Update Explanation on each parameter of MS-Dial 5.qmd

Explanation on each parameter of MS-Dial 5.qmd

@@ -24,43 +24,63 @@ MS-Dial 4: Effective but slower on larger datasets.
 MS-Dial 5: Optimized for faster data processing, especially for large, multi-omics datasets.
 
 **Annotation Capabilities:**
+
 MS-DIAL 4: Limited to using one database and annotation level in a single analysis. Provides comprehensive annotation of metabolites and lipids through spectral matching using established databases.
+
 MS-DIAL 5: Enables the use of multiple databases and annotation levels within the same analysis. Significantly improves annotation accuracy by incorporating ion mobility spectrometry (IMS) data and enhanced spectral deconvolution. MS-DIAL 5 also has better integration with larger and more updated databases, improving the annotation of complex molecules like lipids, metabolites, and isomers.
 
 **Annotation Capabilities:**
+
 MS-DIAL 4: Offers only one possible annotation candidate per analysis.
+
 MS-DIAL 5: Provides multiple annotation candidates from different databases, improving identification accuracy. Adds support for ion mobility spectrometry (IMS), enabling better separation of ions that share the same mass-to-charge ratio (m/z) but have different drift times. This improves separation in complex biological mixtures.
 
 **Isomer Separation:**
+
 MS-Dial 4: It will support basic functionality.
+
 MS-Dial 5: Enhanced separation of isomers and similar molecular species.
 
 **Peak Picking and Alignment:**
+
 MS-Dial 4: Accurate, but sometimes slower or less accurate with noisy data.
+
 MS-Dial 5: Refined peak picking and alignment algorithms for better performance, especially with complex datasets.
 
 **Data Formats:**
+
 MS-Dial 4: Supports only (.ABF) format.
+
 MS-Dial 5: Further extended support for newer formats, including advanced mass spectrometry data.
 
 **Separation Techniques:**
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 MS-DIAL 4: Supports separation methods like LCMS, LCIMMS, and GCMS.
+
 MS-DIAL 5: Adds support for direct infusion MS (DIMS) and ion mobility MS (IMMS), broadening the range of separation techniques.
 
 **Collision Types:**
+
 MS-DIAL 4: Works with CID and HCD collision types.
+
 MS-DIAL 5: Extends support to additional collision types, including ECD, HotECD, EIEIO, EID, and OAD, offering more advanced fragmentation methods.
 
 **Targeted Omics:**
+
 MS-DIAL 4: Focuses on metabolomics and lipidomics analysis.
+
 MS-DIAL 5: Expands its capabilities to include proteomics, in addition to metabolomics and lipidomics.
 
 **Flexibility in MS Methods:**
+
 MS-DIAL 4: Only one MS method (DDA, SWATH, AIF) can be applied in each analysis.
+
 MS-DIAL 5: Allows multiple MS methods to be applied to a single analysis, enabling more comprehensive data analysis.
 
 **Undo/Redo Functionality:**
+
 MS-DIAL 4: Does not offer an undo/redo feature when changing an annotation to unknown.
+
 MS-DIAL 5: Introduces this capability, making it easier to revert or correct annotation changes during data processing.
 
 ## 4.0 Step-by-step guide on how to set up a project in MS-DIAL 5
@@ -81,11 +101,11 @@ For a detailed walkthrough on selecting the acquisition type, refer to the video
 
 {{< video https://youtu.be/2iy-fsbusYI?si=49SP7rO1YIfv1BUO >}}
 
-After selecting the acquisition type, you can further customize your project by setting additional parameters. If your analysis involves multiple batches, you can assign batch numbers to differentiate between them and account for batch effects during data processing. You can also specify the analytical order of your samples, which is useful for tracking trends such as signal drift or other variations that may have occurred throughout the run. Additionally, you can set a dilution factor for each sample, allowing MS-DIAL to adjust the quantification accordingly. If certain samples are not needed for further analysis, you can choose to exclude them from the data processing (figure 3). 
+After selecting the acquisition type, you can further customize your project by setting additional parameters. If your analysis involves multiple batches, you can assign batch numbers to differentiate between them and account for batch effects during data processing. You can also specify the analytical order of your samples, which is useful for tracking trends such as signal drift or other variations that may have occurred throughout the run. Additionally, you can set a dilution factor for each sample, allowing MS-DIAL to adjust the quantification accordingly. If certain samples are not needed for further analysis, you can choose to exclude them from the data processing (Figure 3). 
 
