Update proteomics.qmd

Author: Bujee415

proteomics.qmd

@@ -2,6 +2,64 @@
 title: "Proteomics"
 ---
 
-## 1. Label-free shotgun proteomics
+See [Figure 2](index.qmd#fig-2) for the meanings of the abbreviations used in this chapter.
 
-TBA
+## 1. LC-MS (DDA) for proteomics
+### 1-1 Input data
+The dataset for reproducing this tutorial can be obtained from 
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15369007.svg)](https://zenodo.org/badge/DOI/10.5281/zenodo.15369007)
+This tutorial utilizes 2 raw data files (*.raw) from https://repository.jpostdb.org/entry/JPST000200.
+The human_proteins_ref.fasta was obtained from https://www.uniprot.org/.
+
+### 1-1 Starting up your project
+
+![Figure 1: Starting up a project in MS-DIAL5. First, open the 
+MSDIAL.exe file in the downloaded folder (1). Click on “New 
+project” (2). You can name your project according to your preferences.
+Browse to the location of your experimental files. Click next and then 
+continue to the second left side bar “Raw measurement files”. Here, 
+click browse to access your raw data files.]
+(images/proteomics/Fig1%20Starting%20up%20a%20project.png){#fig-1}
+
+![Figure 2: Importing raw data files and setting up the measurement 
+parameters. Change the type of file according to your vendor format 
+and select the raw data files that you want to import (1). After 
+improting your raw data files, you will be able to further assign 
+identifiers to your measurements by sample “Type” (Sample, Standard, 
+Blank), “Class ID” (according to your experimental setup) set the 
+batch, analytical order, dilution factor, or possibly exclude some 
+samples from further data processing (2, 3). This is because to be able 
+to use all MS-DIAL functions. After clicking next and selecting the 
+“Measurement parameters” in the left side tab, you can specify your 
+analytical setup according to this figure (4).]
+(images/proteomics/Fig2%20Improting%20a%20raw%20data%20files%20and%20setting%20up%20parameters.png){#fig-2}
+
+![Figure 3: Setting other project parameters according to your thoughts. 
+Specifically, in the “Identification” section, FASTA files obtained from 
+Uniprot or other sources can be set as a database. Select the “+” next to 
+“Database setting” (1). Here, select the database type and browse to access 
+your files (Fasta) (2). In addition to this, if you browse the enzyme setting, 
+you can select the enzyme according to your experimental setup (3, 4). Also, 
+you can set modification settings in this entry. In the proteomics mode of 
+MS-DIAL, carbamidomethyl (CAM) of cysteine is considered in the default settings.]
+(images/proteomics/Fig3%20Setting%20up%20analysis%20parameters.png){#fig-3}
+
+![Figure 4: This is the main view of MS-DIAL. Double-clicking on a file name 
+in the file navigator will display the detected peak information in the center 
+window (Peak spot viewer) (1). “Show ion table” window can be displayed both on 
+the alignment result viewer and the peak spot viewer (2). Based on the amino acid 
+sequence information in the Fasta file, the sequence is annotated and mapped as 
+a peptide that is expected to be generated when digested with trypsin, etc. (3). 
+The peak height is visualized in a bar chart for each result. Each peptide result 
+can be marked with a Comment or Tag (4). This result should be retained by saving 
+the project file (5). The annotation of each peptide involves analysis of its 
+tandem mass spectrum. Assuming peptide bond cleavage induced by Collision Induced 
+Dissociation (CID), lists of b-ions and y-ions derived from each peptide sequence 
+are generated and compared. In MS-DIAL, product ions with charges greater than one 
+are also considered. B-ions are displayed in red and y-ions in cyan, shown as paired 
+spectra below the measured spectrum (6).]
+(images/proteomics/Fig4%20Project%20windows%20after%20analysis.png){#fig-4}
+
+The video tutorial for the MS-DAIL5 operation
+
+{{< video https://www.youtube.com/watch?v=kdykKiKPaho >}}