pseudo-MS1 and MS2 spectra are generated. 
+    14.    Results can be exported as Excel table. 

-[[members limit=20]]
-[[download_button]]

+ ### **Quick Start**
+ 1.    Download the desktop executable:
+https://sourceforge.net/projects/sugarbase-x/files/SugarBase_v08032026.zip/download
+
+2. Open the desktop executable:
+ 
+
+3. Download the test data:
+https://sourceforge.net/projects/sugarbase-x/files/Test_data_SugarBase.zip/download
+
+4. Select your input folder. A maximum of three .mzXML files is allowed per analysis. 
+5. Select your output folder.
+6. Enter a sample name.
+7. Select the analysis mode:
+8. 'Targeted' -> requires a Target.xlsx file which should include the chemical formulas of the sugars you want to target, e.g. C6H12O6.
+9. 'Discovery' -> no Target.xlsx file is required. 
+10.    To run the analysis with default parameters, click "Run Analysis":
+
+ 
+
+11.    A tabular output will show up, presenting the identified nucleotide-sugar hits with their total score. 
+12.    The table can be exported as an Excel file, using the "Export" function. 
+
+ 
+
+13.    Each nucleotide-sugar hit can be explored interactively by selecting one of the hits in the table:
+
+ 
+
+14.    For a description of the input and output parameters, the reader is referred to the ReadMe file. 
+
+ 
+### **Citation**
+Van Ede, J.M., Holst Sørensen, M.C., Sorokin, D.Y., van Loosdrecht, M.C.M. and Pabst, M. SugarBase: mapping glycomolecule precursors in microbes. (2026). 
+ 
+###  **Contacts**
+Jitske M. van Ede (J.M.vanEde@tudelft.nl)
+Martin Pabst (M.Pabst@tudelft.nl)

Home modified by glycolab

glycolab — Sun, 01 Mar 2026 03:14:53 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

glycolab (admin)