 ![Click on the browse icon and point MS-DIAL5 to the folder where your raw data is stored (A). Next, select the raw file format as per your analysis (B). Select the raw files for analysis (C). Further, assign identifiers to your measurements and acquisition type (D)](images/Parameters for MS-Dial/Figure_2 Website.png){#fig-3}
 
-After assigning identifiers to the raw measurement files, click Next to proceed to the Measurement Parameters tab. In this section, you will input the analytical and instrumental parameters that were used during data acquisition. These settings are crucial for ensuring accurate data processing and should align exactly with the experimental conditions under which the measurements were taken.
+After assigning identifiers to the raw measurement files, click Next to proceed to the Measurement Parameters tab. In this section, you will input the analytical and instrumental parameters that were used during data acquisition. These settings are crucial for ensuring accurate data processing and should align exactly with the experimental conditions under which the measurements were taken (Figure 4).
 The following sections will offer detailed instructions on how to select and configure each parameter within the Measurement Parameters section
 
 **4.1 Measurement Parameters Section:**
@@ -113,7 +133,7 @@ The following sections will offer detailed instructions on how to select and con
 
 ![Overview of the Measurement parameter settings](images/Parameters for MS-Dial/Figure_3 Website.png){#fig-4}
 
-After configuring each parameter in the Measurement Parameters section, click “Next” to proceed to the Data Collection tab. In this section, you will need to enter the data collection parameters that were used during the acquisition of your samples. These parameters are essential for accurately processing and analyzing your data according to the conditions of your experiment.
+After configuring each parameter in the Measurement Parameters section, click “Next” to proceed to the Data Collection tab. In this section, you will need to enter the data collection parameters that were used during the acquisition of your samples. These parameters are essential for accurately processing and analyzing your data according to the conditions of your experiment (Figure 5).
 The upcoming sections will provide detailed instructions on how to set each parameter in the Data Collection section.
 
 **4.2 Data collection parameters:**
@@ -132,7 +152,7 @@ The upcoming sections will provide detailed instructions on how to set each para
 
 ![Overview of the Data collection parameter setting.](images/Parameters for MS-Dial/Figure_4 Website.png){#fig-5}
 
-Click Next to proceed to the Peak Detection Parameter Settings. In this section, you'll need to enter the parameters used for peak detection in your mass spectrometry data. This includes specifying values such as the minimum peak height, mass peak width, and exclusion mass list.
+Click Next to proceed to the Peak Detection Parameter Settings. In this section, you'll need to enter the parameters used for peak detection in your mass spectrometry data. This includes specifying values such as the minimum peak height, mass peak width, and exclusion mass list (Figure 6).
 The following sections will offer detailed guidance on how to configure each parameter within the Peak Detection section
 
 **4.3 Peak detection parameter:**
@@ -158,7 +178,7 @@ Refer to the tutorial on how to determine the minimum peak height for your analy
 
 ![Overview of the Peak detection parameter settings.](images/Parameters for MS-Dial/Figure_5 Website.png){#fig-6}
 
-Click Next to proceed to the Spectrum Deconvolution Parameter Settings. In this section, you will configure the parameters for deconvoluting your mass spectrometry data. Key settings include the sigma window value, the MS/MS abundance cut-off value, and the option to exclude peaks following the precursor ion.
+Click Next to proceed to the Spectrum Deconvolution Parameter Settings. In this section, you will configure the parameters for deconvoluting your mass spectrometry data. Key settings include the sigma window value, the MS/MS abundance cut-off value, and the option to exclude peaks following the precursor ion (Figure 7).
 The following sections will provide detailed instructions on how to set each parameter within the Spectrum Deconvolution section.
 
 **4.4 Spectrum deconvolution parameter:**
@@ -175,7 +195,7 @@ The following sections will provide detailed instructions on how to set each par
 
 ![Overview of the Spectrum deconvolution parameter settings.](images/Parameters for MS-Dial/Figure_6 Website.png){#fig-7}
 
-Click Next to proceed to the Identification Parameter Settings. In this section, you will configure parameters related to the identification of compounds, including the database type, lipid profiling settings, annotation options, and retention time settings.
+Click Next to proceed to the Identification Parameter Settings. In this section, you will configure parameters related to the identification of compounds, including the database type, lipid profiling settings, annotation options, and retention time settings (Figure 8).
 The following sections will provide detailed instructions on how to set each parameter within the Identification section.
 
 **4.5 Identification parameter:**
@@ -207,7 +227,7 @@ Refer to the tutorial video on MS-DIAL for guidance on how to import a text libr
 ![Overview of the Identification parameter settings. Selecting lipids for the analysis (A). Setting identification parameters (B).](images/Parameters for MS-Dial/Figure_7Website.png){#fig-8}
 
 Click on Next to proceed to the Adduct Ion Parameter Settings. In this section, you will need to select the adduct ions relevant to your analysis.
-The following sections will provide detailed instructions on how to choose and configure adduct ions for your analysis. 
+The following sections will provide detailed instructions on how to choose and configure adduct ions for your analysis (Figure 9). 
 
 **4.6 Adduct ion parameters:**
 
@@ -241,7 +261,7 @@ For Trifluoroacetic acid: TFA, CFCOOH
 
 ![Overview of the Adduct parameter settings.](images/Parameters for MS-Dial/Figure_8Website.png){#fig-9}
 
-Click Next to proceed to the Alignment Parameter Settings. In this section, you'll need to configure various parameters including the reference file, RT tolerance, RT factor, features based on blank information, and peak count filter for adduct ions.
+Click Next to proceed to the Alignment Parameter Settings. In this section, you'll need to configure various parameters including the reference file, RT tolerance, RT factor, features based on blank information, and peak count filter for adduct ions (Figure 10).
 The following sections will provide detailed instructions on how to set each of these parameters for optimal alignment of your data.
 
 **4.7 Alignment parameters:**
@@ -276,7 +296,7 @@ For example, if you have 3 biological replicates with the same peak information
 
 ![Overview of the alignment parameter settings.](images/Parameters for MS-Dial/Figure_9Website.png){#fig-10}
 
-Click Next to proceed to the Isotope Tracking Settings. In this section, you will configure the settings to enable isotope tracking in your data.
+Click Next to proceed to the Isotope Tracking Settings. In this section, you will configure the settings to enable isotope tracking in your data (Figure 11).
 The following sections will provide detailed instructions on how to set up the isotope tracking parameters for your analysis.
 
 **4.8 Isotope tracking parameter:**
@@ -287,7 +307,7 @@ The following sections will provide detailed instructions on how to set up the i
 
 Then you can click Run for the processing of your MS data in MS-Dial 5 and click Save to save the project.
 
-Once you finished the data processing like peak picking, peak identification, and peak annotation. You can click the export icon to export the results in different forms. 
+Once you finished the data processing like peak picking, peak identification, and peak annotation. You can click the export icon to export the results in different forms (Figure 12). 
 The following sections will provide detailed instructions on how to export your results. 
 
 **4.9 Export:**
@@ -314,13 +334,13 @@ Let's consider for lipidomics project:
 
 **1: Meaning of Fill%:**
 
-Fill% refers to the proportion of scans or runs in which a particular ion or feature is detected during mass spectrometry analysis. It indicates how consistently the feature is present across multiple injections or samples.
+Fill% refers to the proportion of scans or runs in which a particular ion or feature is detected during mass spectrometry analysis. It indicates how consistently the feature is present across multiple injections or samples (Figure 13A).
 
 Fill% helps assess the reliability of detection for a particular compound in a sample, indicating how frequently it was detected during analysis.
 
 **2: Meaning of S/N average:**
 
-S/N (Signal-to-Noise) Average refers to the average ratio of the signal's intensity (the compound of interest) to the background noise over multiple scans. A higher S/N ratio indicates a clearer signal against background noise.
+S/N (Signal-to-Noise) Average refers to the average ratio of the signal's intensity (the compound of interest) to the background noise over multiple scans. A higher S/N ratio indicates a clearer signal against background noise (Figure 13B).
 
 A higher S/N ratio means that the signal is clearly distinguishable from the noise, indicating reliable detection of the compound.